ORCID Profile
0000-0002-7319-8922
Current Organisations
The University of Manitoba
,
CancerCare Manitoba
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Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/GIGASCIENCE/GIAC099
Abstract: The advancement of hybrid sequencing technologies is increasingly expanding genome assemblies that are often annotated using hybrid sequencing transcriptomics, leading to improved genome characterization and the identification of novel genes and isoforms in a wide variety of organisms. We developed an easy-to-use genome-guided transcriptome annotation pipeline that uses assembled transcripts from hybrid sequencing data as input and distinguishes between coding and long non-coding RNAs by integration of several bioinformatic approaches, including gene reconciliation with previous annotations in GTF format. We demonstrated the efficiency of this approach by correctly assembling and annotating all exons from the chicken SCO-spondin gene (containing more than 105 exons), including the identification of missing genes in the chicken reference annotations by homology assignments. Our method helps to improve the current transcriptome annotation of the chicken brain. Our pipeline, implemented on Anaconda/Nextflow and Docker is an easy-to-use package that can be applied to a broad range of species, tissues, and research areas helping to improve and reconcile current annotations. The code and datasets are publicly available at farkas/annotate_my_genomes
Publisher: Springer Science and Business Media LLC
Date: 13-10-2022
DOI: 10.1038/S41375-022-01716-9
Abstract: ETP-ALL (Early T cell Progenitor Acute Lymphoblastic Leukemia) represents a high-risk subtype of T cell acute lymphocytic leukemia (T-ALL). Therapeutically, ETP-ALL patients frequently relapse after conventional chemotherapy highlighting the need for alternative therapeutic approaches. Using our ZEB2
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-09-2021
Abstract: Research indicates that the adult mammalian heart does not contain cardiac stem cells and the vast majority of cardiomyocytes do not ide. Heart regeneration is thus limited after injury. The postmitotic nature of cardiomyocytes blocks cardiac tumor formation but at the same time minimizes cardiomyocyte renewal. Chen et al . report that cell type–specific expression of pluripotency factors dedifferentiates adult cardiomyocytes to a state that resembles fetal cardiomyocytes, enabling adult cardiomyocytes to reenter mitosis (see the Perspective by Wang and Blau). Cardiomyocytes can be reprogrammed to a pluripotent state when expression of pluripotency factors is sustained over an extended period. If cardiomyocytes are only partially reprogrammed, the heart regenerates without tumor formation. —BAP
Publisher: Public Library of Science (PLoS)
Date: 22-09-2021
DOI: 10.1371/JOURNAL.PBIO.3001394
Abstract: The ZEB2 transcription factor has been demonstrated to play important roles in hematopoiesis and leukemic transformation. ZEB1 is a close family member of ZEB2 but has remained more enigmatic concerning its roles in hematopoiesis. Here, we show using conditional loss-of-function approaches and bone marrow (BM) reconstitution experiments that ZEB1 plays a cell-autonomous role in hematopoietic lineage differentiation, particularly as a positive regulator of monocyte development in addition to its previously reported important role in T-cell differentiation. Analysis of existing single-cell (sc) RNA sequencing (RNA-seq) data of early hematopoiesis has revealed distinctive expression differences between Zeb1 and Zeb2 in hematopoietic stem and progenitor cell (HSPC) differentiation, with Zeb2 being more highly and broadly expressed than Zeb1 except at a key transition point (short-term HSC [ST-HSC]➔MPP1), whereby Zeb1 appears to be the dominantly expressed family member. Inducible genetic inactivation of both Zeb1 and Zeb2 using a tamoxifen-inducible Cre-mediated approach leads to acute BM failure at this transition point with increased long-term and short-term hematopoietic stem cell numbers and an accompanying decrease in all hematopoietic lineage differentiation. Bioinformatics analysis of RNA-seq data has revealed that ZEB2 acts predominantly as a transcriptional repressor involved in restraining mature hematopoietic lineage gene expression programs from being expressed too early in HSPCs. ZEB1 appears to fine-tune this repressive role during hematopoiesis to ensure hematopoietic lineage fidelity. Analysis of Rosa26 locus–based transgenic models has revealed that Zeb1 as well as Zeb2 cDNA-based overexpression within the hematopoietic system can drive extramedullary hematopoiesis/splenomegaly and enhance monocyte development. Finally, inactivation of Zeb2 alone or Zeb1/2 together was found to enhance survival in secondary MLL-AF9 acute myeloid leukemia (AML) models attesting to the oncogenic role of ZEB1/2 in AML.
Publisher: Cold Spring Harbor Laboratory
Date: 02-04-2023
DOI: 10.1101/2023.03.30.534915
Abstract: Thyroid cancer is the most common endocrine malignancy and several genetic events have been described to promote the development of thyroid carcinogenesis. Besides the effects of specific mutations on thyroid cancer development, the molecular mechanisms controlling tumorigenesis, tumor behavior, and drug resistance are still largely unknown. Cancer organoids have been proposed as a powerful tool to study aspects related to tumor development and progression and appear promising to test in idual responses to therapies. Here, using mESC-derived thyroid organoids, we developed a Braf V637E -inducible model able to recapitulate the features of papillary thyroid cancer in vitro. Overexpression of Braf V637E rapidly leads to MAPK activation, cell dedifferentiation, and disruption of follicular organization. Braf V637E -expressing organoids show a transcriptomic signature for p53, focal adhesion, ECM-receptor interactions, EMT, and inflammatory signaling pathways. Finally, PTC-like thyroid organoids were used for drug screening assays. The combination of MAPK and PI3K inhibitors reversed Braf oncogene-promoted cell dedifferentiation while restoring thyroid follicle organization and function in vitro . Our results demonstrate that pluripotent stem cells-derived thyroid cancer organoids can mimic tumor development and features while providing an efficient tool for testing novel targeted therapies.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 02-12-2022
Abstract: Skeletal precursors are mesenchymal in origin and can give rise to distinct sublineages. Their lineage commitment is modulated by various signaling pathways. The importance of Wnt signaling in skeletal lineage commitment has been implicated by the study of β-catenin–deficient mouse models. Ectopic chondrogenesis caused by the loss of β-catenin leads to a long-standing belief in canonical Wnt signaling that determines skeletal cell fate. As β-catenin has other functions, it remains unclear whether skeletogenic lineage commitment is solely orchestrated by canonical Wnt signaling. The study of the Wnt secretion regulator Gpr177/Wntless also raises concerns about current knowledge. Here, we show that skeletal cell fate is determined by β-catenin but independent of LEF/TCF transcription. Genomic and bioinformatic analyses further identify GATA3 as a mediator for the alternative signaling effects. GATA3 alone is sufficient to promote ectopic cartilage formation, demonstrating its essential role in mediating nonclassical β-catenin signaling in skeletogenic lineage specification.
Publisher: American Society for Clinical Investigation
Date: 08-07-2022
Publisher: American Association for the Advancement of Science (AAAS)
Date: 28-04-2023
Abstract: Aberrant AKT activation occurs in a number of cancers, metabolic syndrome, and immune disorders, making it an important target for the treatment of many diseases. To monitor spatial and temporal AKT activity in a live setting, we generated an Akt-FRET biosensor mouse that allows longitudinal assessment of AKT activity using intravital imaging in conjunction with image stabilization and optical window technology. We demonstrate the sensitivity of the Akt-FRET biosensor mouse using various cancer models and verify its suitability to monitor response to drug targeting in spheroid and organotypic models. We also show that the dynamics of AKT activation can be monitored in real time in erse tissues, including in in idual islets of the pancreas, in the brown and white adipose tissue, and in the skeletal muscle. Thus, the Akt-FRET biosensor mouse provides an important tool to study AKT dynamics in live tissue contexts and has broad preclinical applications.
Start Date: 2011
End Date: 2013
Funder: Belgian Federal Science Policy Office
View Funded ActivityStart Date: 2010
End Date: 2011
Funder: Natural Sciences and Engineering Research Council
View Funded ActivityStart Date: 2010
End Date: 2015
Funder: Ministry of Economic Development, Job Creation and Trade
View Funded ActivityStart Date: 2013
End Date: 2016
Funder: Research Foundation - Flanders
View Funded ActivityStart Date: 2018
End Date: 2020
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 2013
End Date: 2015
Funder: Belgian Federal Science Policy Office
View Funded ActivityStart Date: 2001
End Date: 2004
Funder: Terry Fox Foundation
View Funded ActivityStart Date: 2019
End Date: 2024
Funder: Canadian Institutes of Health Research
View Funded Activity