ORCID Profile
0000-0001-6315-4777
Current Organisations
Murdoch Children's Research Institute
,
Australian Regenerative Medicine Institute
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Developmental Genetics (incl. Sex Determination) | Systems Biology | Genetics | Evolution of Developmental Systems | Gene Expression (incl. Microarray and other genome-wide approaches) | Genome Structure and Regulation | Biochemistry and Cell Biology | Bioinformatics
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Computer Software and Services not elsewhere classified | Expanding Knowledge in the Mathematical Sciences |
Related Links
Publications
Transcriptome analysis of the zebrafishatoh7−/−Mutant,lakritz, highlights Atoh7‐dependent genetic networks with potential implications for human eye diseases
Publisher: Wiley
Date: 27-06-2020
β-catenin drives distinct transcriptional networks in proliferative and non-proliferative cardiomyocytes
Publisher: The Company of Biologists
Date: 2020
DOI: 10.1242/DEV.193417
Abstract: The inability of the adult mammalian heart to regenerate represents a fundamental barrier in heart failure management. In contrast, the neonatal heart retains a transient regenerative capacity, but the underlying mechanisms for the developmental loss of cardiac regenerative capacity in mammals are not fully understood. Wnt/β-catenin signaling has been proposed as a key cardio-regenerative pathway driving cardiomyocyte proliferation. Here, we show that Wnt/β-catenin signaling potentiates neonatal mouse cardiomyocyte proliferation in vivo and immature human pluripotent stem cell-derived cardiomyocyte (hPSC-CM) proliferation in vitro. In contrast, Wnt/β-catenin signaling in adult mice is cardioprotective but fails to induce cardiomyocyte proliferation. Transcriptional profiling and chromatin immunoprecipitation sequencing of neonatal mouse and hPSC-CM revealed a core Wnt/β-catenin-dependent transcriptional network governing cardiomyocyte proliferation. In contrast, β-catenin failed to re-engage this neonatal proliferative gene network in the adult heart despite partial transcriptional re-activation of a neonatal glycolytic gene program. These findings suggest that β-catenin may be repurposed from regenerative to protective functions in the adult heart in a developmental process dependent on the metabolic status of cardiomyocytes.
Cell Type of Origin Dictates the Route to Pluripotency
Publisher: Elsevier BV
Date: 12-2017
DOI: 10.1016/J.CELREP.2017.11.029
Abstract: Our current understanding of induced pluripotent stem cell (iPSC) generation has almost entirely been shaped by studies performed on reprogramming fibroblasts. However, whether the resulting model universally applies to the reprogramming process of other cell types is still largely unknown. By characterizing and profiling the reprogramming pathways of fibroblasts, neutrophils, and keratinocytes, we unveil that key events of the process, including loss of original cell identity, mesenchymal to epithelial transition, the extent of developmental reversion, and reactivation of the pluripotency network, are to a large degree cell-type specific. Thus, we reveal limitations for the use of fibroblasts as a universal model for the study of the reprogramming process and provide crucial insights about iPSC generation from alternative cell sources.
Variable outcomes of human heart attack recapitulated in genetically diverse mice.
Publisher: Springer Science and Business Media LLC
Date: 04-03-2019
DOI: 10.1038/S41536-019-0067-6
Abstract: Clinical variation in patient responses to myocardial infarction (MI) has been difficult to model in laboratory animals. To assess the genetic basis of variation in outcomes after heart attack, we characterized responses to acute MI in the Collaborative Cross (CC), a multi-parental panel of genetically erse mouse strains. Striking differences in post-MI functional, morphological, and myocardial scar features were detected across 32 CC founder and recombinant inbred strains. Transcriptomic analyses revealed a plausible link between increased intrinsic cardiac oxidative phosphorylation levels and MI-induced heart failure. The emergence of significant quantitative trait loci for several post-MI traits indicates that utilizing CC strains is a valid approach for gene network discovery in cardiovascular disease, enabling more accurate clinical risk assessment and prediction.
Point mutations in murine Nkx2-5 phenocopy human congenital heart disease and induce pathogenic Wnt signaling
Publisher: American Society for Clinical Investigation
Date: 23-03-2017
MEPD: a resource for medaka gene expression patterns
Publisher: Oxford University Press (OUP)
Date: 06-05-2005
DOI: 10.1093/BIOINFORMATICS/BTI478
Abstract: The Medaka Expression Pattern Database (MEPD) is a database for gene expression patterns determined by in situ hybridization in the small freshwater fish medaka (Oryzias latipes). Data have been collected from various research groups and MEPD is developing into a central expression pattern depository within the medaka community. Gene expression patterns are described by images and terms of a detailed medaka anatomy ontology of over 4000 terms, which we have developed for this purpose and submitted to Open Biological Ontologies. Sequences have been annotated via BLAST match results and using Gene Ontology terms. These new features will facilitate data analyses using bioinformatics approaches and allow cross-species comparisons of gene expression patterns. Presently, MEPD has 19,757 entries, for 1024 of them the expression pattern has been determined.
New genes in the evolution of the neural crest differentiation program
Publisher: Springer Science and Business Media LLC
Date: 2007
Physical activity levels improve following discharge in people admitted to hospital with an acute exacerbation of chronic obstructive pulmonary disease
Publisher: SAGE Publications
Date: 15-09-2015
Abstract: This study aimed to determine the physical activity level of people admitted to hospital with an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) and whether physical activity changed immediately after discharge and 6 weeks post hospital admission. In this prospective observational study, people admitted to hospital with an AECOPD had physical activity levels monitored using the SenseWear ® Armband (model MF-SW) for 3 days in hospital (T1), during the first week at home following discharge (T2), and at home during the sixth week after admission (T3). Fifty participants (mean age (SD) 71 (10) years) completed the study. There was a linear increase in average steps per day over the three time periods (T1, mean (SD) 1385 (1972) steps/day T2, 2040 (2680) T3, 2328 (2745) analysis of variance (ANOVA) p = 0.001) and time spent in moderate activity (3.0–6.0 metabolic equivalents minutes/day) (T1, mean (SD) 16 (27) minutes/day T2, 32 (46) minutes/day T3, 35 (58) minutes/day ANOVA p = 0.008). For both outcomes, post hoc t-tests showed significant improvements from T1 to T2 and from T1 to T3, but not between T2 and T3. Physical activity was low in hospital and significantly improved in the week after discharge but showed no further significant improvement at 6 weeks following a hospitalized AECOPD.
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods
Publisher: Springer Science and Business Media LLC
Date: 18-09-2023
Cardiac gene expression data and in silico analysis provide novel insights into human and mouse taste receptor gene regulation
Publisher: Springer Science and Business Media LLC
Date: 20-05-2015
DOI: 10.1007/S00210-015-1118-1
Abstract: G protein-coupled receptors are the principal mediators of the sweet, umami, bitter, and fat taste qualities in mammals. Intriguingly, the taste receptors are also expressed outside of the oral cavity, including in the gut, airways, brain, and heart, where they have additional functions and contribute to disease. However, there is little known about the mechanisms governing the transcriptional regulation of taste receptor genes. Following our recent delineation of taste receptors in the heart, we investigated the genomic loci encoding for taste receptors to gain insight into the regulatory mechanisms that drive their expression in the heart. Gene expression analyses of healthy and diseased human and mouse hearts showed coordinated expression for a subset of chromosomally clustered taste receptors. This chromosomal clustering mirrored the cardiac expression profile, suggesting that a common gene regulatory block may control the taste receptor locus. We identified unique domains with strong regulatory potential in the vicinity of taste receptor genes. We also performed de novo motif enrichment in the proximal promoter regions and found several overrepresented DNA motifs in cardiac taste receptor gene promoters corresponding to ubiquitous and cardiac-specific transcription factor binding sites. Thus, combining cardiac gene expression data with bioinformatic analyses, this study has provided insights into the noncoding regulatory landscape for taste GPCRs. These findings also have broader relevance for the study of taste GPCRs outside of the classical gustatory system, where understanding the mechanisms controlling the expression of these receptors may have implications for future therapeutic development.
Kidney Organoids Generated Using an Allelic Series of NPHS2 Point Variants Reveal Distinct Intracellular Podocin Mistrafficking
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 27-09-2022
Abstract: Missense variants of NPHS2 that cause mistrafficking of the encoded protein, PODOCIN, have been associated with steroid-resistant nephrotic syndrome. However, most studies have overexpressed such variants in 2D nonpodocyte cells. This study describes the generation and characterization of human kidney organoids representing an allelic series of homozygous NPHS2 missense variants. The strategy revealed a previously unappreciated reduction in variant PODOCIN protein, variant-specific subcellular localization, and specific effects on NEPHRIN association. All variants showed apoptosis in the absence of endoplasmic reticulum stress. Engineering endogenous NPHS2 variants to model in 3D human organoids provides a more accurate view of the pathobiology and a toolkit to screen compounds for reduction of variant protein degradation and mistrafficking. NPHS2 variants are the most common cause of steroid-resistant nephrotic syndrome in children month old. Missense NPHS2 variants were reported to cause mistrafficking of the encoded protein, PODOCIN, but this conclusion was on the basis of overexpression in some nonpodocyte cell lines. We generated a series of human induced pluripotent stem cell (iPSC) lines bearing pathogenic missense variants of NPHS2 , encoding the protein changes p.G92C, p.P118L, p.R138Q, p.R168H, and p.R291W, and control lines. iPSC lines were also generated from a patient with steroid-resistant nephrotic syndrome (p.R168H homozygote) and a healthy heterozygous parent. All lines were differentiated into kidney organoids. Immunofluorescence assessed PODOCIN expression and subcellular localization. Podocytes were transcriptionally profiled and PODOCIN-NEPHRIN interaction interrogated. All variant lines revealed reduced levels of PODOCIN protein in the absence of reduced transcription. Although wild-type PODOCIN localized to the membrane, distinct variant proteins displayed unique patterns of subcellular protein trafficking, some unreported. P118L and R138Q were preferentially retained in the endoplasmic reticulum (ER) R168H and R291W accumulated in the Golgi. Podocyte profiling demonstrated minimal disease-associated transcriptional change. All variants displayed podocyte-specific apoptosis, which was not linked to ER stress. NEPHRIN-PODOCIN colocalization elucidated the variant-specific effect on NEPHRIN association and hence NEPHRIN trafficking. Specific variants of endogenous NPHS2 result in distinct subcellular PODOCIN localization within organoid podocytes. Understanding the effect of each variant on protein levels and localization and the effect on NEPHRIN provides additional insight into the pathobiology of NPHS2 variants. This article contains a podcast at edirect.mp3/edia odcast/JASN/2023_01_05_JASN2022060707.mp3
Systematic molecular profiling of acute leukemia cancer stem cells allows identification of druggable targets
Publisher: Elsevier BV
Date: 10-2022
Adult mouse fibroblasts retain organ-specific transcriptomic identity
Publisher: eLife Sciences Publications, Ltd
Date: 16-03-2022
DOI: 10.7554/ELIFE.71008
Abstract: Organ fibroblasts are essential components of homeostatic and diseased tissues. They participate in sculpting the extracellular matrix, sensing the microenvironment, and communicating with other resident cells. Recent studies have revealed transcriptomic heterogeneity among fibroblasts within and between organs. To dissect the basis of interorgan heterogeneity, we compare the gene expression of murine fibroblasts from different tissues (tail, skin, lung, liver, heart, kidney, and gonads) and show that they display distinct positional and organ-specific transcriptome signatures that reflect their embryonic origins. We demonstrate that expression of genes typically attributed to the surrounding parenchyma by fibroblasts is established in embryonic development and largely maintained in culture, bioengineered tissues and ectopic transplants. Targeted knockdown of key organ-specific transcription factors affects fibroblast functions, in particular genes involved in the modulation of fibrosis and inflammation. In conclusion, our data reveal that adult fibroblasts maintain an embryonic gene expression signature inherited from their organ of origin, thereby increasing our understanding of adult fibroblast heterogeneity. The knowledge of this tissue-specific gene signature may assist in targeting fibrotic diseases in a more precise, organ-specific manner.
Large-scale expression screening by automated whole-mount in situ hybridization
Publisher: Elsevier BV
Date: 07-2004
NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets
Publisher: eLife Sciences Publications, Ltd
Date: 06-07-2015
DOI: 10.7554/ELIFE.06942
Abstract: We take a functional genomics approach to congenital heart disease mechanism. We used DamID to establish a robust set of target genes for NKX2-5 wild type and disease associated NKX2-5 mutations to model loss-of-function in gene regulatory networks. NKX2-5 mutants, including those with a crippled homeodomain, bound hundreds of targets including NKX2-5 wild type targets and a unique set of "off-targets", and retained partial functionality. NKXΔHD, which lacks the homeodomain completely, could heterodimerize with NKX2-5 wild type and its cofactors, including E26 transformation-specific (ETS) family members, through a tyrosine-rich homophilic interaction domain (YRD). Off-targets of NKX2-5 mutants, but not those of an NKX2-5 YRD mutant, showed overrepresentation of ETS binding sites and were occupied by ETS proteins, as determined by DamID. Analysis of kernel transcription factor and ETS targets show that ETS proteins are highly embedded within the cardiac gene regulatory network. Our study reveals binding and activities of NKX2-5 mutations on WT target and off-targets, guided by interactions with their normal cardiac and general cofactors, and suggest a novel type of gain-of-function in congenital heart disease.
Towards spatio-temporally resolved developmental cardiac gene regulatory networks in zebrafish
Publisher: Oxford University Press (OUP)
Date: 25-06-2021
DOI: 10.1093/BFGP/ELAB030
Abstract: Heart formation in the zebrafish involves a rapid, complex series of morphogenetic events in three-dimensional space that spans cardiac lineage specification through to chamber formation and maturation. This process is tightly orchestrated by a cardiac gene regulatory network (GRN), which ensures the precise spatio-temporal deployment of genes critical for heart formation. Alterations of the timing or spatial localisation of gene expression can have a significant impact in cardiac ontogeny and may lead to heart malformations. Hence, a better understanding of the cellular and molecular basis of congenital heart disease relies on understanding the behaviour of cardiac GRNs with precise spatiotemporal resolution. Here, we review the recent technical advances that have expanded our capacity to interrogate the cardiac GRN in zebrafish. In particular, we focus on studies utilising high-throughput technologies to systematically dissect gene expression patterns, both temporally and spatially during heart development.
MonaGO: a novel Gene Ontology enrichment analysis visualisation system
Publisher: Cold Spring Harbor Laboratory
Date: 29-09-2020
DOI: 10.1101/2020.09.27.316067
Abstract: MonaGO is a novel web-based visualisation system that provides an intuitive, interactive and responsive interface for performing gene ontology (GO) enrichment analysis and visualising the results. MonaGO combines dynamic clustering and interactive visualisation as well as customisation options to assist biologists in obtaining meaningful representation of overrepresented GO terms, producing simplified outputs in an unbiased manner. MonaGO supports gene lists as well as GO terms as inputs. Visualisation results can be exported as high-resolution images or restored in new sessions, allowing reproducibility of the analysis. An extensive comparison between MonaGO and 11 state-of-the-art GO enrichment visualisation tools based on 9 features revealed that MonaGO is the only platform that simultaneously allows interactive visualisation within one single output page, directly accessible through a web browser with customisable display options. In summary, MonaGO will facilitate the interpretation of GO analysis and will assist the biologists into the representation of the results.
Identification of starmaker‐like in medaka as a putative target gene of Pax2 in the otic vesicle
Publisher: Wiley
Date: 30-09-2009
DOI: 10.1002/DVDY.22093
Abstract: Otoliths in bony fishes are involved in the function of the ear in the senses of balance and hearing. In a large-scale random in situ hybridization screen of genes expressed in the medaka developing ear, we identified starmaker-like (stm-l) gene, a novel homologue of zebrafish starmaker and human dentine sialo-phosphoprotein (dspp) gene. Despite the absence of sequence similarity between these genes, here we describe their similar genomic structure and expression patterns hinting for a conserved function. In medaka fry, stm-l is expressed in various organs such as otoliths, teeth, gills, and kidney. Additionally, our results provide evidence that stm-l is a putative downstream target gene of Pax2 transcription factor and Pax2 itself has a promoting function in otolith formation.
The Intercellular Tight Junction and Spontaneous Coronary Artery Dissection
Publisher: Elsevier BV
Date: 10-2018
Drosophila Hrp48 Is Required for Mushroom Body Axon Growth, Branching and Guidance
Publisher: Public Library of Science (PLoS)
Date: 27-08-2015
Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
Publisher: Springer Science and Business Media LLC
Date: 24-06-2007
DOI: 10.1038/NMETH1061
Abstract: We developed Trawler, the fastest computational pipeline to date, to efficiently discover over-represented motifs in chromatin immunoprecipitation (ChIP) experiments and to predict their functional instances. When we applied Trawler to data from yeast and mammals, 83% of the known binding sites were accurately called, often with other additional binding sites, providing hints of combinatorial input. Newly discovered motifs and their features (identity, conservation, position in sequence) are displayed on a web interface.
Metformin intervention prevents cardiac dysfunction in a murine model of adult congenital heart disease
Publisher: Elsevier BV
Date: 02-2019
Author response: Adult mouse fibroblasts retain organ-specific transcriptomic identity
Publisher: eLife Sciences Publications, Ltd
Date: 07-01-2022
Integrated Value of Influence: An Integrative Method for the Identification of the Most Influential Nodes within Networks
Publisher: Elsevier BV
Date: 08-2020
Formation of the Embryonic Head in the Mouse
Publisher: Elsevier
Date: 2016
The RNA-binding protein SRSF3 has an essential role in megakaryocyte maturation and platelet production
Publisher: American Society of Hematology
Date: 03-03-2022
Abstract: RNA processing is increasingly recognized as a critical control point in the regulation of different hematopoietic lineages including megakaryocytes responsible for the production of platelets. Platelets are anucleate cytoplasts that contain a rich repertoire of RNAs encoding proteins with essential platelet functions derived from the parent megakaryocyte. It is largely unknown how RNA binding proteins contribute to the development and functions of megakaryocytes and platelets. We show that serine-arginine–rich splicing factor 3 (SRSF3) is essential for megakaryocyte maturation and generation of functional platelets. Megakaryocyte-specific deletion of Srsf3 in mice led to macrothrombocytopenia characterized by megakaryocyte maturation arrest, dramatically reduced platelet counts, and abnormally large functionally compromised platelets. SRSF3 deficient megakaryocytes failed to reprogram their transcriptome during maturation and to load platelets with RNAs required for normal platelet function. SRSF3 depletion led to nuclear accumulation of megakaryocyte mRNAs, demonstrating that SRSF3 deploys similar RNA regulatory mechanisms in megakaryocytes as in other cell types. Our study further suggests that SRSF3 plays a role in sorting cytoplasmic megakaryocyte RNAs into platelets and demonstrates how SRSF3-mediated RNA processing forms a central part of megakaryocyte gene regulation. Understanding SRSF3 functions in megakaryocytes and platelets provides key insights into normal thrombopoiesis and platelet pathologies as SRSF3 RNA targets in megakaryocytes are associated with platelet diseases.
Navigating the non-coding genome in heart development and Congenital Heart Disease
Publisher: Elsevier BV
Date: 05-2019
DOI: 10.1016/J.DIFF.2019.05.001
Abstract: Congenital Heart Disease (CHD) is characterised by a wide range of cardiac defects, from mild to life-threatening, which occur in babies worldwide. To date, there is no cure to CHD, however, progress in surgery has reduced its mortality allowing children affected by CHD to reach adulthood. In an effort to understand its genetic basis, several studies involving whole-genome sequencing (WGS) of patients with CHD have been undertaken and generated a great wealth of information. The majority of putative causative mutations identified in WGS studies fall into the non-coding part of the genome. Unfortunately, due to the lack of understanding of the function of these non-coding mutations, it is challenging to establish a causal link between the non-coding mutation and the disease. Thus, here we review the state-of-the-art approaches to interpret non-coding mutations in the context of CHD and address the following questions: What are the non-coding sequences important for cardiac function? Which technologies are used to identify them? Which resources are available to analyse them? What mutations are expected in these non-coding sequences? Learning from developmental process, what is their expected role in CHD?
GSD: a genetic screen database
Publisher: Elsevier BV
Date: 07-2004
A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease.
Publisher: Springer Science and Business Media LLC
Date: 12-2021
DOI: 10.1186/S13059-021-02539-0
Abstract: Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis -regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14 , RpS24 , and Rpn8 are associated with heart phenotypes. Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis -regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
Evolutionary relationships and diversification of barhl genes within retinal cell lineages
Publisher: Springer Science and Business Media LLC
Date: 21-11-2011
Abstract: Basic helix-loop-helix and homeodomain transcription factors have been shown to specify all different neuronal cell subtypes composing the vertebrate retina. The appearance of gene paralogs of such retina-specific transcription factors in lower vertebrates, with differently evolved function and/or conserved non-coding elements, might provide an important source for the generation of neuronal ersity within the vertebrate retinal architecture. In line with this hypothesis, we investigated the evolution of the homeobox Barhl family of transcription factors, barhl1 and barhl2 , in the teleost and tetrapod lineages. In tetrapod barhl2 , but not barhl1 , is expressed in the retina and is important for amacrine cell specification. Zebrafish has three barhl paralogs: barhl1.1, barhl1.2 and barhl2 , but their precise spatio-temporal retinal expression, as well as their function is yet unknown. Here we performed a meticulous expression pattern comparison of all known barhl fish paralogs and described a novel barhl paralog in medaka. Our detailed analysis of zebrafish barhl gene expression in wild type and mutant retinas revealed that only barhl1.2 and barhl2 are present in the retina. We also showed that these two paralogs are expressed in distinct neuronal lineages and are differently regulated by Atoh7, a key retinal-specific transcription factor. Finally, we found that the two retained medaka fish barhl paralogs, barhl1 and barhl2 , are both expressed in the retina, in a pattern reminiscent of zebrafish barhl1.2 and barhl2 respectively. By performing phylogenetic and synteny analysis, we provide evidence that barhl retinal expression domain is an ancestral feature, probably lost in tetrapods due to functional redundancy. Functional differences among retained paralogs of key retina-specific transcription factors between teleosts and tetrapods might provide important clues for understanding their potential impact on the generation of retinal neuronal ersity. Intriguingly, within teleosts, retention of zebrafish barhl1.2 and its medaka ortholog barhl1 appears to correlate with the acquisition of distinct signalling mechanisms by the two genes within distinct retinal cell lineages. Our findings provide a starting point for the study of barhl gene evolution in relation to the generation of cell ersity in the vertebrate retina.
From whole-mount to single-cell spatial assessment of gene expression in 3D
Publisher: Springer Science and Business Media LLC
Date: 23-10-2020
DOI: 10.1038/S42003-020-01341-1
Abstract: Unravelling spatio-temporal patterns of gene expression is crucial to understanding core biological principles from embryogenesis to disease. Here we review emerging technologies, providing automated, high-throughput, spatially resolved quantitative gene expression data. Novel techniques expand on current benchmark protocols, expediting their incorporation into ongoing research. These approaches digitally reconstruct patterns of embryonic expression in three dimensions, and have successfully identified novel domains of expression, cell types, and tissue features. Such technologies pave the way for unbiased and exhaustive recapitulation of gene expression levels in spatial and quantitative terms, promoting understanding of the molecular origin of developmental defects, and improving medical diagnostics.
Nuclear transporter Importin-13 plays a key role in the oxidative stress transcriptional response
Publisher: Springer Science and Business Media LLC
Date: 08-10-2021
DOI: 10.1038/S41467-021-26125-X
Abstract: The importin superfamily member Importin-13 is a bidirectional nuclear transporter. To delineate its functional roles, we performed transcriptomic analysis on wild-type and Importin-13-knockout mouse embryonic stem cells, revealing enrichment of differentially expressed genes involved in stress responses and apoptosis regulation. De novo promoter motif analysis on 277 Importin-13-dependent genes responsive to oxidative stress revealed an enrichment of motifs aligned to consensus sites for the transcription factors specificity protein 1, SP1, or Kruppel like factor 4, KLF4. Analysis of embryonic stem cells subjected to oxidative stress revealed that Importin-13-knockout cells were more resistant, with knockdown of SP1 or KLF4 helping protect wild-type embryonic stem cells against stress-induced death. Importin-13 was revealed to bind to SP1 and KLF4 in a cellular context, with a key role in oxidative stress-dependent nuclear export of both transcription factors. The results are integral to understanding stress biology, highlighting the importance of Importin-13 in the stress response.
Genetic networks governing heart development
Publisher: Cold Spring Harbor Laboratory
Date: 03-10-2014
Detection and identification of cis-regulatory elements using change-point and classification algorithms
Publisher: Springer Science and Business Media LLC
Date: 25-01-2022
DOI: 10.1186/S12864-021-08190-0
Abstract: Transcriptional regulation is primarily mediated by the binding of factors to non-coding regions in DNA. Identification of these binding regions enhances understanding of tissue formation and potentially facilitates the development of gene therapies. However, successful identification of binding regions is made difficult by the lack of a universal biological code for their characterisation. We extend an alignment-based method, , and identify clusters of biological significance, through ontology and de novo motif analysis. Further, we apply a Bayesian method to estimate and combine binary classifiers on the clusters we identify to produce a better performing composite. The analysis we describe provides a computational method for identification of conserved binding sites in the human genome and facilitates an alternative interrogation of combinations of existing data sets with alignment data.
Germline Stem Cell Activity Is Sustained by SALL4-Dependent Silencing of Distinct Tumor Suppressor Genes
Publisher: Elsevier BV
Date: 09-2017
Asymmetric inheritance of the apical domain and self-renewal of retinal ganglion cell progenitors depend on Anillin function
Publisher: The Company of Biologists
Date: 2015
DOI: 10.1242/DEV.118612
Abstract: Divisions that generate one neuronal lineage-committed and one self-renewing cell maintain the balance of proliferation and differentiation for the generation of neuronal ersity. The asymmetric inheritance of apical domains and components of the cell ision machinery has been implicated in this process, and might involve interactions with cell fate determinants in regulatory feedback loops of an as yet unknown nature. Here, we report the dynamics of Anillin – an essential F-actin regulator and furrow component – and its contribution to progenitor cell isions in the developing zebrafish retina. We find that asymmetrically iding retinal ganglion cell progenitors position the Anillin-rich midbody at the apical domain of the differentiating daughter. anillin hypomorphic conditions disrupt asymmetric apical domain inheritance and affect daughter cell fate. Consequently, the retinal cell type composition is profoundly affected, such that the ganglion cell layer is dramatically expanded. This study provides the first in vivo evidence for the requirement of Anillin during asymmetric neurogenic isions. It also provides insights into a reciprocal regulation between Anillin and the ganglion cell fate determinant Ath5, suggesting a mechanism whereby the balance of proliferation and differentiation is accomplished during progenitor cell isions in vivo.
Trawler Web
Publisher: Springer Science and Business Media LLC
Date: 05-04-2018
Haematopoietic stem cell induction by somite-derived endothelial cells controlled by meox1
Publisher: Springer Science and Business Media LLC
Date: 13-08-2014
DOI: 10.1038/NATURE13678
Abstract: Haematopoietic stem cells (HSCs) are self-renewing stem cells capable of replenishing all blood lineages. In all vertebrate embryos that have been studied, definitive HSCs are generated initially within the dorsal aorta (DA) of the embryonic vasculature by a series of poorly understood inductive events. Previous studies have identified that signalling relayed from adjacent somites coordinates HSC induction, but the nature of this signal has remained elusive. Here we reveal that somite specification of HSCs occurs via the deployment of a specific endothelial precursor population, which arises within a sub-compartment of the zebrafish somite that we have defined as the endotome. Endothelial cells of the endotome are specified within the nascent somite by the activity of the homeobox gene meox1. Specified endotomal cells consequently migrate and colonize the DA, where they induce HSC formation through the deployment of chemokine signalling activated in these cells during endotome formation. Loss of meox1 activity expands the endotome at the expense of a second somitic cell type, the muscle precursors of the dermomyotomal equivalent in zebrafish, the external cell layer. The resulting increase in endotome-derived cells that migrate to colonize the DA generates a dramatic increase in chemokine-dependent HSC induction. This study reveals the molecular basis for a novel somite lineage restriction mechanism and defines a new paradigm in induction of definitive HSCs.
Control of cardiac jelly dynamics by NOTCH1 and NRG1 defines the building plan for trabeculation
Publisher: Springer Science and Business Media LLC
Date: 05-2018
DOI: 10.1038/S41586-018-0110-6
Abstract: In vertebrate hearts, the ventricular trabecular myocardium develops as a sponge-like network of cardiomyocytes that is critical for contraction and conduction, ventricular septation, papillary muscle formation and wall thickening through the process of compaction
The humanFLT1regulatory element directs vascular expression and modulates angiogenesis pathwaysin vitroandin vivo
Publisher: Cold Spring Harbor Laboratory
Date: 06-03-2021
DOI: 10.1101/2021.03.03.433738
Abstract: There is growing evidence that mutations in non-coding cis -regulatory elements (CREs) disrupt proper development. However, little is known about human CREs that are crucial for cardiovascular development. To address this, we bioinformatically identified cardiovascular CREs based on the occupancy of the CRE by the homeodomain protein NKX2-5 and cardiac chromatin histone modifications. This search defined a highly conserved CRE within the FLT1 locus termed enFLT1 . We show that the human enFLT1 is an enhancer capable of driving reporter transgene expression in vivo throughout the developing cardiovascular system of medaka. Deletion of the human enFLT1 enhancer ( ΔenFLT1 ) triggered molecular perturbations in extracellular matrix organisation and blood vessel morphogenesis in vitro in endothelial cells derived from human embryonic stem cells and vascular defects in vivo in medaka. These findings highlight the crucial role of the human FLT1 enhancer and its function as a regulator and buffer of transcriptional regulation in cardiovascular development.
Close association of olfactory placode precursors and cranial neural crest cells does not predestine cell mixing
Publisher: Wiley
Date: 22-05-2012
DOI: 10.1002/DVDY.23797
Defining the earliest step of cardiovascular progenitor specification during embryonic stem cell differentiation
Publisher: Rockefeller University Press
Date: 07-03-2011
Abstract: During embryonic development and embryonic stem cell (ESC) differentiation, the different cell lineages of the mature heart arise from two types of multipotent cardiovascular progenitors (MCPs), the first and second heart fields. A key question is whether these two MCP populations arise from differentiation of a common progenitor. In this paper, we engineered Mesp1–green fluorescent protein (GFP) ESCs to isolate early MCPs during ESC differentiation. Mesp1-GFP cells are strongly enriched for MCPs, presenting the ability to differentiate into multiple cardiovascular lineages from both heart fields in vitro and in vivo. Transcriptional profiling of Mesp1-GFP cells uncovered cell surface markers expressed by MCPs allowing their prospective isolation. Mesp1 is required for MCP specification and the expression of key cardiovascular transcription factors. Isl1 is expressed in a subset of early Mesp1-expressing cells independently of Mesp1 and acts together with Mesp1 to promote cardiovascular differentiation. Our study identifies the early MCPs residing at the top of the cellular hierarchy of cardiovascular lineages during ESC differentiation.
A gene regulatory network anchored by LIM homeobox 1 for embryonic head development
Publisher: Wiley
Date: 09-2018
DOI: 10.1002/DVG.23246
Abstract: Development of the embryonic head is driven by the activity of gene regulatory networks of transcription factors. LHX1 is a homeobox transcription factor that plays an essential role in the formation of the embryonic head. The loss of LHX1 function results in anterior truncation of the embryo caused by the disruption of morphogenetic movement of tissue precursors and the dysregulation of WNT signaling activity. Profiling the gene expression pattern in the Lhx1 mutant embryo revealed that tissues in anterior germ layers acquire posterior tissue characteristics, suggesting LHX1 activity is required for the allocation and patterning of head precursor tissues. Here, we used LHX1 as an entry point to delineate its transcriptional targets and interactors and construct a LHX1-anchored gene regulatory network. Using a gain-of-function approach, we identified genes that immediately respond to Lhx1 activation. Meta-analysis of the datasets of LHX1-responsive genes and genes expressed in the anterior tissues of mouse embryos at head-fold stage, in conjunction with published Xenopus embryonic LHX1 (Xlim1) ChIP-seq data, has pinpointed the putative transcriptional targets of LHX1 and an array of genetic determinants functioning together in the formation of the mouse embryonic head.
Tyrosine phosphorylation of LRP 6 by Src and Fer inhibits Wnt/β‐catenin signalling
Publisher: EMBO
Date: 12-11-2014
Abstract: Low‐density lipoprotein receptor‐related proteins 5 and 6 ( LRP 5/6) function as transmembrane receptors to transduce Wnt signals. A key mechanism for signalling is Wnt‐induced serine/threonine phosphorylation at conserved PPPSP x S motifs in the LRP 6 cytoplasmic domain, which promotes pathway activation. Conserved tyrosine residues are positioned close to all PPPSP x S motifs, which suggests they have a functional significance. Using a cell culture‐based c DNA expression screen, we identified the non‐receptor tyrosine kinases Src and Fer as novel LRP 6 modifiers. Both Src and Fer associate with LRP 6 and phosphorylate LRP 6 directly. In contrast to the known PPPSP x S Ser/Thr kinases, tyrosine phosphorylation by Src and Fer negatively regulates LRP 6‐Wnt signalling. Epistatically, they function upstream of β‐catenin to inhibit signalling and in agreement with a negative role in regulating LRP 6, MEF cells lacking these kinases show enhanced Wnt signalling. Wnt3a treatment of cells enhances tyrosine phosphorylation of endogenous LRP 6 and, mechanistically, Src reduces cell surface LRP 6 levels and disrupts LRP6 signalosome formation. Interestingly, CK 1γ inhibits Fer‐induced LRP 6 phosphorylation, suggesting a mechanism whereby CK 1γ acts to de‐represses inhibitory LRP 6 tyrosine phosphorylation. We propose that LRP 6 tyrosine phosphorylation by Src and Fer serves a negative regulatory function to prevent over‐activation of Wnt signalling at the level of the Wnt receptor, LRP6.
Transcriptome analysis of the zebrafishatoh7−/−mutant,lakritz, highlights Atoh7-dependent genetic networks with potential implications for human eye diseases
Publisher: Cold Spring Harbor Laboratory
Date: 10-04-2020
DOI: 10.1101/2020.04.09.033704
Abstract: Expression of the bHLH transcription protein Atoh7 is a crucial factor conferring competence to retinal progenitor cells for the development of retinal ganglion cells. A number of studies have emerged establishing ATOH7 as a retinal disease gene. Remarkably, such studies uncovered ATOH7 variants associated with global eye defects including optic nerve hypoplasia, microphthalmia, retinal vascular disorders and glaucoma. The complex genetic networks and cellular decisions arising downstream of atoh7 expression, and how their dysregulation cause development of such disease traits remains unknown. To begin to understand such Atoh7-dependent events in vivo we performed transcriptome analysis of wild type and atoh7 mutant ( lakritz ) zebrafish embryos at the onset of retinal ganglion cell differentiation. We investigated in silico interplays of atoh7 and other disease-related genes and pathways. By network reconstruction analysis of differentially expressed genes we identified gene clusters enriched in retinal development, cell cycle, chromatin remodelling, stress response and Wnt pathways. By weighted gene coexpression network we identified coexpression modules affected by the mutation and enriched in retina development genes tightly connected to atoh7 . We established the groundwork whereby Atoh7-linked cellular and molecular processes can be investigated in the dynamic multi-tissue environment of the developing normal and diseased vertebrate eye.
Expression profiling in mouse fetal thymus reveals clusters of coordinately expressed genes that mark individual stages of T-cell ontogeny
Publisher: Springer Science and Business Media LLC
Date: 10-2002
DOI: 10.1007/S00251-002-0488-Y
Abstract: To search for genes that participate in regulatory networks sustaining mouse embryonic T-cell development, we have performed expression profiling using nylon macroarrays. Labeled s les representative of in idual developmental stages were utilized, taking advantage of cell homogeneity during early thymus ontogeny. cDNAs revealing differential expression were further selected using labeled s les derived from lymphoid versus non-lymphoid tissues, and from mutant thymi exhibiting T-cell developmental defects. We thus identified clusters of coexpressed genes during T-cell embryogenesis and characterized their sequences through bioinformatics. We compare our results with those from other profiling analyses in the immune system, and discuss their implications for the definition of genes whose products are involved in T-cell development.
A novel conditional mouse model for Nkx2-5 reveals transcriptional regulation of cardiac ion channels
Publisher: Elsevier BV
Date: 2016
DOI: 10.1016/J.DIFF.2015.12.003
Abstract: Nkx2-5 is one of the master regulators of cardiac development, homeostasis and disease. This transcription factor has been previously associated with a suite of cardiac congenital malformations and impairment of electrical activity. When disease causative mutations in transcription factors are considered, NKX2-5 gene dysfunction is the most common abnormality found in patients. Here we describe a novel mouse model and subsequent implications of Nkx2-5 loss for aspects of myocardial electrical activity. In this work we have engineered a new Nkx2-5 conditional knockout mouse in which flox sites flank the entire Nkx2-5 locus, and validated this line for the study of heart development, differentiation and disease using a full deletion strategy. While our homozygous knockout mice show typical embryonic malformations previously described for the lack of the Nkx2-5 gene, hearts of heterozygous adult mice show moderate morphological and functional abnormalities that are sufficient to sustain blood supply demands under homeostatic conditions. This study further reveals intriguing aspects of Nkx2-5 function in the control of cardiac electrical activity. Using a combination of mouse genetics, biochemistry, molecular and cell biology, we demonstrate that Nkx2-5 regulates the gene encoding Kcnh2 channel and others, shedding light on potential mechanisms generating electrical abnormalities observed in patients bearing NKX2-5 dysfunction and opening opportunities to the study of novel therapeutic targets for anti-arrhythmogenic therapies.
Imp Promotes Axonal Remodeling by Regulating profilin mRNA during Brain Development
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.CUB.2014.02.038
Abstract: Neuronal remodeling is essential for the refinement of neuronal circuits in response to developmental cues [1-4]. Although this process involves pruning or retraction of axonal projections followed by axonal regrowth and branching, how these steps are controlled is poorly understood. Drosophila mushroom body (MB) γ neurons provide a paradigm for the study of neuronal remodeling, as their larval axonal branches are pruned during metamorphosis and re-extend to form adult-specific branches [5]. Here, we identify the RNA binding protein Imp as a key regulator of axonal remodeling. Imp is the sole fly member of a conserved family of proteins that bind target mRNAs to promote their subcellular targeting [6-12]. We show that whereas Imp is dispensable for the initial growth of MB γ neuron axons, it is required for the regrowth and ramification of axonal branches that have undergone pruning. Furthermore, Imp is actively transported to axons undergoing developmental remodeling. Finally, we demonstrate that profilin mRNA is a direct and functional target of Imp that localizes to axons and controls axonal regrowth. Our study reveals that mRNA localization machineries are actively recruited to axons upon remodeling and suggests a role of mRNA transport in developmentally programmed rewiring of neuronal circuits during brain maturation.
Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics
Publisher: Cold Spring Harbor Laboratory
Date: 02-04-2023
DOI: 10.1101/2023.03.31.535025
Abstract: Spatially resolved transcriptomics (SRT) technologies produce complex, multi-dimensional data sets of gene expression information that can be obtained at subcellular spatial resolution. While several computational tools are available to process and analyse SRT data, no platforms facilitate the visualisation and interaction with SRT data in an immersive manner. Here we present VR-Omics, a computational platform that supports the analysis, visualisation, exploration, and interpretation SRT data compatible with any SRT technology. VR-Omics is the first tool capable of analysing and visualising data generated by multiple SRT platforms in both 2D desktop and virtual reality environments. It incorporates an in-built workflow to automatically pre-process and spatially mine the data within a user-friendly graphical user interface. Benchmarking VR-Omics against other comparable software demonstrates its seamless end-to-end analysis of SRT data, hence making SRT data processing and mining universally accessible. VR-Omics is an open-source software freely available at: ramialison-lab.github.io ages/vromics.html
Combinatorial Ranking of Gene Sets to Predict Disease Relapse: The Retinoic Acid Pathway in Early Prostate Cancer
Publisher: Frontiers Media SA
Date: 15-03-2017
Active Pin1 is a key target of all-trans retinoic acid in acute promyelocytic leukemia and breast cancer
Publisher: Springer Science and Business Media LLC
Date: 13-04-2015
DOI: 10.1038/NM.3839
Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation
Publisher: Springer Science and Business Media LLC
Date: 02-2010
Abstract: Genome-wide location analysis has become a standard technology to unravel gene regulation networks. The accurate characterization of nucleotide signatures in sequences is key to uncovering the regulatory logic but remains a computational challenge. This protocol describes how to best characterize these signatures (motifs) using the new standalone version of Trawler, which was designed and optimized to analyze chromatin immunoprecipitation (ChIP) data sets. In particular, we describe the three main steps of Trawler_standalone (motif discovery, clustering and visualization) and discuss the appropriate parameters to be used in each step depending on the data set and the biological questions addressed. Compared to five other motif discovery programs, Trawler_standalone is in most cases the fastest algorithm to accurately predict the correct motifs especially for large data sets. Its running time ranges within few seconds to several minutes, depending on the size of the data set and the parameters used. This protocol is best suited for bioinformaticians seeking to use Trawler_standalone in a high-throughput manner.
Systems-level investigation of mucopolysaccharidosis IIIA identifies deficient synaptic activity as a key driver of disease progression
Publisher: Cold Spring Harbor Laboratory
Date: 04-10-2022
DOI: 10.1101/2022.10.03.510585
Abstract: Mucopolysaccharidoses are lysosomal storage diseases that collectively represent a major cause of lethal, treatment-refractory childhood dementias 1–7 Clinically-useful interventions are h ered due to an incomplete understanding of their neuropathological origins. Using the zebrafish sgsh model of mucopolysaccharidosis IIIA 8 (MPS IIIA, Sanfilippo syndrome A), we conducted several ‘omics-based analyses, and developed and benchmarked a novel bioinformatic feature classification and ranking model for high-throughput datasets – ExIR – to prioritise important features in the progression of neurological manifestations of the disease. We find that the massive endolysosomal burden resulting from increased lysosomal storage of heparan sulfate and other secondarily accumulating substrates, such as sphingolipids, induces abnormal microtubule organisation and vesicle trafficking in neurons. This results in a gradual impairment of synaptic vesicle localisation at the presynaptic terminal and consequently impaired neuronal activity. Importantly, the endolysosomal phenotype in MPS IIIA zebrafish well-precedes the onset of neural pathology, though the larval MPS IIIA brain was found to be more susceptible to perturbation than wild type siblings. Collectively, these analyses demonstrate the presence of a progressive ‘functional neurodegenerative’ phenotype underpinning neurological disease in MPS IIIA. Our findings provide direct mechanistic evidence linking the well-described lysosomal storage basis for MPS IIIA to its disproportionately severe neural clinical involvement, enabling development and refinement of future therapeutic interventions for this currently untreatable disorder. MPS IIIA represents one of the most common causes of broadly fatal childhood dementia, but the mechanisms underlying disease progression are poorly understood. The first systems-level analyses of disease state and progression in the CNS of an MPS IIIA animal model were performed. Ex perimental data-based I ntegrative R anking (ExIR) was developed to provide unbiased prioritisation and classification of biological data as drivers, biomarkers and mediators of biological processes from high-throughput data at a systems level. Application of ExIR to a transcriptomic and proteomic analyses of a zebrafish model of MPS IIIA implies progressive deficiencies in synaptic activity as a key driver of disease progression correlating with progressive neuronal endolysosomal burden and secondary storage diseases. A novel unifying explanation of pathobiology and progression of MPS IIIA facilitates identification of clinically targetable features and may be generalised to other neuronopathic storage disorders.
A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes
Publisher: Elsevier BV
Date: 07-2004
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools
Publisher: Springer Science and Business Media LLC
Date: 2008
Human Cardiac Transcription Factor Networks
Publisher: Elsevier
Date: 2021
MonaGO: a novel gene ontology enrichment analysis visualisation system
Publisher: Springer Science and Business Media LLC
Date: 14-02-2022
DOI: 10.1186/S12859-022-04594-1
Abstract: Gene ontology (GO) enrichment analysis is frequently undertaken during exploration of various -omics data sets. Despite the wide array of tools available to biologists to perform this analysis, meaningful visualisation of the overrepresented GO in a manner which is easy to interpret is still lacking. Monash Gene Ontology (MonaGO) is a novel web-based visualisation system that provides an intuitive, interactive and responsive interface for performing GO enrichment analysis and visualising the results. MonaGO supports gene lists as well as GO terms as inputs. Visualisation results can be exported as high-resolution images or restored in new sessions, allowing reproducibility of the analysis. An extensive comparison between MonaGO and 11 state-of-the-art GO enrichment visualisation tools based on 9 features revealed that MonaGO is a unique platform that simultaneously allows interactive visualisation within one single output page, directly accessible through a web browser with customisable display options. MonaGO combines dynamic clustering and interactive visualisation as well as customisation options to assist biologists in obtaining meaningful representation of overrepresented GO terms, producing simplified outputs in an unbiased manner. MonaGO will facilitate the interpretation of GO analysis and will assist the biologists into the representation of the results.
Adult fibroblasts retain organ-specific transcriptomic identity
Publisher: Cold Spring Harbor Laboratory
Date: 04-06-2021
DOI: 10.1101/2021.06.03.446915
Abstract: Organ fibroblasts are essential components of homeostatic and diseased tissues. They participate in sculpting the extracellular matrix, sensing the microenvironment and communicating with other resident cells. Recent studies have revealed transcriptomic heterogeneity among fibroblasts within and between organs. To dissect the basis of inter-organ heterogeneity, we compare the gene expression of fibroblasts from different tissues (tail, skin, lung, liver, heart, kidney, gonads) and show that they display distinct positional and organ-specific transcriptome signatures that reflect their embryonic origins. We demonstrate that fibroblasts’ expression of genes typically attributed to the surrounding parenchyma is established in embryonic development and largely maintained in culture, bioengineered tissues, and ectopic transplants. Targeted knockdown of key organ-specific transcription factors affects fibroblasts functions, with modulation of genes related to fibrosis and inflammation. Our data open novel opportunities for the treatment of fibrotic diseases in a more precise, organ-specific manner.
Multicellular Transcriptional Analysis of Mammalian Heart Regeneration
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 19-09-2017
DOI: 10.1161/CIRCULATIONAHA.117.028252
Abstract: The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus nonregenerative (adult) state for the first time. Cardiomyocytes, fibroblasts, leukocytes, and endothelial cells from infarcted and noninfarcted neonatal (P1) and adult (P56) mouse hearts were isolated by enzymatic dissociation and fluorescence-activated cell sorting at day 3 following surgery. RNA sequencing was performed on these cell populations to generate the transcriptome of the major cardiac cell populations during cardiac development, repair, and regeneration. To complement our transcriptomic data, we also surveyed the epigenetic landscape of cardiomyocytes during postnatal maturation by performing deep sequencing of accessible chromatin regions by using the Assay for Transposase-Accessible Chromatin from purified mouse cardiomyocyte nuclei (P1, P14, and P56). Profiling of cardiomyocyte and nonmyocyte transcriptional programs uncovered several injury-responsive genes across regenerative and nonregenerative time points. However, the majority of transcriptional changes in all cardiac cell types resulted from developmental maturation from neonatal stages to adulthood rather than activation of a distinct regeneration-specific gene program. Furthermore, adult leukocytes and fibroblasts were characterized by the expression of a proliferative gene expression network following infarction, which mirrored the neonatal state. In contrast, cardiomyocytes failed to reactivate the neonatal proliferative network following infarction, which was associated with loss of chromatin accessibility around cell cycle genes during postnatal maturation. This work provides a comprehensive framework and transcriptional resource of multiple cardiac cell populations during cardiac development, repair, and regeneration. Our findings define a regulatory program underpinning the neonatal regenerative state and identify alterations in the chromatin landscape that could limit reinduction of the regenerative program in adult cardiomyocytes.
Activation of Nkx2.5 transcriptional program is required for adult myocardial repair
Publisher: Springer Science and Business Media LLC
Date: 27-05-2022
DOI: 10.1038/S41467-022-30468-4
Abstract: The cardiac developmental network has been associated with myocardial regenerative potential. However, the embryonic signals triggered following injury have yet to be fully elucidated. Nkx2.5 is a key causative transcription factor associated with human congenital heart disease and one of the earliest markers of cardiac progenitors, thus it serves as a promising candidate. Here, we show that cardiac-specific RNA-sequencing studies reveal a disrupted embryonic transcriptional profile in the adult Nkx2.5 loss-of-function myocardium. nkx2.5 −/− fish exhibit an impaired ability to recover following ventricular apex utation with diminished dedifferentiation and proliferation. Complex network analyses illuminate that Nkx2.5 is required to provoke proteolytic pathways necessary for sarcomere disassembly and to mount a proliferative response for cardiomyocyte renewal. Moreover, Nkx2.5 targets embedded in these distinct gene regulatory modules coordinate appropriate, multi-faceted injury responses. Altogether, our findings support a previously unrecognized, Nkx2.5-dependent regenerative circuit that invokes myocardial cell cycle re-entry, proteolysis, and mitochondrial metabolism to ensure effective regeneration in the teleost heart.
Cellular Transcriptomic Analysis of Multiple Cardiac Lineages During Heart Development and Regeneration
Publisher: Elsevier BV
Date: 08-2016
Nlcam modulates midline convergence during anterior neural plate morphogenesis
Publisher: Elsevier BV
Date: 03-2010
DOI: 10.1016/J.YDBIO.2009.12.003
Abstract: During development, different cell types must undergo distinct morphogenetic programs so that tissues develop the right dimensions in the appropriate place. In early eye morphogenesis, retinal progenitor cells (RPCs) move first towards the midline, before turning around to migrate out into the evaginating optic vesicles. Neighbouring forebrain cells, however, converge rapidly and then remain at the midline. These differential behaviours are regulated by the transcription factor Rx3. Here, we identify a downstream target of Rx3, the Ig-domain protein Nlcam, and characterise its role in regulating cell migration during the initial phase of optic vesicle morphogenesis. Through sophisticated live imaging and comprehensive cell tracking experiments in zebrafish, we show that ectopic expression of Nlcam in RPCs, as is observed in Rx3 mutants, causes enhanced convergence of these cells. Expression levels of Nlcam therefore regulate the migratory properties of RPCs. Our results provide evidence that the two phases of optic vesicle morphogenesis: slowed convergence and outward-directed migration, are under different genetic control. We propose that Nlcam forms part of the guidance machinery directing rapid midline migration of forebrain precursors, where it is normally expressed, and that its ectopic expression upon loss of Rx3 imparts these migratory characteristics upon RPCs.
Alpha kinase 3 signaling at the M-band maintains sarcomere integrity and proteostasis in striated muscle
Publisher: Springer Science and Business Media LLC
Date: 15-02-2023
DOI: 10.1038/S44161-023-00219-9
Abstract: Muscle contraction is driven by the molecular machinery of the sarcomere. As phosphorylation is a critical regulator of muscle function, the identification of regulatory kinases is important for understanding sarcomere biology. Pathogenic variants in alpha kinase 3 ( ALPK3 ) cause cardiomyopathy and musculoskeletal disease, but little is known about this atypical kinase. Here we show that ALPK3 is an essential component of the M-band of the sarcomere and define the ALPK3-dependent phosphoproteome. ALPK3 deficiency impaired contractility both in human cardiac organoids and in the hearts of mice harboring a pathogenic truncating Alpk3 variant. ALPK3-dependent phosphopeptides were enriched for sarcomeric components of the M-band and the ubiquitin-binding protein sequestosome-1 (SQSTM1) (also known as p62). Analysis of the ALPK3 interactome confirmed binding to M-band proteins including SQSTM1. In human pluripotent stem cell-derived cardiomyocytes modeling cardiomyopathic ALPK3 mutations, sarcomeric organization and M-band localization of SQSTM1 were abnormal suggesting that this mechanism may underly disease pathogenesis.
Cis-regulatory properties of medaka synexpression groups
Publisher: The Company of Biologists
Date: 03-2012
DOI: 10.1242/DEV.071803
Abstract: During embryogenesis, tissue specification is triggered by the expression of a unique combination of developmental genes and their expression in time and space is crucial for successful development. Synexpression groups are batteries of spatiotemporally co-expressed genes that act in shared biological processes through their coordinated expression. Although several synexpression groups have been described in numerous vertebrate species, the regulatory mechanisms that orchestrate their common complex expression pattern remain to be elucidated. Here we performed a pilot screen on 560 genes of the vertebrate model system medaka (Oryzias latipes) to systematically identify synexpression groups and investigate their regulatory properties by searching for common regulatory cues. We find that synexpression groups share DNA motifs that are arranged in various combinations into cis-regulatory modules that drive co-expression. In contrast to previous assumptions that these genes are located randomly in the genome, we discovered that genes belonging to the same synexpression group frequently occur in synexpression clusters in the genome. This work presents a first repertoire of synexpression group common signatures, a resource that will contribute to deciphering developmental gene regulatory networks.
Human specificity encoded in the dark matter of the genome
Publisher: Springer Science and Business Media LLC
Date: 15-09-2022
3D-cardiomics: A spatial transcriptional atlas of the mammalian heart
Publisher: Elsevier BV
Date: 02-2022
DOI: 10.1016/J.YJMCC.2021.09.011
Abstract: Understanding the spatial gene expression and regulation in the heart is key to uncovering its developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information in organs such as the heart, but few utilize intuitive true-to-life three-dimensional representations to analyze and visualise results. Here we combined transcriptomics with 3D-modelling to interrogate spatial gene expression in the mammalian heart. For this, we microdissected and sequenced transcriptome-wide 18 anatomical sections of the adult mouse heart. Our study has unveiled known and novel genes that display complex spatial expression in the heart sub-compartments. We have also created 3D-cardiomics, an interface for spatial transcriptome analysis and visualization that allows the easy exploration of these data in a 3D model of the heart. 3D-cardiomics is accessible from
Analysis of steric effects in DamID profiling of transcription factor target genes
Publisher: Elsevier BV
Date: 03-2017
DOI: 10.1016/J.YGENO.2017.01.006
Abstract: DNA adenine methyltransferase identification (DamID) is an enzymatic technology for detecting DNA regions targeted by chromatin-associated proteins. Proteins are fused to bacterial DNA adenine methyltransferase (Dam) and expressed in cultured cells or whole organisms. Here, we used DamID to detect DNA regions bound by the cardiac-restricted transcription factors (TFs) NKX2-5 and SRF, and ubiquitously-expressed co-factors ELK1 and ELK4. We compared targets bound by these TFs as N- and C-terminal fusions with Dam, for both wild type (WT) NKX2-5 and mutant proteins mimicking those found in congenital heart disease. Overall, DamID is highly robust: while the orientation of WT Dam fusions can affect the size of the target sets, their signatures remained largely reproducible. Furthermore, a severe NKX2-5 mutant lacking the homeodomain showed strong steric effects negatively impacting target discovery. The extent of steric effect is likely to be dependent on the protein in question and the orientation of Dam fusion.
Related Organisations
Heidelberg University And Karlsruhe Institute Of Technology
Location: Germany
European Molecular Biology Laboratory (EMBL) And Heidelberg University
Location: Germany
Related Funding Activities
Discovery Projects - Grant ID: DP190102771
Start Date: 06-2019
End Date: 12-2022
Amount: $376,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP160100933
Start Date: 2016
End Date: 12-2018
Amount: $486,700.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP140101067
Start Date: 02-2014
End Date: 12-2016
Amount: $390,000.00
Funder: Australian Research Council
View Funded Activity