ORCID Profile
0000-0003-1294-0692
Current Organisations
University of South Australia
,
SA Pathology
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Publisher: Elsevier BV
Date: 03-2017
DOI: 10.1016/J.SEMCDB.2017.08.008
Abstract: Interconversions between epithelial and mesenchymal states, often referred to as epithelial mesenchymal transition (EMT) and its reverse MET, play important roles in embryonic development and are recapitulated in various adult pathologies including cancer progression. These conversions are regulated by complex transcriptional and post-transcriptional mechanisms including programs of alternative splicing which are orchestrated by specific splicing factors. This review will focus on the latest developments in our understanding of the splicing factors regulating epithelial mesenchymal plasticity associated with cancer progression and the induction of pluripotency, including potential roles for circular RNAs (circRNAs) which have been recently implicated in these processes.
Publisher: Springer Science and Business Media LLC
Date: 16-04-2020
DOI: 10.1038/S41580-020-0237-9
Abstract: Epithelial–mesenchymal transition (EMT) encompasses dynamic changes in cellular organization from epithelial to mesenchymal phenotypes, which leads to functional changes in cell migration and invasion. EMT occurs in a erse range of physiological and pathological conditions and is driven by a conserved set of inducing signals, transcriptional regulators and downstream effectors. With over 5,700 publications indexed by Web of Science in 2019 alone, research on EMT is expanding rapidly. This growing interest warrants the need for a consensus among researchers when referring to and undertaking research on EMT. This Consensus Statement, mediated by ‘the EMT International Association’ (TEMTIA), is the outcome of a 2-year-long discussion among EMT researchers and aims to both clarify the nomenclature and provide definitions and guidelines for EMT research in future publications. We trust that these guidelines will help to reduce misunderstanding and misinterpretation of research data generated in various experimental models and to promote cross-disciplinary collaboration to identify and address key open questions in this research field. While recognizing the importance of maintaining ersity in experimental approaches and conceptual frameworks, we emphasize that lasting contributions of EMT research to increasing our understanding of developmental processes and combatting cancer and other diseases depend on the adoption of a unified terminology to describe EMT.
Publisher: Elsevier BV
Date: 03-2001
DOI: 10.1016/S0167-4781(01)00167-1
Abstract: Sequencing of rat and human vascular endothelial growth factor (VEGF) cDNA clones has previously identified a 3' untranslated region of approximately 1.9 kb, although the apparent site of polyadenylation differed in the two species, despite a high degree of sequence conservation in the region. Neither site is preceded by a canonical AAUAAA polyadenylation signal, a situation frequently found in genes that are subject to alternative polyadenylation. We have sequenced 2.25 kb of the 3' region of the mouse VEGF gene and mapped the usage of potential polyadenylation sites in fibroblasts cultured under both normoxic and hypoxic conditions. We find that two sites for polyadenylation are present in the mouse VEGF gene but the majority of transcripts contain the longer form of the 3'UTR and that their usage is not effected by environmental oxygen tension.
Publisher: Elsevier BV
Date: 03-2015
DOI: 10.1016/J.CELL.2015.02.014
Abstract: Circular RNAs (circRNAs), formed by non-sequential back-splicing of pre-mRNA transcripts, are a widespread form of non-coding RNA in animal cells. However, it is unclear whether the majority of circRNAs represent splicing by-products without function or are produced in a regulated manner to carry out specific cellular functions. We show that hundreds of circRNAs are regulated during human epithelial-mesenchymal transition (EMT) and find that the production of over one-third of abundant circRNAs is dynamically regulated by the alternative splicing factor, Quaking (QKI), which itself is regulated during EMT. Furthermore, by modulating QKI levels, we show the effect on circRNA abundance is dependent on intronic QKI binding motifs. Critically, the addition of QKI motifs is sufficient to induce de novo circRNA formation from transcripts that are normally linearly spliced. These findings demonstrate circRNAs are both purposefully synthesized and regulated by cell-type specific mechanisms, suggesting they play specific biological roles in EMT.
Publisher: Public Library of Science (PLoS)
Date: 24-01-2013
Publisher: Springer Science and Business Media LLC
Date: 09-12-2022
Publisher: Oxford University Press (OUP)
Date: 07-06-2011
DOI: 10.1093/NAR/GKR330
Publisher: Elsevier BV
Date: 09-2014
Publisher: Life Science Alliance, LLC
Date: 03-08-2023
Abstract: Epithelial–mesenchymal transition is essential for tissue patterning and organization. It involves both regulation of cell motility and alterations in the composition and organization of the ECM—a complex environment of proteoglycans and fibrous proteins essential for tissue homeostasis, signaling in response to chemical and biomechanical stimuli, and is often dysregulated under conditions such as cancer, fibrosis, and chronic wounds. Here, we demonstrate that basonuclin-2 (BNC2), a mesenchymal-expressed gene, that is, strongly associated with cancer and developmental defects across genome-wide association studies, is a novel regulator of ECM composition and degradation. We find that at endogenous levels, BNC2 controls the expression of specific collagens, matrix metalloproteases, and other matrisomal components in breast cancer cells, and in fibroblasts that are primarily responsible for the production and processing of the ECM within the tumour microenvironment. In so doing, BNC2 modulates the motile and invasive properties of cancers, which likely explains the association of high BNC2 expression with increasing cancer grade and poor patient prognosis.
Publisher: American Association for Cancer Research (AACR)
Date: 30-06-2015
DOI: 10.1158/0008-5472.CAN-15-0287
Abstract: microRNAs (miRNA) are well suited to the task of regulating gene expression networks, because any given miRNA has the capacity to target dozens, if not hundreds, of genes. The simultaneous targeting of multiple genes within a pathway may enable miRNAs to more strongly regulate the pathway, or to achieve more subtle control through the targeting of distinct subnetworks of genes. Therefore, as our capacity to discover miRNA targets en masse increases, so must our consideration of the complex networks in which these genes participate. We highlight recent studies in which the comprehensive identification of targets has been used to elucidate miRNA-regulated gene networks in cancer, focusing especially upon miRNAs such as members of the miR-200 family that regulate epithelial–mesenchymal transition (EMT), a reversible phenotypic switch whereby epithelial cells take on the more invasive properties of their mesenchymal counterparts. These studies have expanded our understanding of the roles of miRNAs in EMT, which were already known to form important regulatory loops with key transcription factors to regulate the epithelial or mesenchymal properties of cells. Cancer Res 75(13) 2594–9. ©2015 AACR.
Publisher: Elsevier BV
Date: 07-1987
DOI: 10.1016/0003-9861(87)90461-9
Abstract: A rat spleen cDNA library was prepared and employed for the molecular cloning of the cDNA for thymosin beta 10, a peptide that previously had been found to accompany the closely related peptide, thymosin beta 4, in several species of mammals (S. Erickson-Viitanen, S. Ruggieri, P. Natalini, and B. L. Horecker (1983) Arch. Biochem. Biophys. 225, 407-413). First-round screening with a synthetic oligodeoxynucleotide probe yielded 55 positive clones, and sequence analysis of 11 of these clones revealed that they all coded for a peptide containing the thymosin beta 10 sequence, except for an additional arginyl residue at position 39. This peptide, designated thymosin beta 10arg, had been identified previously in rabbit tissues and reported as a variant of thymosin beta 10 (S. Ruggieri, S. Erickson-Viitanen, and B.L. Horecker (1983) Arch. Biochem. Biophys. 226, 388-392). Analysis of the 55 positive clones using a specific oligodeoxynucleotide probe constructed to correspond to the mRNA sequence, including the codon for Arg39, confirmed that they all coded for the amino acid sequence including Arg39. Based on these results, the existence of a molecular species lacking Arg39 is considered unlikely, and we conclude that thymosin beta 10 contains 43, rather than 42, amino acid residues, with identity to thymosin beta 4 in 32 of the 43 residues. We propose that the name thymosin beta 10 be used to refer to the peptide containing Arg39 and that the designation thymosin beta 10arg be dropped. In the cDNA sequence the codons for Ala1 and Ser43 of thymosin beta 10 are flanked by initiator and terminator codons, respectively thus, both the thymosin beta 4 and thymosin beta 10, which coexist in mammalian cells and tissues, are synthesized without the formation of larger polypeptide precursors.
Publisher: Elsevier BV
Date: 08-1989
DOI: 10.1016/0092-8674(89)90428-5
Abstract: Plant cells do not in general process the introns of transcripts expressed from introduced vertebrate genes. By studying the processing of model introns in transfected plant protoplasts, we have investigated the special requirements for intron recognition by plant cells. Our results indicate that the requirements for intron recognition in plants are different from those of both metazoa and yeast. A synthetic intron of arbitrary sequence but incorporating splice site consensus sequences and a high proportion of U and A nucleotides, a characteristic feature of plant introns, was efficiently spliced in protoplasts. We have studied the effects of various sequence alterations and conclude that AU-rich sequences are necessary for intron recognition. In addition, we find that the criteria for branch site selection are relaxed, as they are in vertebrates, but a polypyrimidine tract is not necessary.
Publisher: Springer Science and Business Media LLC
Date: 06-12-2020
DOI: 10.1038/S41416-019-0669-1
Abstract: Stathmin mediates cell migration and invasion in vitro, and metastasis in vivo. To investigate stathmin’s role on the metastatic process, we performed integrated mRNA–miRNA expression analysis to identify pathways regulated by stathmin. MiRNA and gene arrays followed by miRNA-target-gene integration were performed on stathmin-depleted neuroblastoma cells (Ctrl shRNA vs. Stmn Seq2 shRNA ). The expression of the predicted target PTPN14 was evaluated by RT-qPCR, western blot and immunohistochemistry. Gene-silencing technology was used to assess the role of PTPN14 on proliferation, migration, invasion and signalling pathway. Stathmin levels modulated the expression of genes and miRNA in neuroblastoma cells, leading to a deregulation of migration and invasion pathways. Consistent with gene array data, PTPN14 mRNA and protein expression were downregulated in stathmin- depleted neuroblastoma cells and xenografts. In two independent neuroblastoma cells, suppression of PTPN14 expression led to an increase in cell migration and invasion. PTPN14 and stathmin expression did not act in a feedback regulatory loop in PTPN14- depleted cells, suggesting a complex interplay of signalling pathways. The effect of PTPN14 on YAP pathway activation was cell-type dependent. Our findings demonstrate that stathmin levels can regulate PTPN14 expression, which can modulate neuroblastoma cell migration and invasion.
Publisher: Wiley
Date: 15-01-2004
DOI: 10.1111/J.1432-1033.2003.03968.X
Abstract: Vascular endothelial growth factor (VEGF) is a key regulator of angiogenesis and post-transcriptional regulation plays a major role in VEGF expression. Both the 5'- and 3'-UTR are required for VEGF post-transcriptional regulation but factors binding to functional sequences within the 5'-UTR have not been fully characterized. We report here the identification of complexes, binding to the VEGFmRNA 5'- and 3'-UTR, that contain cold shock domain (CSD) and polypyrimidine tract binding (PTB) RNA binding proteins. Analysis of the CSD/PTB binding sites revealed a potential role in VEGF mRNA stability, in both noninduced and induced conditions, demonstrating a general stabilizing function. Such a stabilizing mechanism had not been reported previously for the VEGF gene. We further found that the CSD/PTB-containing complexes are large multiprotein complexes that are most likely preformed in solution and we demonstrate that PTB is associated with the VEGF mRNA in vivo. Complex formation between CSD proteins and PTB has not been reported previously. Analysis of the CSD/PTB RNA binding sites revealed a novel CSD protein RNA recognition site and also demonstrated that CSD proteins may direct the binding of CSD/PTB complexes. We found the same complexes binding to an RNA-stabilizing element of another growth factor gene, suggesting a broader functional role for the CSD/PTB complexes. Finally, as the VEGF gene is also regulated at the transcriptional level by CSD proteins, we propose a combined transcriptional ost-transcriptional role for these proteins in VEGF and other growth factor gene regulation.
Publisher: Proceedings of the National Academy of Sciences
Date: 12-1983
Abstract: Two peptides related to thymosin alpha 1 have been isolated from preparations of calf thymosin fraction 5. One, lacking four amino acid residues at the COOH terminus, is designated des-(25-28)-thymosin alpha 1. The other, named thymosin alpha 11, contains seven additional amino acid residues at the COOH terminus. The sequence of this peptide is: AcSer-Asp-Ala-Ala-Val-Asp-Thr-Ser-Ser-Glu-Ile-Thr-Thr-Lys-Asp-Leu- Lys-Glu-Lys- Lys-Glu-Val-Val-Glu-Glu-Ala-Glu-Asn-Gly-Arg-Glu-Ala-Pro-Ala-AsnOH. Thymosin alpha 11, in doses of less than 300 ng per mouse, protects susceptible inbred murine strains against opportunistic infections with Candida albicans. It is approximately equal to 30 times as potent as thymosin fraction 5 and approximately equal in potency to thymosin alpha 1.
Publisher: American Association for Cancer Research (AACR)
Date: 15-12-2004
DOI: 10.1158/0008-5472.CAN-04-1437
Abstract: Hypoxia-inducible factor (HIF)-1, a heterodimeric transcription factor composed of HIF-1α and HIF-1β subunits coordinates pathophysiologic responses toward decreased oxygen availability. It is now appreciated that enhanced protein translation of HIF-1α under normoxia accounts for an alternative regulatory circuit to activate HIF-1 by hormones, growth factors, or cytokines such as tumor necrosis factor α (TNF-α). Here, we aimed at understanding molecular details of HIF-1α translation in response to TNF-α. In tubular LLC-PK1 cells, activation of nuclear factor κB (NFκB) by TNF-α resulted in HIF-1α protein synthesis as determined by [35S]methionine pulse experiments. Protein synthesis was attenuated by blocking NFκB, phosphatidylinositol 3′-kinase (PI3k), and mitogen-activated protein kinase (MAPK). Use of a dicistronic reporter with the HIF-1α 5′-untranslated region (5′UTR) between two coding regions indicated that TNF-α promoted an internal ribosome entry site (IRES) rather than a cap-dependent translation. IRES-mediated translation required the functional integrity of the NFκB, PI3k, and MAPK signaling pathways. Although no signal cross-talk was noticed between NFκB, PI3k, and MAPK signaling, these pathways are needed to up-regulate the anti-apoptotic target protein Bcl-2 by TNF-α. Expression of Bcl-2 provoked not only IRES-dependent translation but also HIF-1α protein synthesis. We conclude that Bcl-2 functions as an important determinant in facilitating HIF-1α protein expression by TNF-α via an IRES-dependent translational mechanism. These observations suggest a link between Bcl-2 and HIF-1α expression, a situation with potential relevance to cancer biology.
Publisher: Portland Press Ltd.
Date: 12-1981
DOI: 10.1042/BJ1990603
Abstract: The active site of pyruvate carboxylase, like those of all biotin-dependent carboxylases, is believed to consist of two spatially distinct sub-sites with biotin acting as a mobile carboxy-group carrier oscillating between the two sub-sites. Some of the factors that influence the location and rate of movement of the N-carboxybiotin were studied. The rate of carboxylation of the alternative substrate, 2-oxobutyrate, was measured at 0 degrees C in an assay system where the isolated enzyme--[14C]carboxybiotin was the carboxy-group donor. The results are consistent with the hypothesis that the location of the carboxybiotin in the active site is determined by the presence of Mg2+, acetyl-CoA and the oxo acid substrate. The presence of Mg2+ favours the holding of the complex at the first sub-site, whereas alpha-oxo acids induce the complex to move to the second sub-site. At low concentrations pyruvate induces this movement but does not efficiently act as a carboxy-group acceptor hydroxypyruvate, glyoxylate and oxamate, though not carboxylated, still induce the movement. The allosteric activator acetyl-CoA exerts only a slight stimulation on the rate of translocation to the second sub-site, and this stimulation arises from an increase in the dissociation constant for Mg2+.
Publisher: American Society for Cell Biology (ASCB)
Date: 05-2002
Abstract: HIF-1α is the regulated subunit of the HIF-1 transcription factor, which induces transcription of a number of genes involved in the cellular response to hypoxia. The HIF-1α protein is rapidly degraded in cells supplied with adequate oxygen but is stabilized in hypoxic cells. Using polysome profile analysis, we found that translation of HIF-1α mRNA in NIH3T3 cells is spared the general reduction in translation rate that occurs during hypoxia. To assess whether the 5′UTR of the HIF-1α mRNA contains an internal ribosome entry site (IRES), we constructed a dicistronic reporter with the HIF-1α 5′UTR inserted between two reporter coding regions. We found that the HIF-1α 5′UTR promoted translation of the downstream reporter, indicating the presence of an IRES. The IRES had activity comparable to that of the well-characterized c-myc IRES. IRES activity was not affected by hypoxic conditions that caused a reduction in cap-dependent translation, and IRES activity was less affected by serum-starvation than was cap-dependent translation. These data indicate that the presence of an IRES in the HIF-1α 5′UTR allows translation to be maintained under conditions that are inhibitory to cap-dependent translation.
Publisher: Elsevier BV
Date: 2021
DOI: 10.1016/J.CELREP.2020.108585
Abstract: Potent therapeutic inhibition of the androgen receptor (AR) in prostate adenocarcinoma can lead to the emergence of neuroendocrine prostate cancer (NEPC), a phenomenon associated with enhanced cell plasticity. Here, we show that microRNA-194 (miR-194) is a regulator of epithelial-neuroendocrine transdifferentiation. In clinical prostate cancer s les, miR-194 expression and activity were elevated in NEPC and inversely correlated with AR signaling. miR-194 facilitated the emergence of neuroendocrine features in prostate cancer cells, a process mediated by its ability to directly target a suite of genes involved in cell plasticity. One such target was FOXA1, which encodes a transcription factor with a vital role in maintaining the prostate epithelial lineage. Importantly, a miR-194 inhibitor blocked epithelial-neuroendocrine transdifferentiation and inhibited the growth of cell lines and patient-derived organoids possessing neuroendocrine features. Overall, our study reveals a post-transcriptional mechanism regulating the plasticity of prostate cancer cells and provides a rationale for targeting miR-194 in NEPC.
Publisher: Springer Science and Business Media LLC
Date: 27-01-2009
DOI: 10.1007/S00428-009-0731-0
Abstract: Sessile serrated adenomas are now recognised as precursor lesions of a substantial subset of colorectal cancers arising via a so-called "serrated pathway". However, their biological markers remain to be defined. The aim of our study was to identify differentially expressed genes in sessile serrated adenomas and conventional adenomas. Gene expression analysis demonstrated molecular differences between polyp types. Further studies using quantitative real-time polymerase chain reaction on cathepsin E (CTSE) demonstrated a significantly (p < 0.05) higher expression in sessile serrated adenomas as compared to hyperplastic polyp and tubular adenomas. Trefoil Factor 1 showed the same trend of expression for sessile serrated adenomas as compared to hyperplastic polyps and was significantly higher in both polyps compared to tubular adenomas. Immunohistochemistry for both proteins demonstrated strong cytoplasmic staining of abnormal crypts in all sessile serrated adenomas, while staining in tubular adenomas and hyperplastic polyps was absent or weak and focal. BRAF and KRAS mutation analysis were employed to further validate polyp discrimination. The findings demonstrated the positive association of the BRAF mutation, V600E, with sessile serrated adenomas and KRAS mutations with tubular adenomas (p < 0.05). This study demonstrates the over-expression in CTSE, in particular, and TFF1 in sessile serrated adenomas compared to both hyperplastic polyps and tubular adenomas.
Publisher: Springer Science and Business Media LLC
Date: 22-03-2011
Abstract: Esophageal squamous cell carcinoma (ESCC) is often diagnosed at later stages until they are incurable. MicroRNA (miR) is a small, non-coding RNA that negatively regulates gene expression mainly via translational repression. Accumulating evidence indicates that deregulation of miR is associated with human malignancies including ESCC. The aim of this study was to identify miR that could be specifically expressed and exert distinct biological actions in ESCC. Total RNA was extracted from ESCC cell lines, OE21 and TE10, and a non-malignant human esophageal squamous cell line, Het-1A, and subjected to microarray analysis. Expression levels of miR that showed significant differences between the 2 ESCC and Het-1A cells based on the comprehensive analysis were analyzed by the quantitative reverse transcriptase (RT)-PCR method. Then, functional analyses, including cellular proliferation, apoptosis and Matrigel invasion and the wound healing assay, for the specific miR were conducted. Using ESCC tumor s les and paired surrounding non-cancerous tissue obtained endoscopically, the association with histopathological differentiation was examined with quantitative RT-PCR. Based on the miR microarray analysis, there were 14 miRs that showed significant differences (more than 2-fold) in expression between the 2 ESCC cells and non-malignant Het-1A. Among the significantly altered miRs, miR-205 expression levels were exclusively higher in 5 ESCC cell lines examined than any other types of malignant cell lines and Het-1A. Thus, miR-205 could be a specific miR in ESCC. Modulation of miR-205 expression by transfection with its precursor or anti-miR-205 inhibitor did not affect ESCC cell proliferation and apoptosis, but miR-205 was found to be involved in cell invasion and migration. Western blot revealed that knockdown of miR-205 expression in ESCC cells substantially enhanced expression of zinc finger E-box binding homeobox 2, accompanied by reduction of E-cadherin, a regulator of epithelial mesenchymal transition. The miR-205 expression levels were not associated with histological differentiation of human ESCC. These results imply that miR-205 is an ESCC-specific miR that exerts tumor-suppressive activities with EMT inhibition by targeting ZEB2.
Publisher: Proceedings of the National Academy of Sciences
Date: 02-1984
Abstract: A polypeptide containing approximately equal to 112 amino acid residues, with the thymosin alpha 1 sequence at its NH2 terminus, has been isolated from rat thymus by using a radioimmunoassay with an antibody prepared against synthetic thymosin alpha 1. The new polypeptide, named "prothymosin alpha," was found to be the major substance crossreacting with thymosin alpha 1 antiserum in rat thymus extracts peptides corresponding to thymosin alpha 1 or thymosin alpha 11 were not detected. In gel filtration at pH 2.8, prothymosin alpha emerged as a single symmetrical peak corresponding to an apparent molecular weight of 32,000, approximately 3 times larger than the minimum molecular weight calculated from its amino acid composition. On the same gel filtration columns, synthetic thymosin alpha 1 (calculated Mr = 3108) emerged at a position corresponding to a molecular weight of 10,000-11,000. Thus, both prothymosin alpha and thymosin alpha 1 appear to exist in solution as oligomers, possibly as trimers. Prothymosin alpha and synthetic thymosin alpha 1 also were separated readily in reverse-phase HPLC and in isoelectric focusing the isoelectric point of prothymosin alpha determined by the latter procedure was found to be 3.55, consistent with an unusually high content of glutamic and aspartic acids based on amino acid analyses. Prothymosin alpha appears to represent the native polypeptide from which thymosin alpha 1 and other fragments are generated during the isolation of thymosin fraction 5.
Publisher: Springer Science and Business Media LLC
Date: 12-2009
Publisher: Oxford University Press (OUP)
Date: 02-02-2011
Publisher: Cold Spring Harbor Laboratory
Date: 28-04-2020
DOI: 10.1101/2020.04.26.062794
Abstract: Breast cancer prognosis is challenging due to the heterogeneity of the disease. Various computational methods using bulk RNA-seq data have been proposed for breast cancer prognosis. However, these methods suffer from limited performances or ambiguous biological relevance, as a result of the neglect of intra-tumor heterogeneity. Recently, single cell RNA-sequencing (scRNA-seq) has emerged for studying tumor heterogeneity at cellular levels. In this paper, we propose a novel method, scPrognosis , to improve breast cancer prognosis with scRNA-seq data. scPrognosis uses the scRNA-seq data of the biological process Epithelial-to-Mesenchymal Transition (EMT). It firstly infers the EMT pseudotime and a dynamic gene co-expression network, then uses an integrative model to select genes important in EMT based on their expression variation and differentiation in different stages of EMT, and their roles in the dynamic gene co-expression network. To validate and apply the selected signatures to breast cancer prognosis, we use them as the features to build a prediction model with bulk RNA-seq data. The experimental results show that scPrognosis outperforms other benchmark breast cancer prognosis methods that use bulk RNA-seq data. Moreover, the dynamic changes in the expression of the selected signature genes in EMT may provide clues to the link between EMT and clinical outcomes of breast cancer. scPrognosis will also be useful when applied to scRNA-seq datasets of different biological processes other than EMT. Various computational methods have been developed for breast cancer prognosis. However, those methods mainly use the gene expression data generated by the bulk RNA sequencing techniques, which average the expression level of a gene across different cell types. As breast cancer is a heterogenous disease, the bulk gene expression may not be the ideal resource for cancer prognosis. In this study, we propose a novel method to improve breast cancer prognosis using scRNA-seq data. The proposed method has been applied to the EMT scRNA-seq dataset for identifying breast cancer signatures for prognosis. In comparison with existing bulk expression data based methods in breast cancer prognosis, our method shows a better performance. Our single-cell-based signatures provide clues to the relation between EMT and clinical outcomes of breast cancer. In addition, the proposed method can also be useful when applied to scRNA-seq datasets of different biological processes other than EMT.
Publisher: Elsevier BV
Date: 09-2014
DOI: 10.1016/J.BIOCEL.2014.03.010
Abstract: The function of microRNAs is well characterized in the cytoplasm, where they direct an Argonaute-containing complex to target and repress mRNAs. More recently, regulatory roles for microRNAs and Argonaute have also been reported in the nucleus where microRNAs guide Argonaute to target gene promoters and directly regulate transcription in either a positive or a negative manner. Deep sequencing has revealed a high abundance of endogenous microRNAs within the nucleus, and in silico target prediction suggests thousands of potential microRNA:promoter interaction sites. The predicted high frequency of miRNA:promoter interactions is supported by chromatin immunoprecipitation, indicating the microRNA-dependent recruitment of Argonaute to thousands of transcriptional start sites and the subsequent regulation of RNA polymerase-II occupancy and chromatin modifiers. In this review we discuss the evidence for, and mechanisms associated with, direct transcriptional regulation by microRNAs which may represent a significant and largely unexplored aspect of microRNA function. This article is part of a Directed Issue entitled: The non-coding RNA revolution.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2019
DOI: 10.1158/2159-8290.23854361
Abstract: IL3Rα/βc transcript and protein expression ratio in AML patient s les.
Publisher: Oxford University Press (OUP)
Date: 12-06-2006
DOI: 10.1189/JLB.0206112
Abstract: Mechanisms controlling the balance between proliferation and self-renewal versus growth suppression and differentiation during normal and leukemic myelopoiesis are not understood. We have used the bi-potent FDB1 myeloid cell line model, which is responsive to myelopoietic cytokines and activated mutants of the granulocyte macrophage-colony stimulating factor (GM-CSF) receptor, having differential signaling and leukemogenic activity. This model is suited to large-scale gene-profiling, and we have used a factorial time-course design to generate a substantial and powerful data set. Linear modeling was used to identify gene-expression changes associated with continued proliferation, differentiation, or leukemic receptor signaling. We focused on the changing transcription factor profile, defined a set of novel genes with potential to regulate myeloid growth and differentiation, and demonstrated that the FDB1 cell line model is responsive to forced expression of oncogenes identified in this study. We also identified gene-expression changes associated specifically with the leukemic GM-CSF receptor mutant, V449E. Signaling from this receptor mutant down-regulates CCAAT/enhancer-binding protein α (C/EBPα) target genes and generates changes characteristic of a specific acute myeloid leukemia signature, defined previously by gene-expression profiling and associated with C/EBPα mutations.
Publisher: Springer Science and Business Media LLC
Date: 08-01-2018
DOI: 10.1038/S41598-017-17913-X
Abstract: Complex regulatory networks control epithelial-to-mesenchymal transition (EMT) but the underlying epigenetic control is poorly understood. Lysine-specific demethylase 1 (LSD1) is a key histone demethylase that alters the epigenetic landscape. Here we explored the role of LSD1 in global epigenetic regulation of EMT, cancer stem cells (CSCs), the tumour microenvironment, and therapeutic resistance in breast cancer. LSD1 induced pan-genomic gene expression in networks implicated in EMT and selectively elicits gene expression programs in CSCs whilst repressing non-CSC programs. LSD1 phosphorylation at serine-111 (LSD1-s111p) by chromatin anchored protein kinase C-theta (PKC-θ), is critical for its demethylase and EMT promoting activity and LSD1-s111p is enriched in chemoresistant cells in vivo . LSD1 couples to PKC-θ on the mesenchymal gene epigenetic template promotes LSD1-mediated gene induction. In vivo , chemotherapy reduced tumour volume, and when combined with an LSD1 inhibitor, abrogated the mesenchymal signature and promoted an innate, M1 macrophage-like tumouricidal immune response. Circulating tumour cells (CTCs) from metastatic breast cancer (MBC) patients were enriched with LSD1 and pharmacological blockade of LSD1 suppressed the mesenchymal and stem-like signature in these patient-derived CTCs. Overall, LSD1 inhibition may serve as a promising epigenetic adjuvant therapy to subvert its pleiotropic roles in breast cancer progression and treatment resistance.
Publisher: Oxford University Press (OUP)
Date: 11-09-2017
DOI: 10.1093/NAR/GKX788
Publisher: Elsevier BV
Date: 06-1988
DOI: 10.1016/0003-9861(88)90640-6
Abstract: A rat spleen cDNA library was screened for clones carrying the cDNAs for prothymosin alpha and parathymosin. Sequence analysis of a clone carrying the entire coding region for prothymosin alpha confirmed and completed the amino acid sequence for this polypeptide and established the number of amino acid residues as 111. Rat prothymosin alpha differs from human prothymosin alpha at six positions, including four substitutions and two insertions. The nucleotide sequences of the cDNAs for the rat and human polypeptides are more than 90% identical in the open reading frames, with significant homology extending into the 5' and 3' flanking regions. From the same library, we also isolated a clone carrying 80% of the coding region for rat parathymosin. The number of amino acid residues in rat parathymosin is 101, based on the sequence deduced from the cDNA insert and earlier information on the sequence in the amino-terminal portion of this polypeptide. Despite their similarity in size and amino acid composition, rat prothymosin alpha and rat parathymosin show only limited sequence homology, primarily in the segment including residues 14 through 25, where 10 of 12 positions are identical in the two polypeptides. this is also the region of significant sequence similarity to a 12-amino-acid segment in the p17 protein of the human immunodeficiency disease associated virus (HTLV-IIIB).
Publisher: Springer Science and Business Media LLC
Date: 06-06-2017
DOI: 10.1038/ONC.2016.185
Abstract: MicroRNA-375 (miR-375) is frequently elevated in prostate tumors and cell-free fractions of patient blood, but its role in genesis and progression of prostate cancer is poorly understood. In this study, we demonstrated that miR-375 is inversely correlated with epithelial-mesenchymal transition signatures (EMT) in clinical s les and can drive mesenchymal-epithelial transition (MET) in model systems. Indeed, miR-375 potently inhibited invasion and migration of multiple prostate cancer lines. The transcription factor YAP1 was found to be a direct target of miR-375 in prostate cancer. Knockdown of YAP1 phenocopied miR-375 overexpression, and overexpression of YAP1 rescued anti-invasive effects mediated by miR-375. Furthermore, transcription of the miR-375 gene was shown to be directly repressed by the EMT transcription factor, ZEB1. Analysis of multiple patient cohorts provided evidence for this ZEB1-miR-375-YAP1 regulatory circuit in clinical s les. Despite its anti-invasive and anti-EMT capacities, plasma miR-375 was found to be correlated with circulating tumor cells in men with metastatic disease. Collectively, this study provides new insight into the function of miR-375 in prostate cancer, and more broadly identifies a novel pathway controlling epithelial plasticity and tumor cell invasion in this disease.
Publisher: Wiley
Date: 31-10-1983
DOI: 10.1016/0014-5793(83)81150-8
Abstract: Previous proposals for the mechanism by which biotin-dependent enzymes catalyse the transfer of the carboxyl group from 1'-N-carboxybiotin to acceptor molecules do not appear to be consistent with all of the experimental observations now available. We propose a multi-step mechanism in which (a) substrate and then carboxybiotin bind at the second partial reaction site, (b) a base positioned adjacent to the 3'-N of the carboxybiotin abstracts a proton from the 3'-N and (c) the resulting enolate ion and the acceptor substrate undergo a concerted reaction resulting in carboxyl-group transfer.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 17-02-2015
DOI: 10.1126/SCISIGNAL.2005547
Abstract: Without the protein phosphatase PTPN14, tumor cells secrete more prometastatic factors and send more growth-promoting receptors to the surface.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854361.V1
Abstract: IL3Rα/βc transcript and protein expression ratio in AML patient s les.
Publisher: EMBO
Date: 06-06-2018
Publisher: American Association for the Advancement of Science (AAAS)
Date: 28-02-2006
Abstract: Cellular signal transduction involves an elaborate network of interrelated signaling pathways. Dissecting the components of these signaling pathways and the functional relationships between them is crucial to our understanding of biological processes. This was the central theme of the November 2005 Signaling Networks meeting held in the Barossa Valley, South Australia. The meeting highlighted recent exciting advances in this area, covering topics such as the initiation, integration, regulation, and architecture of signaling networks, and the importance of these pathways in normal physiological functions and pathophysiological processes.
Publisher: Springer Science and Business Media LLC
Date: 14-10-2017
DOI: 10.1038/LEU.2016.279
Abstract: Enforced expression of microRNA-155 (miR-155) in myeloid cells has been shown to have both oncogenic or tumour-suppressor functions in acute myeloid leukaemia (AML). We sought to resolve these contrasting effects of miR-155 overexpression using murine models of AML and human paediatric AML data sets. We show that the highest miR-155 expression levels inhibited proliferation in murine AML models. Over time, enforced miR-155 expression in AML in vitro and in vivo, however, favours selection of intermediate miR-155 expression levels that results in increased tumour burden in mice, without accelerating the onset of disease. Strikingly, we show that intermediate and high miR-155 expression also regulate very different subsets of miR-155 targets and have contrasting downstream effects on the transcriptional environments of AML cells, including genes involved in haematopoiesis and leukaemia. Furthermore, we show that elevated miR-155 expression detected in paediatric AML correlates with intermediate and not high miR-155 expression identified in our experimental models. These findings collectively describe a novel dose-dependent role for miR-155 in the regulation of AML, which may have important therapeutic implications.
Publisher: Public Library of Science (PLoS)
Date: 02-12-2019
Publisher: Oxford University Press (OUP)
Date: 27-04-2021
DOI: 10.1093/BIOINFORMATICS/BTAB262
Abstract: Unravelling cancer driver genes is important in cancer research. Although computational methods have been developed to identify cancer drivers, most of them detect cancer drivers at population level. However, two patients who have the same cancer type and receive the same treatment may have different outcomes because each patient has a different genome and their disease might be driven by different driver genes. Therefore new methods are being developed for discovering cancer drivers at in idual level, but existing personalized methods only focus on coding drivers while microRNAs (miRNAs) have been shown to drive cancer progression as well. Thus, novel methods are required to discover both coding and miRNA cancer drivers at in idual level. We propose the novel method, pDriver, to discover personalized cancer drivers. pDriver includes two stages: (i) constructing gene networks for each cancer patient and (ii) discovering cancer drivers for each patient based on the constructed gene networks. To demonstrate the effectiveness of pDriver, we have applied it to five TCGA cancer datasets and compared it with the state-of-the-art methods. The result indicates that pDriver is more effective than other methods. Furthermore, pDriver can also detect miRNA cancer drivers and most of them have been confirmed to be associated with cancer by literature. We further analyze the predicted personalized drivers for breast cancer patients and the result shows that they are significantly enriched in many GO processes and KEGG pathways involved in breast cancer. pDriver is available at vvhoang Driver. Supplementary data are available at Bioinformatics online.
Publisher: American Society of Hematology
Date: 30-06-2022
Abstract: Inducing cell death by the sphingolipid ceramide is a potential anticancer strategy, but the underlying mechanisms remain poorly defined. In this study, triggering an accumulation of ceramide in acute myeloid leukemia (AML) cells by inhibition of sphingosine kinase induced an apoptotic integrated stress response (ISR) through protein kinase R–mediated activation of the master transcription factor ATF4. This effect led to transcription of the BH3-only protein Noxa and degradation of the prosurvival Mcl-1 protein on which AML cells are highly dependent for survival. Targeting this novel ISR pathway, in combination with the Bcl-2 inhibitor venetoclax, synergistically killed primary AML blasts, including those with venetoclax-resistant mutations, as well as immunophenotypic leukemic stem cells, and reduced leukemic engraftment in patient-derived AML xenografts. Collectively, these findings provide mechanistic insight into the anticancer effects of ceramide and preclinical evidence for new approaches to augment Bcl-2 inhibition in the therapy of AML and other cancers with high Mcl-1 dependency.
Publisher: Springer Netherlands
Date: 19-12-2012
DOI: 10.1007/978-94-007-5590-1_14
Abstract: microRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translation inhibition. They are pivotal regulators of development and cellular homeostasis through their control of erse processes. Recently, great efforts have been made to elucidate many targets that are affected by miRNAs, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles and sequence information to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in. In this chapter, we first briefly review the computational methods for discovering miRNA targets and miRNA-mRNA regulatory modules, and then focus on a method of identifying functional miRNA-mRNA regulatory modules by integrating multiple data sets from different sources.
Publisher: Springer Science and Business Media LLC
Date: 1990
DOI: 10.1007/BF00360447
Abstract: The purpose of this analysis was to assess selected social consequences of maintaining oral health and treating oral diseases. The associations among socioeconomic and demographic factors with time lost from work or school and reductions in normal activities are explored. Data were gathered as part of the 1989 National Health Interview Survey from 50,000 US households (117,000 in iduals), representing 240 million persons. The oral health care supplement was analyzed using the software SUDAAN to produce standard errors for estimates based on complex multistage s le designs. Because of dental visits or problems, 148,000 hours of work were lost per 100,000 workers, 117,000 hours of school were lost per 100,000 school-age children, and 17,000 activity days beyond work and school time were restricted per 100,000 in iduals in 1989. Exploratory analyses suggest that sociodemographic groups have different patterns of such time loss and of reduced normal activities. Overall, there is low social impact in idually from dental visits and oral conditions. At the societal level, however, such problems and treatments among disadvantaged groups appear to have a greater impact.
Publisher: Proceedings of the National Academy of Sciences
Date: 09-08-2004
Abstract: Angiogenesis is a major therapeutic target. Ideal drug targets are genes expressed only in endothelial cells (ECs) or only during the angiogenic process. Here, we describe a gene, p73RhoGAP (p73), that has both of these properties. By using a PCR-based subtraction–hybridization approach to clone cDNAs from ECs undergoing capillary-tube formation, we identified a RhoGAP member, p73. p73 displays GTPase activity to Rho but not to Rac or Cdc42. Knockdown of p73 protein, achieved by adenovirus delivery of p73 antisense and by small interfering RNA into ECs, demonstrated the importance of this protein in EC function. Under such conditions, EC migration, proliferation, and capillary-tube formation were inhibited. Furthermore, angiogenesis in vivo was also inhibited by antisense p73. A mutant R82A alteration achieved a similar phenotype in vitro to the antisense, demonstrating the importance of the GTPase-activating protein activity to p73 function. Expression profiling of p73 shows that it is vascular cell-selective, being highly expressed in ECs and smooth-muscle cells but not in other cell types. Finally, we show that the mRNA of p73 is up-regulated in an angiogenic milieu with little or no regulation seen under nonangiogenic conditions. p73, a vascular cell-specific GTPase-activating protein, is an important modulator of angiogenesis and displays many of features that make it worthy of being a drug target.
Publisher: Royal Society of Chemistry (RSC)
Date: 1999
DOI: 10.1039/A809571J
Publisher: Springer Science and Business Media LLC
Date: 05-1990
DOI: 10.1007/BF00016505
Publisher: Springer Science and Business Media LLC
Date: 20-01-2009
DOI: 10.1007/S00018-009-8750-1
Abstract: For a tumour cell to metastasize it must successfully negotiate a number of events, requiring a series of coordinated changes in the expression of many genes. MicroRNAs are small non-coding RNA molecules that post-transcriptionally control gene expression. As microRNAs are now recognised as master regulators of gene networks and play important roles in tumourigenesis, it is no surprise that microRNAs have recently been demonstrated to have central roles during metastasis. Recent work has also demonstrated critical roles for microRNAs in epithelial-mesenchymal transition, a phenotypic change underlain by altered gene expression patterns that is believed to mirror events in metastatic progression. These findings offer new potential for improved prognostics through expression profiling and may represent novel molecular treatment targets for future therapy. In this review, we summarise the multistep processes of metastasis and epithelial-mesenchymal transition and describe the recent discoveries of microRNAs that participate in controlling these processes.
Publisher: Elsevier BV
Date: 03-1983
DOI: 10.1016/0003-9861(83)90182-0
Abstract: Thymosin beta 4, originally isolated from calf thymus [Low et al., Proc. Nat. Acad. Sci. USA 78, 1162-1166 (1981)] is present in a number of cell lines unrelated to the reticuloendothelium, including myoblasts and fibroblasts. It is also actively synthesized by these cell lines. Its content and rate of synthesis in the cell lines examined appear to be correlated with their ability to adhere and their motility.
Publisher: The Company of Biologists
Date: 2013
DOI: 10.1242/JCS.122275
Abstract: The miR-200 family is a key regulator of EMT, however its role in controlling the transition between cancer stem cell-like and non-stem cell-like phenotypes is not well understood. We utilized immortalized human mammary epithelial cells (HMLE) to investigate the regulation of the miR-200 family during their conversion to a stem-like phenotype. HMLE cells were found to be capable of spontaneous conversion from a non-stem to a stem-like phenotype and this conversion was accompanied by the loss of miR-200 expression. Stem-like cell fractions isolated from metastatic breast cancers also displayed loss of miR-200 indicating similar molecular changes may occur during breast cancer progression. The phenotypic change observed in HMLE cells was directly controlled by miR-200 as restoration of its expression decreased stem-like properties while promoting a transition to an epithelial phenotype. Investigation of the mechanisms controlling miR-200 expression revealed both DNA methylation and histone modifications were significantly altered in the stem-like and non-stem phenotypes. In particular, in the stem-like phenotype, the miR-200b-200a-429 cluster was silenced primarily through polycomb group-mediated histone modifications whereas the miR-200c-141 cluster was repressed by DNA methylation. These results indicate that the miR-200 family plays a critical role in the transition between stem-like and non-stem phenotypes and that distinct epigenetic-based mechanisms regulate each miR-200 gene in this process. Therapy targeted against miR-200 family members and epigenetic modifications may therefore be applicable to breast cancer.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854346.V1
Abstract: The IL-3R dodecamer activates STAT1 to induce cell differentiation.
Publisher: Wiley
Date: 20-09-2005
DOI: 10.1016/J.FEBSLET.2005.08.075
Abstract: The hypoxia responsive region (HRR) of the VEGF promoter plays a key role in regulating VEGF expression. We found that the cold shock domain (Y-box) repressor proteins, dbpA and dbpB/YB-1, bind distinct strands of the human VEGF HRR. We find both dbpA and dbpB are phosphorylated by ERK2 and GSK3beta in vitro, and the binding of dbpB to single-strand VEGF HRR DNA is regulated by this phosphorylation. These findings suggest the ERK/MAPK and PI3K pathways may regulate VEGF expression in part through regulating the action of these repressor proteins.
Publisher: Springer Science and Business Media LLC
Date: 16-07-2012
DOI: 10.1038/ONC.2012.305
Abstract: Loss of p53 function is a critical event during tumorigenesis, with half of all cancers harboring mutations within the TP53 gene. Such events frequently result in the expression of a mutated p53 protein with gain-of-function properties that drive invasion and metastasis. Here, we show that the expression of miR-155 was up-regulated by mutant p53 to drive invasion. The miR-155 host gene was directly repressed by p63, providing the molecular basis for mutant p53 to drive miR-155 expression. Significant overlap was observed between miR-155 targets and the molecular profile of mutant p53-expressing breast tumors in vivo. A search for cancer-related target genes of miR-155 revealed ZNF652, a novel zinc-finger transcriptional repressor. ZNF652 directly repressed key drivers of invasion and metastasis, such as TGFB1, TGFB2, TGFBR2, EGFR, SMAD2 and VIM. Furthermore, silencing of ZNF652 in epithelial cancer cell lines promoted invasion into matrigel. Importantly, loss of ZNF652 expression in primary breast tumors was significantly correlated with increased local invasion and defined a population of breast cancer patients with metastatic tumors. Collectively, these findings suggest that miR-155 targeted therapies may provide an attractive approach to treat mutant p53-expressing tumors.
Publisher: American Association for Cancer Research (AACR)
Date: 11-2013
DOI: 10.1158/1535-7163.MCT-13-0170
Abstract: Elevated expression and activity of the epidermal growth factor receptor (EGFR) is associated with development and progression of head and neck cancer (HNC) and a poor prognosis. Clinical trials with EGFR tyrosine kinase inhibitors (e.g., erlotinib) have been disappointing in HNC. To investigate the mechanisms mediating resistance to these agents, we developed an HNC cell line (HN5-ER) with acquired erlotinib resistance. In contrast to parental HN5 HNC cells, HN5-ER cells exhibited an epithelial–mesenchymal (EMT) phenotype with increased migratory potential, reduced E-cadherin and epithelial-associated microRNAs (miRNA), and elevated vimentin expression. Phosphorylated receptor tyrosine kinase profiling identified Axl activation in HN5-ER cells. Growth and migration of HN5-ER cells were blocked with a specific Axl inhibitor, R428, and R428 resensitized HN5-ER cells to erlotinib. Microarray analysis of HN5-ER cells confirmed the EMT phenotype associated with acquired erlotinib resistance, and identified activation of gene expression associated with cell migration and inflammation pathways. Moreover, increased expression and secretion of interleukin (IL)-6 and IL-8 in HN5-ER cells suggested a role for inflammatory cytokine signaling in EMT and erlotinib resistance. Expression of the tumor suppressor miR-34a was reduced in HN5-ER cells and increasing its expression abrogated Axl expression and reversed erlotinib resistance. Finally, analysis of 302 HNC patients revealed that high tumor Axl mRNA expression was associated with poorer survival (HR = 1.66, P = 0.007). In summary, our results identify Axl as a key mediator of acquired erlotinib resistance in HNC and suggest that therapeutic inhibition of Axl by small molecule drugs or specific miRNAs might overcome anti-EGFR therapy resistance. Mol Cancer Ther 12(11) 2541–58. ©2013 AACR.
Publisher: Oxford University Press (OUP)
Date: 22-03-2011
DOI: 10.1093/NAR/GKR110
Publisher: Springer Science and Business Media LLC
Date: 11-07-2013
DOI: 10.1038/BJC.2013.369
Publisher: Cold Spring Harbor Laboratory
Date: 18-04-2020
DOI: 10.1101/2020.04.18.047571
Abstract: Translation of eukaryotic mRNAs starts with binding of the m 7 G cap to the protein eIF4E followed by recruitment of other translation initiation factors. eIF4E’s essential role in translation suggests the cellular eIF4E-mRNA interactome (or ‘eIF4E cap-ome’) may serve as a faithful proxy of cellular translational activity. Here we describe capCLIP, a novel method to systematically capture and quantify the eIF4E cap-ome. To validate capCLIP, we identified the cap-omes in human cells ± the partial mTORC1 inhibitor rapamycin. As expected, TOP (terminal oligopyrimidine) mRNA representation is systematically reduced in rapamycin-treated cells. capCLIP tag data permits refinement of a 7-nucleotide TOP motif (5′-CUYUYYC-3′). We also apply capCLIP to probe the consequences of phosphorylation of eIF4E, whose function had remained unclear. eIF4E phosphorylation drives an overall reduction in eIF4E-mRNA association strikingly, mRNAs most sensitive to phosphorylation possess short 5′-UTRs. capCLIP provides a sensitive and comprehensive measure of cellular translational activity. We foresee its application as a high-throughput way to assess translation in contexts not amenable to existing methodologies.
Publisher: Oxford University Press (OUP)
Date: 17-10-2010
DOI: 10.1093/BIOINFORMATICS/BTQ576
Abstract: Motivation: MicroRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translational inhibition. They are important regulators of development and cellular homeostasis through their control of erse processes. Recently, great efforts have been made to elucidate their regulatory mechanism, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in. Results: We present a probabilistic graphical model to discover functional miRNA regulatory modules at potential biological levels by integrating heterogeneous datasets, including expression profiles of miRNAs and mRNAs, with or without the prior target binding information. We applied this model to a mouse mammary dataset. It effectively captured several biological process specific modules involving miRNAs and their target mRNAs. Furthermore, without using prior target binding information, the identified miRNAs and mRNAs in each module show a large proportion of overlap with predicted miRNA target relationships, suggesting that expression profiles are crucial for both target identification and discovery of regulatory modules. Contact: bing.liu@unisa.edu.au jiuyong.li@unisa.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709852
Abstract: Data collection and refinement statistics for the IL-3R ternary complex crystal structure.
Publisher: Elsevier BV
Date: 02-2011
Publisher: Springer Science and Business Media LLC
Date: 09-1992
DOI: 10.1007/BF00538698
Publisher: American Physiological Society
Date: 16-06-2005
DOI: 10.1152/PHYSIOLGENOMICS.00278.2004
Abstract: Angiogenesis is a complex multicellular process requiring the orchestration of many events including migration, alignment, proliferation, lumen formation, remodeling, and maturation. Such complexity indicates that not only in idual genes but also entire signaling pathways will be crucial in angiogenesis. To define an angiogenic blueprint of regulated genes, we utilized our well-characterized three-dimensional collagen gel model of in vitro angiogenesis, in which the majority of cells synchronously progress through defined morphological stages culminating in the formation of capillary tubes. We developed a comprehensive three-tiered approach using microarray analysis, which allowed us to identify genes known to be involved in angiogenesis and genes hitherto unlinked to angiogenesis as well as novel genes and has proven especially useful for genes where the magnitude of change is small. Of interest is the ability to recognize complete signaling pathways that are regulated and genes clustering into ontological groups implicating the functional importance of particular processes. We have shown that consecutive members of the mitogen-activated protein kinase and leukemia inhibitory factor signaling pathways are altered at the mRNA level during in vitro angiogenesis. Thus, at least for the mitogen-activated protein kinase pathway, mRNA changes as well as the phosphorylation changes of these gene products may be important in the control of blood vessel morphogenesis. Furthermore, in this study, we demonstrated the power of virtual Northern blot analysis, as an alternative to quantitative RT-PCR, for measuring the magnitudes of differential gene expression.
Publisher: Elsevier BV
Date: 07-2018
DOI: 10.1016/J.CELS.2018.05.019
Abstract: MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression, functioning in part by facilitating the degradation of target mRNAs. They have an established role in controlling epithelial-mesenchymal transition (EMT), a reversible phenotypic program underlying normal and pathological processes. Many studies demonstrate the role of in idual miRNAs using overexpression at levels greatly exceeding physiological abundance. This can influence transcripts with relatively poor targeting and may in part explain why over 130 different miRNAs are directly implicated as EMT regulators. Analyzing a human mammary cell model of EMT we found evidence that a set of miRNAs, including the miR-200 and miR-182/183 family members, co-operate in post-transcriptional regulation, both reinforcing and buffering transcriptional output. Investigating this, we demonstrate that combinatorial treatment altered cellular phenotype with miRNA concentrations much closer to endogenous levels and with less off-target effects. This suggests that co-operative targeting by miRNAs is important for their physiological function and future work classifying miRNAs should consider such combinatorial effects.
Publisher: American Association for Cancer Research (AACR)
Date: 16-05-2023
DOI: 10.1158/2159-8290.CD-22-1396
Abstract: Stemness is a hallmark of many cancers and is largely responsible for disease emergence, progression, and relapse. Our finding that clinically significant stemness programs in AML are directly regulated by different stoichiometries of cytokine receptors represents a hitherto unexplained mechanism underlying cell-fate decisions in cancer stem cell hierarchies. This article is highlighted in the In This Issue feature, p. 1749
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854355.V1
Abstract: Key interactions between distinct residues in the IL-3R ternary complex crystal structure.
Publisher: Elsevier
Date: 1990
Publisher: Springer Science and Business Media LLC
Date: 25-11-2013
DOI: 10.1038/ONC.2013.502
Abstract: Sphingosine kinase 1 (SK1) is a lipid kinase that catalyses the formation of sphingosine-1-phosphate (S1P). Considerable evidence has implicated elevated cellular SK1 in tumour development, progression and disease severity. In particular, SK1 has been shown to enhance cell survival and proliferation and induce neoplastic transformation. Although S1P has been found to have both cell-surface G-protein-coupled receptors and intracellular targets, the specific downstream pathways mediating oncogenic signalling by SK1 remain poorly defined. Here, using a gene expression array approach, we have demonstrated a novel mechanism whereby SK1 regulates cell survival, proliferation and neoplastic transformation through enhancing expression of transferrin receptor 1 (TFR1). We showed that elevated levels of SK1 enhanced total as well as cell-surface TFR1 expression, resulting in increased transferrin uptake into cells. Notably, we also found that SK1 activation and localization to the plasma membrane, which are critical for its oncogenic effects, are necessary for regulation of TFR1 expression specifically through engagement of the S1P G-protein coupled receptor, S1P2. Furthermore, we showed that blocking TFR1 function with a neutralizing antibody inhibits SK1-induced cell proliferation, survival and neoplastic transformation of NIH3T3 fibroblasts. Similar effects were observed following antagonism of S1P2. Together these findings suggest that TFR1 has an important role in SK1-mediated oncogenesis.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709858
Abstract: Increasing IL3Rα/βc ratios lead to hexameric receptor assembly and augmented quiescence.
Publisher: Springer Science and Business Media LLC
Date: 11-07-2012
DOI: 10.1038/ONC.2011.293
Abstract: The transcription factor FOXP3 has been identified as a tumour suppressor in the breast and prostate epithelia, but little is known about its specific mechanism of action. We have identified a feed-forward regulatory loop in which FOXP3 suppresses the expression of the oncogene SATB1. In particular, we demonstrate that SATB1 is not only a direct target of FOXP3 repression, but that FOXP3 also induces two miRs, miR-7 and miR-155, which specifically target the 3'-UTR of SATB1 to further regulate its expression. We conclude that FOXP3-regulated miRs form part of the mechanism by which FOXP3 prevents the transformation of the healthy breast epithelium to a cancerous phenotype. Approaches aimed at restoring FOXP3 function and the miRs it regulates could help provide new approaches to target breast cancer.
Publisher: Oxford University Press (OUP)
Date: 30-01-2013
DOI: 10.1093/BIOINFORMATICS/BTT048
Abstract: Motivation: microRNAs (miRNAs) are known to play an essential role in the post-transcriptional gene regulation in plants and animals. Currently, several computational approaches have been developed with a shared aim to elucidate miRNA–mRNA regulatory relationships. Although these existing computational methods discover the statistical relationships, such as correlations and associations between miRNAs and mRNAs at data level, such statistical relationships are not necessarily the real causal regulatory relationships that would ultimately provide useful insights into the causes of gene regulations. The standard method for determining causal relationships is randomized controlled perturbation experiments. In practice, however, such experiments are expensive and time consuming. Our motivation for this study is to discover the miRNA–mRNA causal regulatory relationships from observational data. Results: We present a causality discovery-based method to uncover the causal regulatory relationship between miRNAs and mRNAs, using expression profiles of miRNAs and mRNAs without taking into consideration the previous target information. We apply this method to the epithelial-to-mesenchymal transition (EMT) datasets and validate the computational discoveries by a controlled biological experiment for the miR-200 family. A significant portion of the regulatory relationships discovered in data is consistent with those identified by experiments. In addition, the top genes that are causally regulated by miRNAs are highly relevant to the biological conditions of the datasets. The results indicate that the causal discovery method effectively discovers miRNA regulatory relationships in data. Although computational predictions may not completely replace intervention experiments, the accurate and reliable discoveries in data are cost effective for the design of miRNA experiments and the understanding of miRNA–mRNA regulatory relationships. Availability: The R scripts are in the Supplementary material. Contact: thuc_duy.le@mymail.unisa.edu.au or jiuyong.li@unisa.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: EMBO
Date: 28-07-2014
Abstract: The micro RNA s of the miR‐200 family maintain the central characteristics of epithelia and inhibit tumor cell motility and invasiveness. Using the Ago‐ HITS ‐ CLIP technology for transcriptome‐wide identification of direct micro RNA targets in living cells, along with extensive validation to verify the reliability of the approach, we have identified hundreds of miR‐200a and miR‐200b targets, providing insights into general features of mi RNA target site selection. Gene ontology analysis revealed a predominant effect of miR‐200 targets in widespread coordinate control of actin cytoskeleton dynamics. Functional characterization of the miR‐200 targets indicates that they constitute subnetworks that underlie the ability of cancer cells to migrate and invade, including coordinate effects on Rho‐ ROCK signaling, invadopodia formation, MMP activity, and focal adhesions. Thus, the miR‐200 family maintains the central characteristics of the epithelial phenotype by acting on numerous targets at multiple levels, encompassing both cytoskeletal effectors that control actin filament organization and dynamics, and upstream signals that locally regulate the cytoskeleton to maintain cell morphology and prevent cell migration.
Publisher: Wiley
Date: 17-03-2022
DOI: 10.1002/WRNA.1724
Abstract: The RNA-binding protein Quaking (QKI) has emerged as a potent regulator of cellular differentiation in developmental and pathological processes. The QKI gene is itself alternatively spliced to produce three major isoforms, QKI-5, QKI-6, and QKI-7, that possess very distinct functions. Here, we highlight roles of the different QKI isoforms in neuronal, vascular, muscle, and monocyte cell differentiation, and during epithelial-mesenchymal transition in cancer progression. QKI isoforms control cell differentiation through regulating alternative splicing, mRNA stability and translation, with activities in gene transcription now also becoming evident. These erse functions of the QKI isoforms contribute to their broad influences on RNA metabolism and cellular differentiation. This article is categorized under: RNA Interactions with Proteins and Other Molecules Protein-RNA Interactions: Functional Implications RNA Processing Splicing Regulation/Alternative Splicing RNA in Disease and Development RNA in Development.
Publisher: Cold Spring Harbor Laboratory
Date: 02-12-2022
DOI: 10.1101/2022.12.01.518773
Abstract: Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3’ end anchored RNA sequencing, we mapped the alternative polyadenylation landscape (APA) following TGF-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3’UTR lengthening during this cell state transition. Analysis of the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, revealed enrichment of its binding adjacent to cleavage and polyadenylation sites within 3’UTRs. Following QKI knockdown, APA of many transcripts are altered to produce predominantly shorter 3’UTRs associated with reduced gene expression. Among these, QKI binds to its own cleavage site to produce a transcript with a longer 3’UTR. These findings reveal extensive changes in APA occur during EMT and identify a novel function for QKI in this process.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709855
Abstract: Increasing IL3Rα/βc ratios and enforced hexamer signaling lead to reduced differentiation in in vivo engraftments.
Publisher: Wiley
Date: 06-1985
DOI: 10.1111/J.1749-6632.1985.TB18436.X
Abstract: Data from isotopic exchange studies and from experiments with 32P- and 14C-labeled enzyme-bound intermediates support the following description of the first partial reaction: (Formula: see text). From studies of the transfer of the carboxyl-group from ENZ-biotin-CO2- to pyruvate or its analogues we propose that binding of the acceptor substrate induces the translation of carboxybiotin from the first to the second partial reaction site. The studies on the translocation of carboxybiotin can be summarized in the following reaction scheme: (Formula: see text). Where k+3 less than k+1, k-1, k+2 and k-2. Thus, the rate-limited step is governed by k+3 which represents the movement of carboxybiotin from the first subsite to the second.
Publisher: Wiley
Date: 1995
DOI: 10.1002/J.1460-2075.1995.TB07012.X
Abstract: We have performed a systematic study of the effect of artificial hairpins on pre-mRNA splicing in protoplasts of a dicot plant, Nicotiana plumbaginifolia. Hairpins with a potential to form 18 or 24 bp stems strongly inhibit splicing when they sequester the 5' splice site or are placed in the middle of short introns. However, similar 24 bp hairpins sequestering the 3' splice site do not prevent this site from being used as an acceptor. Utilization of the stem-located 3' site requires that the base of the stem is separated from the upstream 5' splice site by a minimum of approximately 45 nucleotides and that another 'helper' 3' splice site is present downstream of the stem. The results indicate that the spliceosome or factors associated with it may have a potential to unfold secondary structure present in the downstream portion of the intron, prior to or at the step of the 3' splice site selection. The finding that the helper 3' site is required for utilization of the stem-located acceptor confirms and extends previous observations, obtained with HeLa cell in vitro splicing systems, indicating that the 3' splice site may be recognized at least twice during spliceosome assembly.
Publisher: Oxford University Press (OUP)
Date: 12-2020
DOI: 10.1093/BIOINFORMATICS/BTAA797
Abstract: Identifying cancer driver genes is a key task in cancer informatics. Most existing methods are focused on in idual cancer drivers which regulate biological processes leading to cancer. However, the effect of a single gene may not be sufficient to drive cancer progression. Here, we hypothesize that there are driver gene groups that work in concert to regulate cancer, and we develop a novel computational method to detect those driver gene groups. We develop a novel method named DriverGroup to detect driver gene groups by using gene expression and gene interaction data. The proposed method has three stages: (i) constructing the gene network, (ii) discovering critical nodes of the constructed network and (iii) identifying driver gene groups based on the discovered critical nodes. Before evaluating the performance of DriverGroup in detecting cancer driver groups, we firstly assess its performance in detecting the influence of gene groups, a key step of DriverGroup. The application of DriverGroup to DREAM4 data demonstrates that it is more effective than other methods in detecting the regulation of gene groups. We then apply DriverGroup to the BRCA dataset to identify driver groups for breast cancer. The identified driver groups are promising as several group members are confirmed to be related to cancer in literature. We further use the predicted driver groups in survival analysis and the results show that the survival curves of patient subpopulations classified using the predicted driver groups are significantly differentiated, indicating the usefulness of DriverGroup. DriverGroup is available at vvhoang/DriverGroup Supplementary data are available at Bioinformatics online.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709873.V1
Abstract: IL3Rα/βc transcript and protein expression ratio in AML patient s les.
Publisher: American Diabetes Association
Date: 14-04-2010
DOI: 10.2337/DB09-1736
Abstract: Increased deposition of extracellular matrix (ECM) within the kidney is driven by profibrotic mediators including transforming growth factor-β (TGF-β) and connective tissue growth factor (CTGF). We investigated whether some of their effects may be mediated through changes in expression of certain microRNAs (miRNAs). Proximal tubular cells, primary rat mesangial cells, and human podocytes were analyzed for changes in the expression of key genes, ECM proteins, and miRNA after exposure to TGF-β (1–10 ng/μl). Tubular cells were also infected with CTGF-adenovirus. Kidneys from diabetic apoE mice were also analyzed for changes in gene expression and miRNA levels. TGF-β treatment was associated with morphologic and phenotypic changes typical of epithelial-mesenchymal transition (EMT) including increased fibrogenesis in all renal cell types and decreased E-cadherin expression in tubular cells. TGF-β treatment also modulated the expression of certain miRNAs, including decreased expression of miR-192/215 in tubular cells, mesangial cells, which are also decreased in diabetic kidney. Ectopic expression of miR-192/215 increased E-cadherin levels via repressed translation of ZEB2 mRNA, in the presence and absence of TGF-β, as demonstrated by a ZEB2 3′-untranslated region luciferase reporter assay. However, ectopic expression of miR-192/215 did not affect the expression of matrix proteins or their induction by TGF-β. In contrast, CTGF increased miR-192/215 levels, causing a decrease in ZEB2, and consequently increased E-cadherin mRNA. These data demonstrate the linking role of miRNA-192/215 and ZEB2 in TGF-β/CTGF–mediated changes in E-cadherin expression. These changes appear to occur independently of augmentation of matrix protein synthesis, suggesting that a multistep EMT program is not necessary for fibrogenesis to occur.
Publisher: Cold Spring Harbor Laboratory
Date: 15-09-2009
DOI: 10.1101/GAD.1820209
Abstract: Metastatic disease is a primary cause of cancer-related death, and factors governing tumor cell metastasis have not been fully elucidated. Here, we address this question by using tumor cell lines derived from mice that develop metastatic lung adenocarcinoma owing to expression of mutant K-ras and p53 . Despite having widespread somatic genetic alterations, the metastasis-prone tumor cells retained a marked plasticity. They transited reversibly between epithelial and mesenchymal states, forming highly polarized epithelial spheres in three-dimensional culture that underwent epithelial-to-mesenchymal transition (EMT) following treatment with transforming growth factor-β or injection into syngeneic mice. This transition was entirely dependent on the microRNA (miR)-200 family, which decreased during EMT. Forced expression of miR-200 abrogated the capacity of these tumor cells to undergo EMT, invade, and metastasize, and conferred transcriptional features of metastasis-incompetent tumor cells. We conclude that tumor cell metastasis is regulated by miR-200 expression, which changes in response to contextual extracellular cues.
Publisher: Elsevier BV
Date: 04-2014
Publisher: Elsevier BV
Date: 10-2012
DOI: 10.1016/J.BBRC.2012.09.059
Abstract: Matrigel is a medium rich in extracellular matrix (ECM) components used for three-dimensional cell culture and is known to alter cellular phenotypes and gene expression. microRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression and have roles in cancer. While miRNA profiles of numerous cell lines cultured on plastic have been reported, the influence of Matrigel-based culture on cancer cell miRNA expression is largely unknown. This study investigated the influence of Matrigel on the expression of miRNAs that might facilitate ECM-associated cancer cell growth. We performed miRNA profiling by microarray using two colon cancer cell lines (SW480 and SW620), identifying significant differential expression of miRNAs between cells cultured in Matrigel and on plastic. Many of these miRNAs have previously been implicated in cancer-related processes. A common Matrigel-induced miRNA signature comprised of up-regulated miR-1290 and miR-210 and down-regulated miR-29b and miR-32 was identified using RT-qPCR across five epithelial cancer cell lines (SW480, SW620, HT-29, A549 and MDA-MB-231). Experimental modulation of these miRNAs altered expression of their known target mRNAs involved in cell adhesion, proliferation and invasion, in colon cancer cell lines. Furthermore, ITGA5 was identified as a novel putative target of miR-32 that may facilitate cancer cell interactions with the ECM. We propose that culture of cancer cell lines in Matrigel more accurately recapitulates miRNA expression and function in cancer than culture on plastic and thus is a valuable approach to the in vitro study of miRNAs.
Publisher: Impact Journals, LLC
Date: 18-04-2015
Abstract: SKBR3-cells, characterized by ERBB2/RARA co- lification, represent a subgroup of HER2+ breast-cancers sensitive to all-trans retinoic acid (ATRA) and Lapatinib. In this model, the two agents alone or in combination modulate the expression of 174 microRNAs (miRs). These miRs and predicted target-transcripts are organized in four interconnected modules (Module-1 to -4). Module-1 and Module-3 consist of ATRA/Lapatinib up-regulated and potentially anti-oncogenic miRs, while Module-2 contains ATRA/Lapatinib down-regulated and potentially pro-oncogenic miRs. Consistent with this, the expression levels of Module-1/-3 and Module-2 miRs are higher and lower, respectively, in normal mammary tissues relative to ductal-carcinoma-in-situ, invasive-ductal-carcinoma and metastases. This indicates associations between tumor-progression and the expression profiles of Module-1 to -3 miRs. Similar associations are observed with tumor proliferation-scores, staging, size and overall-survival using TCGA (The Cancer Genome Atlas) data. Forced expression of Module-1 miRs, (miR-29a-3p miR-874-3p) inhibit SKBR3-cell growth and Module-3 miRs (miR-575 miR-1225-5p) reduce growth and motility. Module-2 miRs (miR-125a miR-193 miR-210) increase SKBR3 cell growth, survival and motility. Some of these effects are of general significance, being replicated in other breast cancer cell lines representing the heterogeneity of this disease. Finally, our study demonstrates that HIPK2-kinase and the PLCXD1-phospholipase-C are novel targets of miR-193a-5p/miR-210-3p and miR-575/miR-1225-5p, respectively.
Publisher: Wiley
Date: 04-09-1998
DOI: 10.1016/S0014-5793(98)01025-4
Abstract: Vascular endothelial growth factor (VEGF), an essential regulator of angiogenesis during early development as well as during the growth of solid tumours, bears an unusually large 5' untranslated region (5'-UTR) in the mRNA of over 1000 nucleotides. We found that the VEGF 5'-UTR, despite being GC-rich and containing an upstream short open reading frame, promotes efficient translation of a luciferase reporter. The VEGF 5'-UTR also allowed translation of luciferase from a dicistronic mRNA when placed between the two cistrons, demonstrating that it contains an internal ribosome entry site. Deletion analysis indicated that the IRES resides towards the 3' end of the 5'-UTR.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854352.V1
Abstract: IL3Rα P248 at the IL-3R assembly interface is critical for cell differentiation.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709849
Abstract: Summary of the key interactions in the IL-3R ternary complex in the IL-3R ternary complex crystal structure.
Publisher: Elsevier BV
Date: 07-2023
Publisher: Informa UK Limited
Date: 1992
DOI: 10.3109/08977199209046923
Abstract: Granulocyte-colony stimulating factor (G-CSF) is a haemopoietic growth factor produced by mesenchymal cells but not T lymphocytes after stimulation with specific cytokines or mitogens. A 330 bp promoter fragment of the human G-CSF gene induced reporter gene expression in human embryonic lung fibroblasts in response to tumor necrosis factor-alpha (TNF-alpha) or interleukin-1 beta (IL-1 beta). The same promoter fragment was not active in Jurkat T cells nor did it respond to phorbol ester in either cell type. At least three distinct elements, the CK-1 sequence, a decanucleotide present in haemopoietic growth factor genes, an NF-IL-6 consensus sequence and a consensus octamer sequence, were essential in the G-CSF promoter for TNF-alpha and IL-1 beta response. Mutation of any of these sequences abolished promoter function. In contrast, mutation of two other consensus protein binding sequences, i.e. a Pu-1 site and a CK-2-like sequence, did not eliminate promoter function. Both the CK-1 and octamer sequences acted independently as TNF-alpha and IL-1 beta responsive elements upstream of a heterologous promoter. The response of the octamer sequence and the 330 bp promoter but not the CK-1 sequence was greater with IL-1 beta than TNF-alpha reflecting a similar response of the endogenous gene.
Publisher: Springer Science and Business Media LLC
Date: 26-08-2013
DOI: 10.1038/ONC.2013.332
Publisher: Wiley
Date: 23-01-2014
DOI: 10.1002/WRNA.1217
Abstract: In recent times, microRNA (miRNA) have emerged as primary regulators of fundamental biological processes including cellular differentiation, proliferation, apoptosis, as well as synaptic plasticity. However, miRNAs bind their targets with only partial complementarity, making it very challenging to determine exactly how a miRNA is functioning in specific biological environments. This review discusses key principles of miRNA target recognition and function which have emerged through the progressive advancement of biological and bioinformatics approaches. Ultimately, the integration of gene expression and biochemical methods with sequence- and systems-based bioinformatics approaches will reveal profound insights regarding the importance of target contextual features in determining miRNA target recognition and regulatory outcome, as well as the importance of RNA interaction networks in enabling miRNA to regulate different target genes and functions in specific biological contexts. There is therefore a demand for the elegant design of future experiments such that principles of context-specific miRNA target recognition and regulatory outcome can be accurately modeled in normal developmental and disease states.
Publisher: Oxford University Press (OUP)
Date: 23-07-2014
DOI: 10.1093/BIOINFORMATICS/BTU489
Abstract: Motivation: MicroRNAs (miRNAs) play crucial roles in complex cellular networks by binding to the messenger RNAs (mRNAs) of protein coding genes. It has been found that miRNA regulation is often condition-specific. A number of computational approaches have been developed to identify miRNA activity specific to a condition of interest using gene expression data. However, most of the methods only use the data in a single condition, and thus, the activity discovered may not be unique to the condition of interest. Additionally, these methods are based on statistical associations between the gene expression levels of miRNAs and mRNAs, so they may not be able to reveal real gene regulatory relationships, which are causal relationships. Results: We propose a novel method to infer condition-specific miRNA activity by considering (i) the difference between the regulatory behavior that an miRNA has in the condition of interest and its behavior in the other conditions (ii) the causal semantics of miRNA–mRNA relationships. The method is applied to the epithelial–mesenchymal transition (EMT) and multi-class cancer (MCC) datasets. The validation by the results of transfection experiments shows that our approach is effective in discovering significant miRNA–mRNA interactions. Functional and pathway analysis and literature validation indicate that the identified active miRNAs are closely associated with the specific biological processes, diseases and pathways. More detailed analysis of the activity of the active miRNAs implies that some active miRNAs show different regulation types in different conditions, but some have the same regulation types and their activity only differs in different conditions in the strengths of regulation. Availability and implementation: The R and Matlab scripts are in the Supplementary materials . Contact: jiuyong.li@unisa.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709849.V1
Abstract: Summary of the key interactions in the IL-3R ternary complex in the IL-3R ternary complex crystal structure.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854334
Abstract: Increasing IL3Rα/βc ratios lead to hexameric receptor assembly and augmented quiescence.
Publisher: Elsevier BV
Date: 1985
DOI: 10.1016/0003-9861(85)90646-0
Abstract: The sequence of a 523-bp cDNA, isolated from a clone bank prepared from partially purified rat spleen mRNA coding for thymosin beta 4, was described. The 3' sequence extended through the poly(A) segment and the 5' sequence included 36 bp preceding the translated sequence. The putative amino acid sequence coded by this segment possesses some of the features of a signal peptide.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854331
Abstract: Increasing IL3Rα/βc ratios and enforced hexamer signaling lead to reduced differentiation in in vivo engraftments.
Publisher: American Association for Cancer Research (AACR)
Date: 30-09-2008
DOI: 10.1158/0008-5472.CAN-08-1942
Abstract: Epithelial to mesenchymal transition occurs during embryologic development to allow tissue remodeling and is proposed to be a key step in the metastasis of epithelial-derived tumors. The miR-200 family of microRNAs plays a major role in specifying the epithelial phenotype by preventing expression of the transcription repressors, ZEB1/δEF1 and SIP1/ZEB2. We show here that miR-200a, miR-200b, and the related miR-429 are all encoded on a 7.5-kb polycistronic primary miRNA (pri-miR) transcript. We show that the promoter for the pri-miR is located within a 300-bp segment located 4 kb upstream of miR-200b. This promoter region is sufficient to confer expression in epithelial cells and is repressed in mesenchymal cells by ZEB1 and SIP1 through their binding to a conserved pair of ZEB-type E-box elements located proximal to the transcription start site. These findings establish a double-negative feedback loop controlling ZEB1-SIP1 and miR-200 family expression that regulates cellular phenotype and has direct relevance to the role of these factors in tumor progression. [Cancer Res 2008 (19):7846–54]
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709855.V1
Abstract: Increasing IL3Rα/βc ratios and enforced hexamer signaling lead to reduced differentiation in in vivo engraftments.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854325.V1
Abstract: Summary of the key interactions in the IL-3R ternary complex in the IL-3R ternary complex crystal structure.
Publisher: Future Science Ltd
Date: 08-2008
DOI: 10.2144/000112896
Abstract: Tetracycline-regulated expression systems have been widely used for inducible protein expression in cultured mammalian cells. With these systems, however, leakiness in expression of the target gene in the absence of the inducing agent is a frequent problem. Here we describe a novel approach to overcome this problem that involves the incorporation of AU-rich mRNA destabilizing elements (AREs) into the 3′ untranslated regions of the tetracycline-inducible constructs. Using the inducible expression of sphingosine kinase 1 and 2 in HEK293 cells as model systems, we found this ARE approach to be remarkably successful in ablating expression of these proteins in the absence of doxycycline through decreasing stability of their mRNAs. We show that this undemanding and flexible process results in a substantial decrease in the leakiness of the tetracycline-inducible expression system while maintaining a high level of target protein expression following induction.
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.JBI.2014.08.005
Abstract: Discovering the regulatory relationships between microRNAs (miRNAs) and mRNAs is an important problem that interests many biologists and medical researchers. A number of computational methods have been proposed to infer miRNA-mRNA regulatory relationships, and are mostly based on the statistical associations between miRNAs and mRNAs discovered in observational data. The miRNA-mRNA regulatory relationships identified by these methods can be both direct and indirect regulations. However, differentiating direct regulatory relationships from indirect ones is important for biologists in experimental designs. In this paper, we present a causal discovery based framework (called DirectTarget) to infer direct miRNA-mRNA causal regulatory relationships in heterogeneous data, including expression profiles of miRNAs and mRNAs, and miRNA target information. DirectTarget is applied to the Epithelial to Mesenchymal Transition (EMT) datasets. The validation by experimentally confirmed target databases suggests that the proposed method can effectively identify direct miRNA-mRNA regulatory relationships. To explore the upstream regulators of miRNA regulation, we further identify the causal feedforward patterns (CFFPs) of TF-miRNA-mRNA to provide insights into the miRNA regulation in EMT. DirectTarget has the potential to be applied to other datasets to elucidate the direct miRNA-mRNA causal regulatory relationships and to explore the regulatory patterns.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709870.V1
Abstract: Key interactions between distinct residues in the IL-3R ternary complex crystal structure.
Publisher: Springer Science and Business Media LLC
Date: 31-10-2016
DOI: 10.1038/NRG.2016.134
Abstract: MicroRNAs (miRNAs) participate in most aspects of cellular differentiation and homeostasis, and consequently have roles in many pathologies, including cancer. These small non-coding RNAs exert their effects in the context of complex regulatory networks, often made all the more extensive by the inclusion of transcription factors as their direct targets. In recent years, the increased availability of gene expression data and the development of methodologies that profile miRNA targets en masse have fuelled our understanding of miRNA functions, and of the sources and consequences of miRNA dysregulation. Advances in experimental and computational approaches are revealing not just cancer pathways controlled by single miRNAs but also intermeshed regulatory networks controlled by multiple miRNAs, which often engage in reciprocal feedback interactions with the targets that they regulate.
Publisher: American Society for Clinical Investigation
Date: 04-2011
DOI: 10.1172/JCI42579
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.ABB.2019.108169
Abstract: Pyruvate carboxylase (PC) is a biotin-containing enzyme that converts pyruvate to oxaloacetate. We have previously shown that PC is overexpressed in highly invasive cancer cell lines where it supports biosynthesis during rapid cell growth. Here, we show that miR-143-3p suppresses the expression of PC in MDA-MB-231 cells by targeting its conserved binding site in the 3'-untranslated region (UTR) of human PC mRNA. Incorporation of the PC 3'UTR into a luciferase reporter gene inhibited expression of luciferase by 50% while mutation of the miR-143-3p binding site abrogated this inhibitory effect in MDA-MB-231 cells but not in low aggressive MCF-7 cell line. Transfection of miR-143-3p mimic or overexpression of miR-143-3p using tetracycline-inducible system in MDA-MB-231 cells down-regulated expression of both endogenous PC mRNA and protein by 40% and 50% respectively, confirming the regulatory role of miR-143-3p in PC expression. Induction of miR-143-3p expression at low and high levels lowered proliferation, metabolic activity and migration of MDA-MB-231 cells, in a dose-dependent manner. Re-expression of PC in MDA-MB-231 cells which were induced to express miR-143-3p partially restored migration but not proliferation, indicating that miR-143-3p regulates proliferation and migration through multiple pathways.
Publisher: Springer Science and Business Media LLC
Date: 30-03-2008
DOI: 10.1038/NCB1722
Abstract: Epithelial to mesenchymal transition (EMT) facilitates tissue remodelling during embryonic development and is viewed as an essential early step in tumour metastasis. We found that all five members of the microRNA-200 family (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) and miR-205 were markedly downregulated in cells that had undergone EMT in response to transforming growth factor (TGF)-beta or to ectopic expression of the protein tyrosine phosphatase Pez. Enforced expression of the miR-200 family alone was sufficient to prevent TGF-beta-induced EMT. Together, these microRNAs cooperatively regulate expression of the E-cadherin transcriptional repressors ZEB1 (also known as deltaEF1) and SIP1 (also known as ZEB2), factors previously implicated in EMT and tumour metastasis. Inhibition of the microRNAs was sufficient to induce EMT in a process requiring upregulation of ZEB1 and/or SIP1. Conversely, ectopic expression of these microRNAs in mesenchymal cells initiated mesenchymal to epithelial transition (MET). Consistent with their role in regulating EMT, expression of these microRNAs was found to be lost in invasive breast cancer cell lines with mesenchymal phenotype. Expression of the miR-200 family was also lost in regions of metaplastic breast cancer specimens lacking E-cadherin. These data suggest that downregulation of the microRNAs may be an important step in tumour progression.
Publisher: Informa UK Limited
Date: 08-2014
DOI: 10.1128/MCB.01693-13
Publisher: Cold Spring Harbor Laboratory
Date: 28-11-2019
Abstract: Most microRNAs (miRNAs) are expressed as a mix of length isoforms (referred to as isomiRs). IsomiR stoichiometry can be differentially impacted upon cell stimulation, as recently evidenced by our group in the context of immune responses induced by type-I interferon (IFN). Here, we revisit published RNA-seq data sets of human and mouse macrophages stimulated with bacterial products at the isomiR level. We demonstrate that for several miRNAs, macrophage stimulation induces changes in isomiR stoichiometry. Critically, we find that changes in miRNA expression can be misinterpreted when miRNAs are quantified by RT-qPCR, as primers directed against canonical miRNA sequences may not equally target the different isomiRs that are regulated endogenously. Beyond the case of phagocyte stimulation, our analyses reinforce the concept that analysis of miRNA expression at the isoform level should become standard practice.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709873
Abstract: IL3Rα/βc transcript and protein expression ratio in AML patient s les.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709870
Abstract: Key interactions between distinct residues in the IL-3R ternary complex crystal structure.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709858.V1
Abstract: Increasing IL3Rα/βc ratios lead to hexameric receptor assembly and augmented quiescence.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709861.V1
Abstract: Enrichment of the IL-3R hexamer versus dodecamer gene signature in primitive normal and leukemic stem cells.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854334.V1
Abstract: Increasing IL3Rα/βc ratios lead to hexameric receptor assembly and augmented quiescence.
Publisher: American Association for Cancer Research (AACR)
Date: 20-08-0006
DOI: 10.1158/2159-8290.23854328.V1
Abstract: Data collection and refinement statistics for the IL-3R ternary complex crystal structure.
Publisher: Proceedings of the National Academy of Sciences
Date: 12-1993
Abstract: Interleukin (IL)-3 stimulates hemopoiesis in vitro. However, IL-3 is not normally found in bone marrow, raising doubts as to the in vivo role of IL-3. We have found that human umbilical vein endothelial cells (HUVEC) express functional high-affinity receptors for IL-3 after stimulation with tumor necrosis factor alpha (TNF-alpha), IL-1 beta, or lipopolysaccharide, and that this receptor is involved in inflammatory phenomena. TNF-alpha caused time- and dose-dependent up-regulation of mRNA for the IL-3 receptor alpha and beta chains, with maximal effects occurring 16-36 h after stimulation with TNF-alpha at 100 units/ml. Induction of mRNA correlated with protein expression on the cell surface as judged by monoclonal antibody staining and by the ability of HUVEC to specifically bind 125I-labeled IL-3. Scatchard analysis under optimal conditions of TNF-alpha stimulation revealed approximately 1500 IL-3 receptors per cell, which were of a high-affinity class (Kd = 500 pM) only. In contrast to a previous report, receptors for granulocyte-macrophage colony-stimulating factor could not be detected. IL-3 binding to TNF-alpha-activated HUVEC enhanced IL-8 production, E-selection expression, and neutrophil transmigration. The selective induction of a functional IL-3 receptor on endothelial cells suggests that, beyond hemopoiesis, IL-3 may have an important role in chronic inflammation and in allergic diseases.
Publisher: MDPI AG
Date: 23-10-2021
Abstract: Circular RNAs are regulatory molecules involved in numerous cellular processes and may be involved in tumour growth and diffusion. Here, we define the expression of 15 selected circular RNAs, which may control the process of epithelial-to-mesenchymal transition, using a panel of 18 breast cancer cell lines recapitulating the heterogeneity of these tumours and consisting of three groups according to the mesenchymal/epithelial phenotype. A circular RNA from the DOCK1 gene (hsa_circ_0020397) shows low/undetectable levels in triple-negative mesenchymal cell lines, while its content is high in epithelial cell lines, independent of estrogen receptor or HER2 positivity. RNA-sequencing experiments performed on the triple-negative/mesenchymal MDA-MB-231 and MDA-MB-157 cell lines engineered to overexpress hsa_circ_0020397 demonstrate that the circRNA influences the expression of 110 common genes. Pathway analysis of these genes indicates that overexpression of the circular RNA differentiates the two mesenchymal cell lines along the epithelial pathway and increases cell-to-cell adhesion. This is accompanied by growth inhibition and a reduction in the random/directional motility of the cell lines. The upregulated AGR2, ENPP1, and PPP1R9A genes as well as the downregulated APOE, AQP3, CD99L2, and IGFBP4 genes show an opposite regulation by hsa_circ_0020397 silencing in luminal CAMA1 cells. The results provide novel insights into the role played by specific circular RNAs in the generation rogression of breast cancer.
Publisher: Impact Journals, LLC
Date: 12-06-2018
Publisher: Proceedings of the National Academy of Sciences
Date: 26-11-1996
Abstract: The control of mRNA stability is crucial to the regulation of cytokine expression. We describe here a novel, potent destabilizing element found in the 3′ untranslated region of granulocyte colony-stimulating factor mRNA. This element, which appears to require at least one stem–loop structure, we term the stem–loop destabilizing element (SLDE). Functionally equivalent elements appear to also exist in the interleukin 2 and interleukin 6 mRNAs. The SLDE is functionally distinct from the A+U-rich elements, which are also present in these and other cytokine mRNAs, because it destabilizes a chimeric mRNA in a tumor cell line in which A+U-rich elements do not function. In addition, the effect of the SLDE is insensitive to calcium ionophore and is therefore regulated independently of A+U destabilizing elements. The existence of two distinct mRNA-destabilizing elements provides an additional mechanism for the differential regulation of cytokine expression.
Publisher: Springer Science and Business Media LLC
Date: 20-10-2020
DOI: 10.1038/S41568-020-00306-0
Abstract: While the processing of mRNA is essential for gene expression, recent findings have highlighted that RNA processing is systematically altered in cancer. Mutations in RNA splicing factor genes and the shortening of 3' untranslated regions are widely observed. Moreover, evidence is accumulating that other types of RNAs, including circular RNAs, can contribute to tumorigenesis. In this Review, we highlight how altered processing or activity of coding and non-coding RNAs contributes to cancer. We introduce the regulation of gene expression by coding and non-coding RNA and discuss both established roles (microRNAs and long non-coding RNAs) and emerging roles (selective mRNA processing and circular RNAs) for RNAs, highlighting the potential mechanisms by which these RNA subtypes contribute to cancer. The widespread alteration of coding and non-coding RNA demonstrates that altered RNA biogenesis contributes to multiple hallmarks of cancer.
Publisher: Elsevier BV
Date: 11-2012
DOI: 10.1016/J.TIG.2012.07.005
Abstract: The development of deep sequencing has enabled the identification of novel microRNAs (miRNAs), leading to a growing appreciation for the fact that in idual miRNAs can be heterogeneous in length and/or sequence. These variants, termed isomiRs, can be expressed in a cell-specific manner, and numerous recent studies suggest that at least some isomiRs may affect target selection, miRNA stability, or loading into the RNA-induced silencing complex (RISC). Reports indicating differential functionality for isomiRs are currently confined to several specific variants, and although isomiRs are common, their broader biological significance is yet to be fully resolved. Here we review the growing body of evidence suggesting that isomiRs have functional differences, of which at least some appear biologically relevant, and caution researchers to take miRNA isoforms into consideration in their experiments.
Publisher: Informa UK Limited
Date: 03-2002
Publisher: Hindawi Limited
Date: 2008
DOI: 10.1100/TSW.2008.115
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.CONTRACEPTION.2013.11.002
Abstract: Sino-implant (II) is a two-rod subcutaneous contraceptive implant used up to 4 years, containing 150 mg of levonorgestrel. We conducted two observational studies of Sino-implant (II) to evaluate its performance in routine service delivery settings. We enrolled 1326 women age 18-44 who had Sino-implant (II) inserted at clinics in Pakistan and Kenya. Women were followed-up using either an active or passive follow-up scheme in each study. Study outcomes were: one-year cumulative pregnancy and discontinuation rates rates of insertion and removal complications adverse event and side effect rates reasons for discontinuation and implant acceptability and satisfaction with clinic services. A total of 754 women returned for at least one follow-up visit. The overall Pearl pregnancy rate was 0.4 per 100 woman-years [95% confidence interval (CI) 0.1, 0.9] resulting from 1 confirmed post-insertion pregnancy in Kenya and 4 in Pakistan. Country-specific Pearl rates were 0.2 (95% CI 0.0, 0.9) in Kenya and 0.6 (95% CI 0.2, 1.6) in Pakistan. The total cumulative 12-month probability of removal was 7.6% (95% CI 6.1, 9.1), with country-specific removal probabilities of 3.7% in Kenya (95% CI 2.1, 5.3) and 10.8% in Pakistan (95% CI 8.5, 13.2). Four serious adverse events occurred in Kenya and none occurred in Pakistan one SAE (an ectopic pregnancy) was possibly related to Sino-implant (II). Most women in both countries said they would recommend the implant to others. The results from these studies reveal high effectiveness and favorable safety and acceptability during the first year of use of Sino-implant. The favorable Sino-implant (II) findings from Kenya and Pakistan provide further evidence from disparate regions that Sino-implant (II) is safe, effective and acceptable during routine service delivery.
Publisher: Informa UK Limited
Date: 1993
DOI: 10.3109/08977199309046929
Abstract: The high affinity receptors for GM-CSF, IL-3 and IL-5 are heterodimers consisting of a ligand-specific alpha chain and a common beta chain. These proteins are members of a family of proteins known as the "cytokine receptor family" which is characterized by the presence of a 200-residue ligand-binding module. The GM-CSF, IL-3 and IL-5 receptor alpha chains constitute a distinct subgroup and share features not found in other members of the cytokine receptor family, features which we propose to be important for their interaction with the common beta chain and for their binding of the structurally-related ligands. The growth hormone receptor is a well-characterized member of the cytokine receptor family. Based on the structure of the complex between growth hormone and its receptor, we have proposed sites of contact between the GM-CSF, IL-3 and IL-5 receptors and their cognate ligands.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709867.V1
Abstract: IL3Rα P248 at the IL-3R assembly interface is critical for cell differentiation.
Publisher: American Society for Cell Biology (ASCB)
Date: 15-05-2011
Abstract: Epithelial-mesenchymal transition (EMT) is a form of cellular plasticity that is critical for embryonic development and tumor metastasis. A double-negative feedback loop involving the miR-200 family and ZEB (zinc finger E-box-binding homeobox) transcription factors has been postulated to control the balance between epithelial and mesenchymal states. Here we demonstrate using the epithelial Madin Darby canine kidney cell line model that, although manipulation of the ZEB/miR-200 balance is able to repeatedly switch cells between epithelial and mesenchymal states, the induction and maintenance of a stable mesenchymal phenotype requires the establishment of autocrine transforming growth factor-β (TGF-β) signaling to drive sustained ZEB expression. Furthermore, we show that prolonged autocrine TGF-β signaling induced reversible DNA methylation of the miR-200 loci with corresponding changes in miR-200 levels. Collectively, these findings demonstrate the existence of an autocrine TGF-β/ZEB/miR-200 signaling network that regulates plasticity between epithelial and mesenchymal states. We find a strong correlation between ZEBs and TGF-β and negative correlations between miR-200 and TGF-β and between miR-200 and ZEBs, in invasive ductal carcinomas, consistent with an autocrine TGF-β/ZEB/miR-200 signaling network being active in breast cancers.
Publisher: Elsevier BV
Date: 02-2013
DOI: 10.1593/NEO.121828
Publisher: Springer New York
Date: 2018
DOI: 10.1007/978-1-4939-7562-4_8
Abstract: Circular RNAs (circRNAs) constitute an emerging class of widespread, abundant, and evolutionarily conserved noncoding RNA. They play important and erse roles in cell development, growth, and tumorigenesis, but functions of the majority of circRNAs remain enigmatic. In order to investigate circRNA function it is necessary to manipulate its expression. While various standard approaches exist for circRNA knockdown, here we present cloning vectors for simplifying the laborious process of cloning circRNAs to achieve high-efficiency overexpression in mammalian cell lines.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709864
Abstract: The IL-3R dodecamer activates STAT1 to induce cell differentiation.
Publisher: American Society for Clinical Investigation
Date: 04-09-2012
DOI: 10.1172/JCI63608
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709861
Abstract: Enrichment of the IL-3R hexamer versus dodecamer gene signature in primitive normal and leukemic stem cells.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709864.V1
Abstract: The IL-3R dodecamer activates STAT1 to induce cell differentiation.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854340.V1
Abstract: Enrichment of the IL-3R hexamer versus dodecamer gene signature in primitive normal and leukemic stem cells.
Publisher: American Association for Cancer Research (AACR)
Date: 14-03-2018
DOI: 10.1158/1078-0432.CCR-17-2485
Abstract: Purpose: The majority of gastric cancer patients are diagnosed with late-stage disease, for which distinct molecular subtypes have been identified that are potentially amenable to targeted therapies. However, there exists no molecular classification system with prognostic power for early-stage gastric cancer (EGC) because the molecular events promoting gastric cancer initiation remain ill-defined. Experimental Design: miRNA microarrays were performed on gastric tissue from the gp130F/F preclinical EGC mouse model, prior to tumor initiation. Computation prediction algorithms were performed on multiple data sets and independent gastric cancer patient cohorts. Quantitative real-time PCR expression profiling was undertaken in gp130F/F-based mouse strains and human gastric cancer cells genetically engineered for suppressed activation of the oncogenic latent transcription factor STAT3. Human gastric cancer cells with modulated expression of the miR-200 family member miR-429 were also assessed for their proliferative response. Results: Increased expression of miR-200 family members is associated with both tumor initiation in a STAT3-dependent manner in gp130F/F mice and EGC (i.e., stage IA) in patient cohorts. Overexpression of miR-429 also elicited contrasting pro- and antiproliferative responses in human gastric cancer cells depending on their cellular histologic subtype. We also identified a miR-200 family–regulated 15-gene signature that integrates multiple key current indicators of EGC, namely tumor invasion depth, differentiation, histology, and stage, and provides superior predictive power for overall survival compared with each EGC indicator alone. Conclusions: Collectively, our discovery of a STAT3-regulated, miR-200 family–associated gene signature specific for EGC, with predictive power, provides a molecular rationale to classify and stratify EGC patients for endoscopic treatment. Clin Cancer Res 24(6) 1459–72. ©2018 AACR.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854328
Abstract: Data collection and refinement statistics for the IL-3R ternary complex crystal structure.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709867
Abstract: IL3Rα P248 at the IL-3R assembly interface is critical for cell differentiation.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854325
Abstract: Summary of the key interactions in the IL-3R ternary complex in the IL-3R ternary complex crystal structure.
Publisher: Springer Science and Business Media LLC
Date: 03-09-2020
DOI: 10.1038/S41598-020-71323-0
Abstract: The attachment of unique molecular identifiers (UMIs) to RNA molecules prior to PCR lification and sequencing, makes it possible to lify libraries to a level that is sufficient to identify rare molecules, whilst simultaneously eliminating PCR bias through the identification of duplicated reads. Accurate de-duplication is dependent upon a sufficiently complex pool of UMIs to allow unique labelling. In applications dealing with complex libraries, such as total RNA-seq, only a limited variety of UMIs are required as the variation in molecules to be sequenced is enormous. However, when sequencing a less complex library, such as small RNAs for which there is a more limited range of possible sequences, we find increased variation in UMIs are required, even beyond that provided in a commercial kit specifically designed for the preparation of small RNA libraries for sequencing. We show that a pool of UMIs randomly varying across eight nucleotides is not of sufficient depth to uniquely tag the microRNAs to be sequenced. This results in over de-duplication of reads and the marked under-estimation of expression of the more abundant microRNAs. Whilst still arguing for the utility of UMIs, this work demonstrates the importance of their considered design to avoid errors in the estimation of gene expression in libraries derived from select regions of the transcriptome or small genomes.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.C.6749895.V2
Abstract: Abstract Leukemia stem cells (LSC) possess distinct self-renewal and arrested differentiation properties that are responsible for disease emergence, therapy failure, and recurrence in acute myeloid leukemia (AML). Despite AML displaying extensive biological and clinical heterogeneity, LSC with high interleukin-3 receptor (IL3R) levels are a constant yet puzzling feature, as this receptor lacks tyrosine kinase activity. Here, we show that the heterodimeric IL3Rα/βc receptor assembles into hexamers and dodecamers through a unique interface in the 3D structure, where high IL3Rα/βc ratios bias hexamer formation. Importantly, receptor stoichiometry is clinically relevant as it varies across the in idual cells in the AML hierarchy, in which high IL3Rα/βc ratios in LSCs drive hexamer-mediated stemness programs and poor patient survival, while low ratios mediate differentiation. Our study establishes a new paradigm in which alternative cytokine receptor stoichiometries differentially regulate cell fate, a signaling mechanism that may be generalizable to other transformed cellular hierarchies and of potential therapeutic significance. Significance: Stemness is a hallmark of many cancers and is largely responsible for disease emergence, progression, and relapse. Our finding that clinically significant stemness programs in AML are directly regulated by different stoichiometries of cytokine receptors represents a hitherto unexplained mechanism underlying cell-fate decisions in cancer stem cell hierarchies. i a href="ancerdiscovery/article/doi/10.1158/2159-8290.CD-13-8-ITI" target="_blank" This article is highlighted in the In This Issue feature, p. 1749 /a /i /
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.C.6749895.V1
Abstract: Abstract Leukemia stem cells (LSC) possess distinct self-renewal and arrested differentiation properties that are responsible for disease emergence, therapy failure, and recurrence in acute myeloid leukemia (AML). Despite AML displaying extensive biological and clinical heterogeneity, LSC with high interleukin-3 receptor (IL3R) levels are a constant yet puzzling feature, as this receptor lacks tyrosine kinase activity. Here, we show that the heterodimeric IL3Rα/βc receptor assembles into hexamers and dodecamers through a unique interface in the 3D structure, where high IL3Rα/βc ratios bias hexamer formation. Importantly, receptor stoichiometry is clinically relevant as it varies across the in idual cells in the AML hierarchy, in which high IL3Rα/βc ratios in LSCs drive hexamer-mediated stemness programs and poor patient survival, while low ratios mediate differentiation. Our study establishes a new paradigm in which alternative cytokine receptor stoichiometries differentially regulate cell fate, a signaling mechanism that may be generalizable to other transformed cellular hierarchies and of potential therapeutic significance. Significance: Stemness is a hallmark of many cancers and is largely responsible for disease emergence, progression, and relapse. Our finding that clinically significant stemness programs in AML are directly regulated by different stoichiometries of cytokine receptors represents a hitherto unexplained mechanism underlying cell-fate decisions in cancer stem cell hierarchies. /
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854355
Abstract: Key interactions between distinct residues in the IL-3R ternary complex crystal structure.
Publisher: Springer Science and Business Media LLC
Date: 07-1990
DOI: 10.1007/BF00633841
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854352
Abstract: IL3Rα P248 at the IL-3R assembly interface is critical for cell differentiation.
Publisher: Elsevier BV
Date: 08-1996
Publisher: Informa UK Limited
Date: 06-1996
Publisher: Public Library of Science (PLoS)
Date: 10-06-2015
Publisher: Elsevier
Date: 1985
Publisher: Oxford University Press (OUP)
Date: 12-2014
DOI: 10.1093/NAR/GKU1242
Publisher: Massachusetts Medical Society
Date: 27-07-2000
Publisher: EMBO
Date: 11-04-2008
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.C.6749895
Abstract: Abstract Leukemia stem cells (LSC) possess distinct self-renewal and arrested differentiation properties that are responsible for disease emergence, therapy failure, and recurrence in acute myeloid leukemia (AML). Despite AML displaying extensive biological and clinical heterogeneity, LSC with high interleukin-3 receptor (IL3R) levels are a constant yet puzzling feature, as this receptor lacks tyrosine kinase activity. Here, we show that the heterodimeric IL3Rα/βc receptor assembles into hexamers and dodecamers through a unique interface in the 3D structure, where high IL3Rα/βc ratios bias hexamer formation. Importantly, receptor stoichiometry is clinically relevant as it varies across the in idual cells in the AML hierarchy, in which high IL3Rα/βc ratios in LSCs drive hexamer-mediated stemness programs and poor patient survival, while low ratios mediate differentiation. Our study establishes a new paradigm in which alternative cytokine receptor stoichiometries differentially regulate cell fate, a signaling mechanism that may be generalizable to other transformed cellular hierarchies and of potential therapeutic significance. Significance: Stemness is a hallmark of many cancers and is largely responsible for disease emergence, progression, and relapse. Our finding that clinically significant stemness programs in AML are directly regulated by different stoichiometries of cytokine receptors represents a hitherto unexplained mechanism underlying cell-fate decisions in cancer stem cell hierarchies. i a href="ancerdiscovery/article/doi/10.1158/2159-8290.CD-13-8-ITI" target="_blank" This article is highlighted in the In This Issue feature, p. 1749 /a /i /
Publisher: American Society of Hematology
Date: 17-10-2013
DOI: 10.1182/BLOOD-2012-12-473017
Abstract: Blockmirs are designed against the miR-27 binding site in VE-cadherin and display restricted specificity. Blockmirs regulate VE-cadherin and endothelial cell junctions, inhibit edema, and promote angiogenesis associated with ischemia.
Publisher: Springer Science and Business Media LLC
Date: 02-2012
DOI: 10.1038/NCB2431
Publisher: Public Library of Science (PLoS)
Date: 24-08-2020
Publisher: Public Library of Science (PLoS)
Date: 25-09-2013
Publisher: Springer Science and Business Media LLC
Date: 21-02-2010
DOI: 10.1038/NCB0310-209
Abstract: The microRNA miR-9 is induced by Myc in breast cancer cells where it targets the major epithelial adherens junction protein, E-cadherin. This primes the cancer cells for epithelial-mesenchymal transition (EMT) and also stimulates angiogenesis in tumours.
Publisher: Rockefeller University Press
Date: 07-01-2021
Abstract: Receptor degradation terminates signaling by activated receptor tyrosine kinases. Degradation of EGFR occurs in lysosomes and requires the switching of RAB5 for RAB7 on late endosomes to enable their fusion with the lysosome, but what controls this critical switching is poorly understood. We show that the tyrosine kinase FER alters PKCδ function by phosphorylating it on Y374, and that phospho-Y374-PKCδ prevents RAB5 release from nascent late endosomes, thereby inhibiting EGFR degradation and promoting the recycling of endosomal EGFR to the cell surface. The rapid association of phospho-Y374-PKCδ with EGFR-containing endosomes is diminished by PTPN14, which dephosphorylates phospho-Y374-PKCδ. In triple-negative breast cancer cells, the FER-dependent phosphorylation of PKCδ enhances EGFR signaling and promotes anchorage-independent cell growth. Importantly, increased Y374-PKCδ phosphorylation correlating with arrested late endosome maturation was identified in ∼25% of triple-negative breast cancer patients, suggesting that dysregulation of this pathway may contribute to their pathology.
Publisher: Oxford University Press (OUP)
Date: 31-07-2023
DOI: 10.1093/NAR/GKAD645
Abstract: MiRNAs post-transcriptionally repress gene expression by binding to mRNA 3′UTRs, but the extent to which they act through protein coding regions (CDS regions) is less well established. MiRNA interaction studies show a substantial proportion of binding occurs in CDS regions, however sequencing studies show much weaker effects on mRNA levels than from 3′UTR interactions, presumably due to competition from the translating ribosome. Consequently, most target prediction algorithms consider only 3′UTR interactions. However, the consequences of CDS interactions may have been underestimated, with the reporting of a novel mode of miRNA-CDS interaction requiring base pairing of the miRNA 3′ end, but not the canonical seed site, leading to repression of translation with little effect on mRNA turnover. Using extensive reporter, western blotting and bioinformatic analyses, we confirm that miRNAs can indeed suppress genes through CDS-interaction in special circumstances. However, in contrast to that previously reported, we find repression requires extensive base-pairing, including of the canonical seed, but does not strictly require base pairing of the 3′ miRNA terminus and is mediated through reducing mRNA levels. We conclude that suppression of endogenous genes can occur through miRNAs binding to CDS, but the requirement for extensive base-pairing likely limits the regulatory impacts to modest effects on a small subset of targets.
Publisher: Informa UK Limited
Date: 1995
DOI: 10.3109/10428199509059635
Abstract: Haemopoietic cytokines regulate haemopoietic cell function via specific cell surface receptors. These receptors are members of a large superfamily of transmembrane proteins and are characterised by a 200 amino acid extracellular sequence encoding the ligand binding domain. Several of the genes for members of this superfamily have now been characterised at the molecular level revealing a highly conserved organisation and a number of these genes have been localised cytogenetically. The recent finding that genes for the IL-3 and GM-CSF receptor alpha chain subunits colocalise to a small region of the pseudoautosomal region and the observation that the LIF receptor locus is present in a cluster of receptor genes on chromosome 5 suggest the possibility that subsets of cytokine receptor genes may be organised into clusters. This possibility is discussed and the potential significance of cytokine receptor gene clusters is assessed. Several of the receptor genes are known to be involved in inherited disorders and there is evidence to suggest lesions in cytokine receptor genes could have a role in leukaemia. We review the gene organisation, localisation and involvement in disease for the known cytokine receptor loci. This large family of receptors is expanding with the steady discovery of new members--all of which have the potential to be involved in human disorders.
Publisher: American Society of Hematology
Date: 26-11-2009
DOI: 10.1182/BLOOD-2009-02-204818
Abstract: Deregulated cell survival programs are a classic hallmark of cancer. We have previously identified a serine residue (Ser585) in the βc subunit of the granulocyte-macrophage colony-stimulating factor receptor that selectively and independently promotes cell survival. We now show that Ser585 phosphorylation is constitutive in 20 (87%) of 23 acute myeloid leukemia (AML) patient s les, indicating that this survival-only pathway is frequently deregulated in leukemia. We performed a global expression screen to identify gene targets of this survival pathway and report a 138-gene βc Ser585-regulated transcriptome. Pathway analysis defines a gene network enriched for PI3-kinase target genes and a cluster of genes involved in cancer and cell survival. We show that one such gene, osteopontin (OPN), is a functionally relevant target of the Ser585-survival pathway as shown by siRNA-mediated knockdown of OPN expression that induces cell death in both AML blasts and CD34+CD38−CD123+ leukemic progenitors. Increased expression of OPN at diagnosis is associated with poor prognosis with multivariate analysis indicating that it is an independent predictor of overall patient survival in normal karyotype AML (n = 60 HR = 2.2 P = .01). These results delineate a novel cytokine-regulated Ser585/PI3-kinase signaling network that is deregulated in AML and identify OPN as a potential prognostic and therapeutic target.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854346
Abstract: The IL-3R dodecamer activates STAT1 to induce cell differentiation.
Publisher: Informa UK Limited
Date: 15-10-2008
DOI: 10.4161/CC.7.20.6851
Abstract: Epithelial-mesenchymal transition (EMT) describes the molecular reprogramming and phenotypic changes involved in the conversion of polarised immotile epithelial cells to motile mesenchymal cells. This process allows the remodelling of tissues during embryonic development and is implicated in the promotion of tumor invasion and metastasis. Several recent studies have identified the miR-200 family and miR-205 as key regulators of EMT and enforcers of the epithelial phenotype. The miR-200 family participates in a signalling network with the E-cadherin transcriptional repressors ZEB1/deltaEF1 and ZEB2/SIP1, and TGFbeta2 that is postulated to facilitate maintenance of stable epithelial or mesenchymal states but also allow reversible switching between these states in response to EMT effectors (such as TGFbeta). This review summarises these recent findings and their implications in both developmental EMT and tumor progression.
Publisher: Wiley
Date: 15-02-2012
Publisher: Oxford University Press (OUP)
Date: 15-11-2002
DOI: 10.1093/NAR/GKF615
Abstract: Overexpression of vascular endothelial growth factor (VEGF) is implicated in a number of diseases. It is therefore critical that mechanisms exist to strictly regulate VEGF expression. A hypoxia-responsive (HR) region of the VEGF promoter which binds the HIF-1 transcription factor is a target for many signals that up-regulate VEGF transcription. Repressors targeting the HIF-1 transcription factor have been identified but no repressors directly binding the HR promoter region had been reported. We now report a novel mechanism of repression of the VEGF HR region involving DNA binding. We find that single strand DNA-specific cold shock domain (CSD or Y-box) proteins repress the HR region via a binding site downstream of the HIF-1 site. The repressor site is functional in unstimulated, normoxic fibroblasts and represents a novel means to prevent expression of VEGF in the absence of appropriate stimuli. We characterized complexes forming on the VEGF repressor site and identified a previously unreported nuclear CSD protein complex containing dbpA. Nuclear dbpA appears to bind as a dimer and we determined a means by which nuclear CSD proteins may enter double strand DNA to bind to their single strand sites to bring about repression of the VEGF HR region.
Publisher: Oxford University Press (OUP)
Date: 02-08-2019
DOI: 10.1093/NAR/GKZ664
Abstract: Epithelial–mesenchymal transition (EMT) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. Although EMT-regulatory roles for numerous miRNAs and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct miRNA targets from complex datasets and in deciding how to incorporate ‘indirect’ miRNA effects that may, or may not, represent biologically relevant information. To better understand how miRNAs exert effects throughout the transcriptome during EMT, we employed Exon–Intron Split Analysis (EISA), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of RNA-Seq reads mapping to exons and introns. We find that in response to the manipulation of miRNAs, a major effect on gene expression is transcriptional. We also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both EMT and mesenchymal to epithelial transition (MET) in response to TGF-β or miR-200c respectively. The prominent transcriptional influence of miRNAs was also observed in other datasets where miRNA levels were perturbed. This work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of EISA to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms.
Publisher: Informa UK Limited
Date: 12-1994
Abstract: AU-rich elements (AREs) in the 3' untranslated regions of several cytokine and oncogene mRNAs have been shown to function as signals for rapid mRNA degradation, and it is assumed that the many other cytokine and oncogene mRNAs that contain AU-rich sequences in the 3' untranslated region are similarly targeted for rapid turnover. We have used a chimeric gene composed mostly of growth hormone sequences with expression driven by the c-fos promoter to investigate the minimal sequence required to act as a functional destabilizing element and to monitor the effect of these sequences on early steps in the degradation pathway. We find that neither AUUUA, UAUUUA, nor AUUUAU can function as a destabilizing element. However, the sequence UAUUUAU, when present in three copies, is sufficient to destabilize a chimeric mRNA. We propose that this sequence functions by virtue of being a sufficient portion of the larger sequence, UUAUUUA(U/A)(U/A), that we propose forms the optimal binding site for a destabilizing factor. The destabilizing effect depends on the number of copies of this proposed binding site and their degree of mismatch in the first two and last two positions, with mismatches in the AUUUA sequence not being tolerated. We found a strict correlation between the effect of an ARE on degradation rate and the effect on the rate of poly(A) shortening, consistent with deadenylation being the first and rate-limiting step in degradation, and the step stimulated by destabilizing AREs. Deadenylation was observed to occur in at least two phases, with an oligo(A) intermediate transiently accumulating, consistent with the suggestion that the degradation processes may be similar in yeast and mammalian cells. AREs that are especially U rich and contain no UUAUUUA(U/A)(U/A) motifs failed to influence the degradation rate or the deadenylation rate, either when downstream of suboptimal destabilizing AREs or when alone.
Publisher: American Chemical Society (ACS)
Date: 1996
DOI: 10.1021/BI961700C
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854340
Abstract: Enrichment of the IL-3R hexamer versus dodecamer gene signature in primitive normal and leukemic stem cells.
Publisher: American Association for Cancer Research (AACR)
Date: 19-07-2023
DOI: 10.1158/2159-8290.23709852.V1
Abstract: Data collection and refinement statistics for the IL-3R ternary complex crystal structure.
Publisher: Springer Science and Business Media LLC
Date: 25-05-2010
DOI: 10.1007/S10911-010-9183-Z
Abstract: MicroRNAs are master regulators of gene expression in many biological and pathological processes, including mammary gland development and breast cancer. The differentiation program termed the epithelial to mesenchymal transition (EMT) involves changes in a number of microRNAs. Some of these microRNAs have been shown to control cellular plasticity through the suppression of EMT-inducers or to influence cellular phenotype through the suppression of genes involved in defining the epithelial and mesenchymal cell states. This has led to the suggestion that microRNAs maybe a novel therapeutic target for the treatment of breast cancer. In this review, we will discuss microRNAs that are involved in EMT in mammary cells and breast cancer.
Publisher: The American Association of Immunologists
Date: 15-07-2010
Abstract: The transcription factor FOXP3 is essential for the formation and function of regulatory T cells (Tregs), and Tregs are essential for maintaining immune homeostasis and tolerance. This is demonstrated by a lethal autoimmune defect in mice lacking Foxp3 and in immunodysregulation polyendocrinopathy enteropathy X-linked syndrome patients. However, little is known about the molecular basis of human FOXP3 function or the relationship between direct and indirect targets of FOXP3 in human Tregs. To investigate this, we have performed a comprehensive genome-wide analysis for human FOXP3 target genes from cord blood Tregs using chromatin immunoprecipitation array profiling and expression profiling. We have identified 5579 human FOXP3 target genes and derived a core Treg gene signature conserved across species using mouse chromatin immunoprecipitation data sets. A total of 739 of the 5579 FOXP3 target genes were differentially regulated in Tregs compared with Th cells, thus allowing the identification of a number of pathways and biological functions overrepresented in Tregs. We have identified gene families including cell surface molecules and microRNAs that are differentially expressed in FOXP3+ Tregs. In particular, we have identified a novel role for peptidase inhibitor 16, which is expressed on the cell surface of & % of resting human CD25+FOXP3+ Tregs, suggesting that in conjunction with CD25 peptidase inhibitor 16 may be a surrogate surface marker for Tregs with potential clinical application.
Publisher: Wiley
Date: 09-1991
DOI: 10.1002/J.1460-2075.1991.TB07806.X
Abstract: We have found previously that the sequences important for recognition of pre-mRNA introns in dicot plants differ from those in the introns of vertebrates and yeast. Neither a conserved branch point nor a polypyrimidine tract, found in yeast and vertebrate introns respectively, are required. Instead, AU-rich sequences, a characteristic feature of dicot plant introns, are essential. Here we show that splicing in protoplasts of maize, a monocot, differs significantly from splicing in a dicot, Nicotiana plumbaginifolia. As in the case of dicots, a conserved branch point and a polypyrimidine tract are not required for intron processing in maize. However, unlike in dicots, AU-rich sequences are not essential, although their presence facilitates splicing if the splice site sequences are not optimal. The lack of an absolute requirement for AU-rich stretches in monocot introns in reflected in the occurrence of GC-rich introns in monocots but not in dicots. We also show that maize protoplasts are able to process a mammalian intron and short introns containing stem--loops, neither of which are spliced in N.plumbaginifolia protoplasts. The ability of maize, but not of N.plumbaginifolia to process stem--loop-containing or GC-rich introns suggests that one of the functions of AU-rich sequences during splicing of dicot plant pre-mRNAs may be to minimize secondary structure within the intron.
Publisher: Proceedings of the National Academy of Sciences
Date: 12-1986
Abstract: A cDNA library was constructed from human spleen mRNA and screened for clones containing cDNAs coding for prothymosin alpha. A clone containing a 503-base-pair insert including the entire coding sequence for the translated portion of the mRNA was isolated. The deduced amino acid sequence confirms and completes the partial sequence of human prothymosin alpha determined by protein sequencing methods. The presence of an initiator codon immediately preceding the codon for the NH2-terminal serine residue and of a terminator codon immediately following the codon for Asp-109, the COOH-terminal residue, suggests that prothymosin alpha is synthesized without formation of a larger precursor polypeptide. Analysis of the 5' sequence preceding the initiator methionine codon excluded the presence of a signal peptide in the translated sequence.
Publisher: Cold Spring Harbor Laboratory
Date: 02-11-2010
Abstract: The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5′ capping. Here, we show that post-transcriptional cleavage of RNA contributes to the ersification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage- and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome.
Publisher: Springer Science and Business Media LLC
Date: 11-03-2013
Publisher: Springer Science and Business Media LLC
Date: 16-09-2014
DOI: 10.1038/ONC.2013.370
Abstract: The microRNA-200 (miR-200) family has a critical role in regulating epithelial-mesenchymal transition and cancer cell invasion through inhibition of the E-cadherin transcriptional repressors ZEB1 and ZEB2. Recent studies have indicated that the miR-200 family may exert their effects at distinct stages in the metastatic process, with an overall effect of enhancing metastasis in a syngeneic mouse breast cancer model. We find in a xenograft orthotopic model of breast cancer metastasis that ectopic expression of members of the miR-200b/200c/429, but not the miR-141/200a, functional groups limits tumour cell invasion and metastasis. Despite modulation of the ZEB1-E-cadherin axis, restoration of ZEB1 in miR-200b-expressing cells was not able to alter metastatic potential suggesting that other targets contribute to this process. Instead, we found that miR-200b repressed several actin-associated genes, with the knockdown of the ezrin-radixin-moesin family member moesin alone phenocopying the repression of cell invasion by miR-200b. Moesin was verified to be directly targeted by miR-200b, and restoration of moesin in miR-200b-expressing cells was sufficient to alleviate metastatic repression. In breast cancer cell lines and patient s les, the expression of moesin significantly inversely correlated with miR-200 expression, and high levels of moesin were associated with poor relapse-free survival. These findings highlight the context-dependent effects of miR-200 in breast cancer metastasis and demonstrate the existence of a moesin-dependent pathway, distinct from the ZEB1-E-cadherin axis, through which miR-200 can regulate tumour cell plasticity and metastasis.
Publisher: Wiley
Date: 19-12-2003
DOI: 10.1046/J.1432-1033.2003.03945.X
Abstract: Poly(A) binding protein (PABP) binds mRNA poly(A) tails and affects mRNA stability and translation. We show here that there is little free PABP in NIH3T3 cells, with the vast majority complexed with RNA. We found that PABP in NIH3T3 cytoplasmic lysates and recombinant human PABP can bind to AU-rich RNA with high affinity. Human PABP bound an AU-rich RNA with Kd in the nm range, which was only sixfold weaker than the affinity for oligo(A) RNA. Truncated PABP containing RNA recognition motif domains 3 and 4 retained binding to both AU-rich and oligo(A) RNA, whereas a truncated PABP containing RNA recognition motif domains 1 and 2 was highly selective for oligo(A) RNA. The inducible PABP, iPABP, was found to be even less discriminating than PABP in RNA binding, with affinities for AU-rich and oligo(A) RNAs differing by only twofold. These data suggest that iPABP and PABP may in some situations interact with other RNA regions in addition to the poly(A) tail.
Publisher: Springer Science and Business Media LLC
Date: 14-02-2019
DOI: 10.1038/S41598-018-37037-0
Abstract: Circular RNAs (circRNAs) exhibit unique properties due to their covalently closed nature. Models of circRNAs synthesis and function are emerging but much remains undefined about this surprisingly prevalent class of RNA. Here, we identified exonic circRNAs from human and mouse RNA-sequencing datasets, documenting multiple new ex les. Addressing function, we found that many circRNAs co-sediment with ribosomes, indicative of their translation potential. By contrast, circRNAs with potential to act as microRNA sponges were scarce, with some support for a collective sponge function by groups of circRNAs. Addressing circRNA biogenesis, we delineated several features commonly associated with circRNA occurrence. CircRNA-producing genes tend to be longer and to contain more exons than average. Back-splice acceptor exons are strongly enriched at ordinal position 2 within genes, and circRNAs typically have a short exon span with two exons being the most prevalent. The flanking introns either side of circRNA loci are exceptionally long. Of note also, single-exon circRNAs derive from unusually long exons while multi-exon circRNAs are mostly generated from exons of regular length. These findings independently validate and extend similar observations made in a number of prior studies. Furthermore, we analysed high-resolution RNA polymerase II occupancy data from two separate human cell lines to reveal distinctive transcription dynamics at circRNA-producing genes. Specifically, RNA polymerase II traverses the introns of these genes at above average speed concomitant with an accentuated slow-down at exons. Collectively, these features indicate how a perturbed balance between transcription and linear splicing creates important preconditions for circRNA production. We speculate that these preconditions need to be in place so that looping interactions between flanking introns can promote back-splicing to raise circRNA production to appreciable levels.
Publisher: American Association for Cancer Research (AACR)
Date: 04-08-2023
DOI: 10.1158/2159-8290.23854331.V1
Abstract: Increasing IL3Rα/βc ratios and enforced hexamer signaling lead to reduced differentiation in in vivo engraftments.
Publisher: Cold Spring Harbor Laboratory
Date: 20-12-2018
Abstract: Endogenous microRNAs (miRNAs) often exist as multiple isoforms (known as “isomiRs”) with predominant variation around their 3′-end. Increasing evidence suggests that different isomiRs of the same family can have erse functional roles, as recently demonstrated with the ex le of miR-222-3p 3′-end variants. While isomiR levels from a same miRNA family can vary between tissues and cell types, change of templated isomiR stoichiometry to stimulation has not been reported to date. Relying on small RNA-sequencing analyses, we demonstrate here that miR-222-3p 3′-end variants nt are specifically decreased upon interferon (IFN) β stimulation of human fibroblasts, while shorter isoforms are spared. This length-dependent dynamic regulation of long miR-222-3p 3′-isoforms and other miRNA families was confirmed in human monocyte-derived dendritic cells following infection with Salmonella Typhimurium, underlining the breadth of 3′-length regulation by infection, beyond the ex le of miR-222-3p. We further show that stem–loop miRNA Taqman RT-qPCR exhibits selectivity between 3′-isoforms, according to their length, and that this can lead to misinterpretation of results when these isoforms are differentially regulated. Collectively, and to our knowledge, this work constitutes the first demonstration that the stoichiometry of highly abundant templated 3′-isoforms of a same miRNA family can be dynamically regulated by a stimulus. Given that such 3′-isomiRs can have different functions, our study underlines the need to consider isomiRs when investigating miRNA-based regulation.
No related grants have been discovered for Gregory Goodall.