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Thakur A, Park K, Cullum R, Fuglerud BM, Khoshnoodi M, Drissler S, Stephan TL, Lotto J, Kim D, Gonzalez FJ, Hoodless PA. HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements. Commun Biol 2024; 7:144. [PMID: 38297077 PMCID: PMC10830483 DOI: 10.1038/s42003-024-05835-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Hepatocyte nuclear factor 4A (HNF4A/NR2a1), a transcriptional regulator of hepatocyte identity, controls genes that are crucial for liver functions, primarily through binding to enhancers. In mammalian cells, active and primed enhancers are marked by monomethylation of histone 3 (H3) at lysine 4 (K4) (H3K4me1) in a cell type-specific manner. How this modification is established and maintained at enhancers in connection with transcription factors (TFs) remains unknown. Using analysis of genome-wide histone modifications, TF binding, chromatin accessibility and gene expression, we show that HNF4A is essential for an active chromatin state. Using HNF4A loss and gain of function experiments in vivo and in cell lines in vitro, we show that HNF4A affects H3K4me1, H3K27ac and chromatin accessibility, highlighting its contribution to the establishment and maintenance of a transcriptionally permissive epigenetic state. Mechanistically, HNF4A interacts with the mixed-lineage leukaemia 4 (MLL4) complex facilitating recruitment to HNF4A-bound regions. Our findings indicate that HNF4A enriches H3K4me1, H3K27ac and establishes chromatin opening at transcriptional regulatory regions.
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Affiliation(s)
- Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Kwangjin Park
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | | | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Donghwan Kim
- Center of Cancer Research, National Cancer Institute, Bethesda, 2089, USA
| | - Frank J Gonzalez
- Center of Cancer Research, National Cancer Institute, Bethesda, 2089, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, V6T 1Z4, Canada.
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2
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Lotto J, Cullum R, Drissler S, Arostegui M, Garside VC, Fuglerud BM, Clement-Ranney M, Thakur A, Underhill TM, Hoodless PA. Cell diversity and plasticity during atrioventricular heart valve EMTs. Nat Commun 2023; 14:5567. [PMID: 37689753 PMCID: PMC10492828 DOI: 10.1038/s41467-023-41279-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/29/2023] [Indexed: 09/11/2023] Open
Abstract
Epithelial-to-mesenchymal transitions (EMTs) of both endocardium and epicardium guide atrioventricular heart valve formation, but the cellular complexity and small scale of this tissue have restricted analyses. To circumvent these issues, we analyzed over 50,000 murine single-cell transcriptomes from embryonic day (E)7.75 hearts to E12.5 atrioventricular canals. We delineate mesenchymal and endocardial bifurcation during endocardial EMT, identify a distinct, transdifferentiating epicardial population during epicardial EMT, and reveal the activation of epithelial-mesenchymal plasticity during both processes. In Sox9-deficient valves, we observe increased epithelial-mesenchymal plasticity, indicating a role for SOX9 in promoting endothelial and mesenchymal cell fate decisions. Lastly, we deconvolve cell interactions guiding the initiation and progression of cardiac valve EMTs. Overall, these data reveal mechanisms of emergence of mesenchyme from endocardium or epicardium at single-cell resolution and will serve as an atlas of EMT initiation and progression with broad implications in regenerative medicine and cancer biology.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | | | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Martin Arostegui
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Victoria C Garside
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - T Michael Underhill
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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3
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Abstract
The metabolic, digestive and homeostatic roles of the liver are dependent on proper crosstalk and organization of hepatic cell lineages. These hepatic cell lineages are derived from their respective progenitors early in organogenesis in a spatiotemporally controlled manner, contributing to the liver's specialized and diverse microarchitecture. Advances in genomics, lineage tracing and microscopy have led to seminal discoveries in the past decade that have elucidated liver cell lineage hierarchies. In particular, single-cell genomics has enabled researchers to explore diversity within the liver, especially early in development when the application of bulk genomics was previously constrained due to the organ's small scale, resulting in low cell numbers. These discoveries have substantially advanced our understanding of cell differentiation trajectories, cell fate decisions, cell lineage plasticity and the signalling microenvironment underlying the formation of the liver. In addition, they have provided insights into the pathogenesis of liver disease and cancer, in which developmental processes participate in disease emergence and regeneration. Future work will focus on the translation of this knowledge to optimize in vitro models of liver development and fine-tune regenerative medicine strategies to treat liver disease. In this Review, we discuss the emergence of hepatic parenchymal and non-parenchymal cells, advances that have been made in in vitro modelling of liver development and draw parallels between developmental and pathological processes.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC, Canada.
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4
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Fuglerud BM, Drissler S, Lotto J, Stephan TL, Thakur A, Cullum R, Hoodless PA. SOX9 reprograms endothelial cells by altering the chromatin landscape. Nucleic Acids Res 2022; 50:8547-8565. [PMID: 35904801 PMCID: PMC9410909 DOI: 10.1093/nar/gkac652] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 01/08/2023] Open
Abstract
The transcription factor SOX9 is activated at the onset of endothelial-to-mesenchymal transition (EndMT) during embryonic development and in pathological conditions. Its roles in regulating these processes, however, are not clear. Using human umbilical vein endothelial cells (HUVECs) as an EndMT model, we show that SOX9 expression alone is sufficient to activate mesenchymal genes and steer endothelial cells towards a mesenchymal fate. By genome-wide mapping of the chromatin landscape, we show that SOX9 displays features of a pioneer transcription factor, such as opening of chromatin and leading to deposition of active histone modifications at silent chromatin regions, guided by SOX dimer motifs and H2A.Z enrichment. We further observe highly transient and dynamic SOX9 binding, possibly promoted through its eviction by histone phosphorylation. However, while SOX9 binding is dynamic, changes in the chromatin landscape and cell fate induced by SOX9 are persistent. Finally, our analysis of single-cell chromatin accessibility indicates that SOX9 opens chromatin to drive EndMT in atherosclerotic lesions in vivo. This study provides new insight into key molecular functions of SOX9 and mechanisms of EndMT and highlights the crucial developmental role of SOX9 and relevance to human disease.
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Affiliation(s)
- Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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5
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Takata K, Chong LC, Ennishi D, Aoki T, Li MY, Thakur A, Healy S, Viganò E, Dao T, Kwon D, Duns G, Nielsen JS, Ben-Neriah S, Tse E, Hung SS, Boyle M, Mun SS, Bourne CM, Woolcock B, Telenius AH, Kishida M, Rai S, Zhang AW, Bashashati A, Saberi S, D' Antonio G, Nelson BH, Shah SP, Hoodless PA, Melnick AM, Gascoyne RD, Connors JM, Scheinberg DA, Béguelin W, Scott DW, Steidl C. Tumor associated antigen PRAME exhibits dualistic functions that are targetable in diffuse large B-cell lymphoma. J Clin Invest 2022; 132:145343. [PMID: 35380993 PMCID: PMC9106353 DOI: 10.1172/jci145343] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/29/2022] [Indexed: 11/26/2022] Open
Abstract
PRAME is a prominent member of the cancer testis antigen family of proteins, which triggers autologous T cell–mediated immune responses. Integrative genomic analysis in diffuse large B cell lymphoma (DLBCL) uncovered recurrent and highly focal deletions of 22q11.22, including the PRAME gene, which were associated with poor outcome. PRAME-deleted tumors showed cytotoxic T cell immune escape and were associated with cold tumor microenvironments. In addition, PRAME downmodulation was strongly associated with somatic EZH2 Y641 mutations in DLBCL. In turn, PRC2-regulated genes were repressed in isogenic PRAME-KO lymphoma cell lines, and PRAME was found to directly interact with EZH2 as a negative regulator. EZH2 inhibition with EPZ-6438 abrogated these extrinsic and intrinsic effects, leading to PRAME expression and microenvironment restoration in vivo. Our data highlight multiple functions of PRAME during lymphomagenesis and provide a preclinical rationale for synergistic therapies combining epigenetic reprogramming with PRAME-targeted therapies.
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Affiliation(s)
| | - Lauren C Chong
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Daisuke Ennishi
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Tomohiro Aoki
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Michael Yu Li
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Avinash Thakur
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Shannon Healy
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Elena Viganò
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Daniel Kwon
- Molecular Oncology, BC Cancer Research, Vancouver, Canada
| | - Gerben Duns
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Julie S Nielsen
- Trev and Joyce Deeley Research Centre, BC Cancer Research, Vancouver, Canada
| | | | - Ethan Tse
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Stacy S Hung
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Merrill Boyle
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Sung Soo Mun
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Christopher M Bourne
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Bruce Woolcock
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | | | - Makoto Kishida
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Shinya Rai
- Lymphoid Cancer Research, BC Cancer Research, Vancouver, Canada
| | - Allen W Zhang
- Department of Molecular Oncology, BC Cancer Research, Vancouver, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer Research, Vancouver, Canada
| | - Saeed Saberi
- Department of Molecular Oncology, BC Cancer Research, Vancouver, Canada
| | - Gianluca D' Antonio
- Trev and Joyce Deeley Research Centre, BC Cancer Research, Vancouver, Canada
| | - Brad H Nelson
- Trev and Joyce Deeley Research Centre, BC Cancer Research, Vancouver, Canada
| | - Sohrab P Shah
- Department of Epidemiology and Biostatistics, Weill Cornell Medical College, New York, United States of America
| | | | - Ari M Melnick
- Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | | | | | - David A Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Wendy Béguelin
- Department of Medicine, Weill Cornell Medical College, New York, United States of America
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Research, Vancouver, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Research, Vancouver, Canada
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6
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Cheng JC, Fang L, Li Y, Thakur A, Hoodless PA, Guo Y, Wang Z, Wu Z, Yan Y, Jia Q, Gao Y, Han X, Yu Y, Sun YP. G protein-coupled estrogen receptor stimulates human trophoblast cell invasion via YAP-mediated ANGPTL4 expression. Commun Biol 2021; 4:1285. [PMID: 34773076 PMCID: PMC8589964 DOI: 10.1038/s42003-021-02816-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Insufficient invasion of trophoblast cells into the uterine decidua is associated with preeclampsia (PE). G protein-coupled estrogen receptor (GPER) is a membrane estrogen receptor involved in non-genomic estrogen signaling. GPER is expressed in human trophoblast cells and downregulated GPER levels are noted in PE. However, to date, the role of GPER in trophoblast cells remains largely unknown. Here, we applied RNA sequencing (RNA-seq) to HTR-8/SVneo human trophoblast cells in response to G1, an agonist of GPER, and identified angiopoietin-like 4 (ANGPTL4) as a target gene of GPER. Treatment of trophoblast cells with G1 or 17β-estradiol (E2) activated Yes-associated protein (YAP), the major downstream effector of the Hippo pathway, via GPER but in a mammalian STE20-like protein kinase 1 (MST1)-independent manner. Using pharmacological inhibitors as well as loss- and gain-of-function approaches, our results revealed that YAP activation was required for GPER-stimulated ANGPTL4 expression. Transwell invasion assays demonstrated that activation of GPER-induced ANGPTL4 promoted cell invasion. In addition, the expression levels of GPER, YAP, and ANGPTL4 were downregulated in the placenta of patients with PE. Our findings reveal a mechanism by which GPER exerts its stimulatory effect on human trophoblast cell invasion by upregulating YAP-mediated ANGPTL4 expression. Cheng, Fan, Li et al. identified ANGPTL4 as a G1-induced target gene of GPER/YAP in HRT8 cells using RNA-seq and highlighted its importance in regulating trophoblast cell invasion. The authors also reported GPER downregulation in the placenta and lower estradiol levels in patients who developed preeclampsia.
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Affiliation(s)
- Jung-Chien Cheng
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Lanlan Fang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yuxi Li
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada, V5Z 1L3.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada, V5Z 1L3.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Yanjie Guo
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Zhen Wang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Ze Wu
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yang Yan
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Qiongqiong Jia
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yibo Gao
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Xiaoyu Han
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yiping Yu
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Ying-Pu Sun
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
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7
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Campbell SA, Stephan TL, Lotto J, Cullum R, Drissler S, Hoodless PA. Signalling pathways and transcriptional regulators orchestrating liver development and cancer. Development 2021; 148:272023. [PMID: 34478514 DOI: 10.1242/dev.199814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Liver development is controlled by key signals and transcription factors that drive cell proliferation, migration, differentiation and functional maturation. In the adult liver, cell maturity can be perturbed by genetic and environmental factors that disrupt hepatic identity and function. Developmental signals and fetal genetic programmes are often dysregulated or reactivated, leading to dedifferentiation and disease. Here, we highlight signalling pathways and transcriptional regulators that drive liver cell development and primary liver cancers. We also discuss emerging models derived from pluripotent stem cells, 3D organoids and bioengineering for improved studies of signalling pathways in liver cancer and regenerative medicine.
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Affiliation(s)
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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8
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Lotto J, Drissler S, Cullum R, Wei W, Setty M, Bell EM, Boutet SC, Nowotschin S, Kuo YY, Garg V, Pe'er D, Church DM, Hadjantonakis AK, Hoodless PA. Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages. Cell 2020; 183:702-716.e14. [PMID: 33125890 PMCID: PMC7643810 DOI: 10.1016/j.cell.2020.09.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 07/06/2020] [Accepted: 09/01/2020] [Indexed: 02/08/2023]
Abstract
The cellular complexity and scale of the early liver have constrained analyses examining its emergence during organogenesis. To circumvent these issues, we analyzed 45,334 single-cell transcriptomes from embryonic day (E)7.5, when endoderm progenitors are specified, to E10.5 liver, when liver parenchymal and non-parenchymal cell lineages emerge. Our data detail divergence of vascular and sinusoidal endothelia, including a distinct transcriptional profile for sinusoidal endothelial specification by E8.75. We characterize two distinct mesothelial cell types as well as early hepatic stellate cells and reveal distinct spatiotemporal distributions for these populations. We capture transcriptional profiles for hepatoblast specification and migration, including the emergence of a hepatomesenchymal cell type and evidence for hepatoblast collective cell migration. Further, we identify cell-cell interactions during the organization of the primitive sinusoid. This study provides a comprehensive atlas of liver lineage establishment from the endoderm and mesoderm through to the organization of the primitive sinusoid at single-cell resolution.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Manu Setty
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erin M Bell
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | | | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ying-Yi Kuo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe'er
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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9
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Coulombe P, Paliouras GN, Clayton A, Hussainkhel A, Fuller M, Jovanovic V, Dauphinee S, Umlandt P, Xiang P, Kyle AH, Minchinton AI, Humphries RK, Hoodless PA, Parker JDK, Wright JL, Karsan A. Endothelial Sash1 Is Required for Lung Maturation through Nitric Oxide Signaling. Cell Rep 2020; 27:1769-1780.e4. [PMID: 31067462 DOI: 10.1016/j.celrep.2019.04.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 03/07/2019] [Accepted: 04/05/2019] [Indexed: 12/19/2022] Open
Abstract
The sterile alpha motif (SAM) and SRC homology 3 (SH3) domain containing protein 1 (Sash1) acts as a scaffold in TLR4 signaling. We generated Sash1-/- mice, which die in the perinatal period due to respiratory distress. Constitutive or endothelial-restricted Sash1 loss leads to a delay in maturation of alveolar epithelial cells causing reduced surfactant-associated protein synthesis. We show that Sash1 interacts with β-arrestin 1 downstream of the TLR4 pathway to activate Akt and endothelial nitric oxide synthase (eNOS) in microvascular endothelial cells. Generation of nitric oxide downstream of Sash1 in endothelial cells affects alveolar epithelial cells in a cGMP-dependent manner, inducing maturation of alveolar type 1 and 2 cells. Thus, we identify a critical cell nonautonomous function for Sash1 in embryonic development in which endothelial Sash1 regulates alveolar epithelial cell maturation and promotes pulmonary surfactant production through nitric oxide signaling. Lung immaturity is a major cause of respiratory distress and mortality in preterm infants, and these findings identify the endothelium as a potential target for therapy.
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Affiliation(s)
- Patrick Coulombe
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Experimental Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Grigorios N Paliouras
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Ashley Clayton
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Experimental Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Angela Hussainkhel
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada; Program of Interdisciplinary Oncology, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Vida Jovanovic
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Shauna Dauphinee
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Experimental Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Patricia Umlandt
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Ping Xiang
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Alistair H Kyle
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Andrew I Minchinton
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - R Keith Humphries
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Terry Fox Laboratory, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Pamela A Hoodless
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Terry Fox Laboratory, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Jeremy D K Parker
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Joanne L Wright
- Department of Pathology, University of British Colombia, Vancouver, BC V6T 2B5, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Experimental Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Program of Interdisciplinary Oncology, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Pathology, University of British Colombia, Vancouver, BC V6T 2B5, Canada.
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10
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Thakur A, Hoodless PA. Repressive Epigenetic Signatures Safeguard the Liver. Dev Cell 2020; 50:3-4. [PMID: 31265811 DOI: 10.1016/j.devcel.2019.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To date, how epigenetic changes are regulated during liver regeneration remains unclear. In this issue of Developmental Cell, Wang and colleagues (2019) employed transcriptomic and epigenomic profiling to explore how Uhrf1, an epigenetic regulator of DNA methylation, functions in liver regeneration using a mouse model of partial hepatectomy.
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Affiliation(s)
- Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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11
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Thakur A, Wong JCH, Wang EY, Lotto J, Kim D, Cheng JC, Mingay M, Cullum R, Moudgil V, Ahmed N, Tsai SH, Wei W, Walsh CP, Stephan T, Bilenky M, Fuglerud BM, Karimi MM, Gonzalez FJ, Hirst M, Hoodless PA. Hepatocyte Nuclear Factor 4-Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver. Hepatology 2019; 70:1360-1376. [PMID: 30933372 PMCID: PMC6773525 DOI: 10.1002/hep.30631] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 03/27/2019] [Indexed: 12/11/2022]
Abstract
Cell-fate determination is influenced by interactions between master transcription factors (TFs) and cis-regulatory elements. Hepatocyte nuclear factor 4 alpha (HNF4A), a liver-enriched TF, acts as a master controller in specification of hepatic progenitor cells by regulating a network of TFs to control onset of hepatocyte cell fate. Using analysis of genome-wide histone modifications, DNA methylation, and hydroxymethylation in mouse hepatocytes, we show that HNF4A occupies active enhancers in hepatocytes and is essential for active histone and DNA signatures, especially acetylation of lysine 27 of histone 3 (H3K27ac) and 5-hydroxymethylcytosine (5hmC). In mice lacking HNF4A protein in hepatocytes, we observed a decrease in both H3K27ac and hydroxymethylation at regions bound by HNF4A. Mechanistically, HNF4A-associated hydroxymethylation (5hmC) requires its interaction with ten-eleven translocation methylcytosine dioxygenase 3 (TET3), a protein responsible for oxidation from 5mC to 5hmC. Furthermore, HNF4A regulates TET3 expression in liver by directly binding to an enhancer region. Conclusion: In conclusion, we identified that HNF4A is required for the active epigenetic state at enhancers that amplifies transcription of genes in hepatocytes.
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Affiliation(s)
- Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3,Department of Medical Genetics, University of British Columbia, Vancouver, Canada, V6T 1Z4
| | - Jasper C. H. Wong
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Y. Wang
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Donghwan Kim
- Center of Cancer Research, National Cancer Institute, Bethesda MD 2089
| | - Jung-Chien Cheng
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Matthew Mingay
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Vaishali Moudgil
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Nafeel Ahmed
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Shu-Huei Tsai
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Colum P. Walsh
- Genomic Medicine Research Group, Centre for Molecular Biosciences, Biomedical Sciences Research Institute, Ulster University, Coleraine, BT52 1SA, UK
| | - Tabea Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Misha Bilenky
- Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Bettina M. Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3,Department of Biosciences, University of Oslo, Oslo, Norway, 0316
| | | | - Frank J. Gonzalez
- Center of Cancer Research, National Cancer Institute, Bethesda MD 2089
| | - Martin Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada,Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada, V5Z 1L3,Department of Medical Genetics, University of British Columbia, Vancouver, Canada, V6T 1Z4,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada, V6T 1Z4
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12
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Wang EY, Cheng JC, Thakur A, Yi Y, Tsai SH, Hoodless PA. YAP transcriptionally regulates ErbB2 to promote liver cell proliferation. Biochim Biophys Acta Gene Regul Mech 2018; 1861:S1874-9399(18)30039-7. [PMID: 30025876 DOI: 10.1016/j.bbagrm.2018.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/04/2018] [Accepted: 07/09/2018] [Indexed: 01/20/2023]
Abstract
The Hippo signaling pathway is implicated in regulation of liver size and dysregulation of this pathway contributes to tumorigenesis. The transcriptional targets and downstream pathways of the Hippo pathway effector YAP that contribute to liver growth have yet to be well-characterized. We examined the liver transcriptome in response to YAP overexpression and identify the ErbB signaling pathway as a mediator of cell growth downstream of YAP. ErbB2 is transcriptionally regulated by YAP in both the mouse liver and in HepG2 human hepatoma cells. Knockdown of YAP or pharmacological inhibition with verteporfin reduced ERBB2 levels in HepG2 cells. Analysis of ChIP-seq data revealed enrichment of the transcription factor TEAD4 at the ERBB2 promoter. Using luciferase reporter and chromatin immunoprecipitation assays, we show that YAP and TEAD4 directly bind to and activate a regulatory element in the ErbB2 promoter in both the mouse liver and HepG2 cells. Functionally, knockdown of YAP reduced EGF-induced ERBB2-mediated HepG2 cell proliferation and PI3K/AKT activation. Our findings highlight a mechanism by which YAP exerts its effects on liver cell proliferation through the ErbB signaling pathway by directly regulating the transcription of ErbB2.
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Affiliation(s)
- Evan Y Wang
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jung-Chien Cheng
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Yuyin Yi
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Shu-Huei Tsai
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z4, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada.
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13
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Cheng JC, Wang EY, Yi Y, Thakur A, Tsai SH, Hoodless PA. S1P Stimulates Proliferation by Upregulating CTGF Expression through S1PR2-Mediated YAP Activation. Mol Cancer Res 2018; 16:1543-1555. [DOI: 10.1158/1541-7786.mcr-17-0681] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 04/06/2018] [Accepted: 05/31/2018] [Indexed: 11/16/2022]
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14
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Freyer L, Hsu CW, Nowotschin S, Pauli A, Ishida J, Kuba K, Fukamizu A, Schier AF, Hoodless PA, Dickinson ME, Hadjantonakis AK. Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives. Cell Rep 2018; 20:2116-2130. [PMID: 28854362 DOI: 10.1016/j.celrep.2017.08.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 06/22/2017] [Accepted: 08/01/2017] [Indexed: 01/22/2023] Open
Abstract
Apela (also known as Elabela, Ende, and Toddler) is a small signaling peptide that activates the G-protein-coupled receptor Aplnr to stimulate cell migration during zebrafish gastrulation. Here, using CRISPR/Cas9 to generate a null, reporter-expressing allele, we study the role of Apela in the developing mouse embryo. We found that loss of Apela results in low-penetrance cardiovascular defects that manifest after the onset of circulation. Three-dimensional micro-computed tomography revealed a higher penetrance of vascular remodeling defects, from which some mutants recover, and identified extraembryonic anomalies as the earliest morphological distinction in Apela mutant embryos. Transcriptomics at late gastrulation identified aberrant upregulation of erythroid and myeloid markers in mutant embryos prior to the appearance of physical malformations. Double-mutant analyses showed that loss of Apela signaling impacts early Aplnr-expressing mesodermal populations independently of the alternative ligand Apelin, leading to lethal cardiac defects in some Apela null embryos.
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Affiliation(s)
- Laina Freyer
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Andrea Pauli
- The Research Institute of Molecular Pathology, Vienna BioCenter, 1030 Vienna, Austria
| | - Junji Ishida
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Akita University, Akita 010-8543, Japan
| | - Akiyoshi Fukamizu
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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15
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Wei W, Lotto J, Hoodless PA. Expression patterns of Yes-associated protein 1 in the developing mouse liver. Gene Expr Patterns 2018; 29:10-17. [PMID: 29627454 DOI: 10.1016/j.gep.2018.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 01/26/2023]
Abstract
The Hippo signaling pathway regulates many cellular processes, but has been specifically associated with control organ size and tumor growth. Yes-associated protein 1 (YAP1) is a transcriptional cofactor, in the Hippo pathway, that regulates gene expression when localized in the nucleus. Elevated expression of YAP1 in adult mouse liver leads to hepatomegaly and can cause hepatocellular carcinoma; while the loss of function studies reveal its importance in regulating cholangiocyte development. Here, we report the expression of YAP1 in mouse embryonic and postnatal hepatic cells, using AFP-GFP transgenic mice to identify the hepatocyte lineage. At embryonic day (E) 8.5, YAP1 is highly expressed in the endoderm, but is not present in the nucleus. Between E9.5-12.5, hepatic cells display low levels of nuclear and non-nuclear YAP1. The nuclear expression of YAP1 is first detected in a small subset of hepatic cells starting at E13.5 when the hepatoblasts begin to differentiate into hepatocytes and cholangiocytes. At E18.5, nuclear YAP1 is nearly undetectable in hepatoblasts and hepatocytes, but enriched within the nuclei of cholangiocytes. These levels remain similar postnatally, consistent with the role of YAP1 in cholangiocyte specification and maintenance.
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Affiliation(s)
- Wei Wei
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada; Department of Medical Genetics and the School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
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16
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Yi Y, Tsai SH, Cheng JC, Wang EY, Anglesio MS, Cochrane DR, Fuller M, Gibb EA, Wei W, Huntsman DG, Karsan A, Hoodless PA. APELA promotes tumour growth and cell migration in ovarian cancer in a p53-dependent manner. Gynecol Oncol 2017; 147:663-671. [DOI: 10.1016/j.ygyno.2017.10.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/07/2017] [Accepted: 10/11/2017] [Indexed: 01/23/2023]
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17
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Wilcox SM, Arora H, Munro L, Xin J, Fenninger F, Johnson LA, Pfeifer CG, Choi KB, Hou J, Hoodless PA, Jefferies WA. The role of the innate immune response regulatory gene ABCF1 in mammalian embryogenesis and development. PLoS One 2017; 12:e0175918. [PMID: 28542262 PMCID: PMC5438103 DOI: 10.1371/journal.pone.0175918] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/03/2017] [Indexed: 12/15/2022] Open
Abstract
ABCF1 is an ABC transporter family protein that has been shown to regulate innate immune response and is a risk gene for autoimmune pancreatitis and arthritis. Unlike other members of ABC transporter family, ABCF1 lacks trans-membrane domains and is thought to function in translation initiation through an interaction with eukaryotic translation initiation factor 2 (eIF2). To study ABCF1 expression and function in development and disease, we used a single gene trap insertion in the Abcf1 gene in murine embryonic stem cells (ES cells) that allowed lineage tracing of the endogenous Abcf1 promoter by following the expression of a β-galactosidase reporter gene. From the ES cells, heterozygous mice (Abcf1+/-) were produced. No live born Abcf1-/- progeny were ever generated, and the lethality was not mouse strain-specific. Thus, we have determined that Abcf1 is an essential gene in development. Abcf1-/- mice were found to be embryonic lethal at 3.5 days post coitum (dpc), while Abcf1+/- mice appeared developmentally normal. Abcf1+/- mice were fertile and showed no significant differences in their anatomy when compared with their wild type littermates. The Abcf1 promoter was found to be active in all organs in adult mice, but varies in levels of expression in specific cell types within tissues. Furthermore, we observed high promoter activity in the blastocysts and embryos. Overall, Abcf1 expression in embryos is required for development and its expression in adults was highly correlated with actively proliferating and differentiating cell types.
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Affiliation(s)
- Sara M. Wilcox
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Hitesh Arora
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lonna Munro
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jian Xin
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Franz Fenninger
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura A. Johnson
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Cheryl G. Pfeifer
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung Bok Choi
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Juan Hou
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Developmental and Cell Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Wilfred A. Jefferies
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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18
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Garside VC, Cullum R, Alder O, Lu DY, Vander Werff R, Bilenky M, Zhao Y, Jones SJM, Marra MA, Underhill TM, Hoodless PA. SOX9 modulates the expression of key transcription factors required for heart valve development. Development 2015; 142:4340-50. [PMID: 26525672 DOI: 10.1242/dev.125252] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/28/2015] [Indexed: 01/10/2023]
Abstract
Heart valve formation initiates when endothelial cells of the heart transform into mesenchyme and populate the cardiac cushions. The transcription factor SOX9 is highly expressed in the cardiac cushion mesenchyme, and is essential for heart valve development. Loss of Sox9 in mouse cardiac cushion mesenchyme alters cell proliferation, embryonic survival, and valve formation. Despite this important role, little is known about how SOX9 regulates heart valve formation or its transcriptional targets. Therefore, we mapped putative SOX9 binding sites by ChIP-Seq in E12.5 heart valves, a stage at which the valve mesenchyme is actively proliferating and initiating differentiation. Embryonic heart valves have been shown to express a high number of genes that are associated with chondrogenesis, including several extracellular matrix proteins and transcription factors that regulate chondrogenesis. Therefore, we compared regions of putative SOX9 DNA binding between E12.5 heart valves and E12.5 limb buds. We identified context-dependent and context-independent SOX9-interacting regions throughout the genome. Analysis of context-independent SOX9 binding suggests an extensive role for SOX9 across tissues in regulating proliferation-associated genes including key components of the AP-1 complex. Integrative analysis of tissue-specific SOX9-interacting regions and gene expression profiles on Sox9-deficient heart valves demonstrated that SOX9 controls the expression of several transcription factors with previously identified roles in heart valve development, including Twist1, Sox4, Mecom and Pitx2. Together, our data identify SOX9-coordinated transcriptional hierarchies that control cell proliferation and differentiation during valve formation.
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Affiliation(s)
- Victoria C Garside
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Program in Cell and Developmental Biology, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Olivia Alder
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Daphne Y Lu
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Ryan Vander Werff
- Biomedical Research Centre, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Mikhail Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada V5A 1S6
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - T Michael Underhill
- Program in Cell and Developmental Biology, University of British Columbia, Vancouver, Canada V6T 1Z4 Biomedical Research Centre, University of British Columbia, Vancouver, Canada V6T 1Z4 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Program in Cell and Developmental Biology, University of British Columbia, Vancouver, Canada V6T 1Z4 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4
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Sanders SS, Hou J, Sutton LM, Garside VC, Mui KKN, Singaraja RR, Hayden MR, Hoodless PA. Huntingtin interacting proteins 14 and 14-like are required for chorioallantoic fusion during early placental development. Dev Biol 2015; 397:257-66. [PMID: 25478910 DOI: 10.1016/j.ydbio.2014.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/01/2014] [Accepted: 11/12/2014] [Indexed: 11/17/2022]
Abstract
Huntington disease (HD) is an adult-onset neurodegenerative disease characterized by motor, cognitive, and psychiatric symptoms that is caused by a CAG expansion in the HTT gene. Palmitoylation is the addition of saturated fatty acids to proteins by DHHC palmitoylacyl transferases. HTT is palmitoylated by huntingtin interacting proteins 14 and 14-like (HIP14 and HIP14L or ZDHHC17 and 13 respectively). Mutant HTT is less palmitoylated and this reduction of palmitoylation accelerates its aggregation and increases cellular toxicity. Mouse models deficient in either Hip14 (Hip14(-/-)) or Hip14l (Hip14l(-/-)) develop HD-like phenotypes. The biological function of HTT palmitoylation and the role that loss of HTT palmitoylation plays in the pathogenesis of HD are unknown. To address these questions mice deficient for both genes were created. Loss of Hip14 and Hip14l leads to early embryonic lethality at day embryonic day 10-11 due to failed chorioallantoic fusion. The chorion is thickened and disorganized and the allantois does not fuse correctly with the chorion and forms a balloon-like shape compared to Hip14l(-/-); Hip14(+/+) littermate control embryos. Interestingly, the Hip14(-/-) ; Hip14(-/-) embryos share many features with the Htt(-/-) embryos, including folding of the yolk sac, a bulb shaped allantois, and a thickened and disorganized chorion. This may be due to a decrease in HTT palmitoylation. In Hip14(-/-); Hip14l(-/-) mouse embryonic fibroblasts show a 25% decrease in HTT palmitoylation compared to wild type cells. This is the first description of a double PAT deficient mouse model where loss of a PAT or multiple PATs results in embryonic lethality in mammals. These results reinforce the physiological importance of palmitoylation during embryogenesis.
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Affiliation(s)
- Shaun S Sanders
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia, 950 28th Avenue West, Vancouver, British Columbia, Canada V5Z 4H4
| | - Juan Hou
- Terry Fox Laboratory, BC Cancer Agency, 675 10th Ave West, Vancouver, British Columbia, Canada V5Z 1L3
| | - Liza M Sutton
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia, 950 28th Avenue West, Vancouver, British Columbia, Canada V5Z 4H4
| | - Victoria C Garside
- Terry Fox Laboratory, BC Cancer Agency, 675 10th Ave West, Vancouver, British Columbia, Canada V5Z 1L3
| | - Katherine K N Mui
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia, 950 28th Avenue West, Vancouver, British Columbia, Canada V5Z 4H4
| | - Roshni R Singaraja
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia, 950 28th Avenue West, Vancouver, British Columbia, Canada V5Z 4H4
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child & Family Research Institute, University of British Columbia, 950 28th Avenue West, Vancouver, British Columbia, Canada V5Z 4H4.
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, 675 10th Ave West, Vancouver, British Columbia, Canada V5Z 1L3
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20
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Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Garside VC, Bilenky M, Griffith M, Morrissy AS, Robertson GA, Thiessen N, Zhao Y, Chen Q, Pan D, Jones SJM, Marra MA, Hoodless PA. Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation. Cell Rep 2014; 9:261-271. [PMID: 25263553 PMCID: PMC4612615 DOI: 10.1016/j.celrep.2014.08.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/11/2014] [Accepted: 08/20/2014] [Indexed: 12/28/2022] Open
Abstract
Cell fate acquisition is heavily influenced by direct interactions between master regulators and tissue-specific enhancers. However, it remains unclear how lineage-specifying transcription factors, which are often expressed in both progenitor and mature cell populations, influence cell differentiation. Using in vivo mouse liver development as a model, we identified thousands of enhancers that are bound by the master regulators HNF4A and FOXA2 in a differentiation-dependent manner, subject to chromatin remodeling, and associated with differentially expressed target genes. Enhancers exclusively occupied in the embryo were found to be responsive to developmentally regulated TEAD2 and coactivator YAP1. Our data suggest that Hippo signaling may affect hepatocyte differentiation by influencing HNF4A and FOXA2 interactions with temporal enhancers. In summary, transcription factor-enhancer interactions are not only tissue specific but also differentiation dependent, which is an important consideration for researchers studying cancer biology or mammalian development and/or using transformed cell lines.
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Affiliation(s)
- Olivia Alder
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Sam Lee
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Arohumam C Kan
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Yuyin Yi
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | | | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Malachi Griffith
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - A Sorana Morrissy
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gordon A Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Qian Chen
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Duojia Pan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z4H4, Canada.
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21
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Hou J, Wei W, Saund RS, Xiang P, Cunningham TJ, Yi Y, Alder O, Lu DYD, Savory JGA, Krentz NAJ, Montpetit R, Cullum R, Hofs N, Lohnes D, Humphries RK, Yamanaka Y, Duester G, Saijoh Y, Hoodless PA. A regulatory network controls nephrocan expression and midgut patterning. Development 2014; 141:3772-81. [PMID: 25209250 DOI: 10.1242/dev.108274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although many regulatory networks involved in defining definitive endoderm have been identified, the mechanisms through which these networks interact to pattern the endoderm are less well understood. To explore the mechanisms involved in midgut patterning, we dissected the transcriptional regulatory elements of nephrocan (Nepn), the earliest known midgut specific gene in mice. We observed that Nepn expression is dramatically reduced in Sox17(-/-) and Raldh2(-/-) embryos compared with wild-type embryos. We further show that Nepn is directly regulated by Sox17 and the retinoic acid (RA) receptor via two enhancer elements located upstream of the gene. Moreover, Nepn expression is modulated by Activin signaling, with high levels inhibiting and low levels enhancing RA-dependent expression. In Foxh1(-/-) embryos in which Nodal signaling is reduced, the Nepn expression domain is expanded into the anterior gut region, confirming that Nodal signaling can modulate its expression in vivo. Together, Sox17 is required for Nepn expression in the definitive endoderm, while RA signaling restricts expression to the midgut region. A balance of Nodal/Activin signaling regulates the anterior boundary of the midgut expression domain.
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Affiliation(s)
- Juan Hou
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Ranajeet S Saund
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Ping Xiang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Thomas J Cunningham
- Development, Aging and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yuyin Yi
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Olivia Alder
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Daphne Y D Lu
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Joanne G A Savory
- Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Nicole A J Krentz
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rachel Montpetit
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Nicole Hofs
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - David Lohnes
- Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Experimental Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yojiro Yamanaka
- Goodman Cancer Research Centre, Department of Human Genetics, McGill University, Montreal, Quebec H2W 1S6, Canada
| | - Gregg Duester
- Development, Aging and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yukio Saijoh
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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22
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Chang AC, Garside VC, Fournier M, Smrz J, Vrljicak P, Umlandt P, Fuller M, Robertson G, Zhao Y, Tam A, Jones SJM, Marra MA, Hoodless PA, Karsan A. A Notch-dependent transcriptional hierarchy promotes mesenchymal transdifferentiation in the cardiac cushion. Dev Dyn 2014; 243:894-905. [DOI: 10.1002/dvdy.24127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/11/2014] [Accepted: 03/11/2014] [Indexed: 12/26/2022] Open
Affiliation(s)
- Alex C.Y. Chang
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
| | - Victoria C. Garside
- Terry Fox Laboratory; British Columbia Cancer Agency; Vancouver Canada
- Cell and Developmental Biology Program; University of British Columbia; Vancouver Canada
| | - Michele Fournier
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver Canada
| | - Justin Smrz
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
| | - Pavle Vrljicak
- Terry Fox Laboratory; British Columbia Cancer Agency; Vancouver Canada
| | - Patricia Umlandt
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver Canada
| | - Gordon Robertson
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
| | - Yongjun Zhao
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
| | - Angela Tam
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
| | - Steven J. M. Jones
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
- Department of Medical Genetics; University of British Columbia; Vancouver Canada
| | - Marco A. Marra
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
- Department of Medical Genetics; University of British Columbia; Vancouver Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory; British Columbia Cancer Agency; Vancouver Canada
- Department of Medical Genetics; University of British Columbia; Vancouver Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre; British Columbia Cancer Agency; Vancouver Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver Canada
- Department of Pathology and Laboratory Medicine; British Columbia Cancer Agency; Vancouver Canada
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23
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Ye X, Zhang HM, Qiu Y, Hanson PJ, Hemida MG, Wei W, Hoodless PA, Chu F, Yang D. Coxsackievirus-induced miR-21 disrupts cardiomyocyte interactions via the downregulation of intercalated disk components. PLoS Pathog 2014; 10:e1004070. [PMID: 24722419 PMCID: PMC3983067 DOI: 10.1371/journal.ppat.1004070] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 02/25/2014] [Indexed: 01/28/2023] Open
Abstract
Intercalated disks (ICDs) are substantial connections maintaining cardiac structures and mediating signal communications among cardiomyocytes. Deficiency in ICD components such as desmosomes, fascia adherens and gap junctions leads to heart dysfunction. Coxsackievirus B3 (CVB3) infection induces cardiac failure but its pathogenic effect on ICDs is unclear. Here we show that CVB3-induced miR-21 expression affects ICD structure, i.e., upregulated miR-21 targets YOD1, a deubiquitinating enzyme, to enhance the K48-linked ubiquitination and degradation of desmin, resulting in disruption of desmosomes. Inhibition of miR-21 preserves desmin during CVB3 infection. Treatment with proteasome inhibitors blocks miR-21-mediated desmin degradation. Transfection of miR-21 or knockdown of YOD1 triggers co-localization of desmin with proteasomes. We also identified K108 and K406 as important sites for desmin ubiquintination and degradation. In addition, miR-21 directly targets vinculin, leading to disturbed fascia adherens evidenced by the suppression and disorientation of pan-cadherin and α-E-catenin proteins, two fascia adherens-components. Our findings suggest a new mechanism of miR-21 in modulating cell-cell interactions of cardiomyocytes during CVB3 infection. Coxsackievirus B3 (CVB3) is one of most common causes of heart inflammation and failure. However, the mechanism by which CVB3 induces cardiac damage has not been fully elucidated. Particularly, the involvement of microRNAs (miRNAs), a family of small RNAs controlling the progression of a wide range of diseases, in CVB3 infection is still unclear. These small RNAs are essential to understand the CVB3-caused heart muscle cell injury and have great potential to serve therapeutic purposes. Here, we systematically analyzed the miRNA changes during CVB3 infection and found that miR-21 is increased by viral infection. We further demonstrated that the CVB3-induced miR-21 triggers heart muscle cell damage by interfering with the cell-cell interactions. miR-21 suppresses the levels of components in cell-cell interactions by either promoting the degradation of those proteins or directly inhibiting the protein production. Inhibition of miR-21 can reduce the host injury caused by CVB3 infection. Our findings will shed new lights on the pathogenesis of CVB3-induced heart failure.
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Affiliation(s)
- Xin Ye
- Department of Pathology and Laboratory Medicine, University of British Columbia, The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Huifang Mary Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Ye Qiu
- Department of Pathology and Laboratory Medicine, University of British Columbia, The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Paul J. Hanson
- Department of Pathology and Laboratory Medicine, University of British Columbia, The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Maged Gomaa Hemida
- Department of Pathology and Laboratory Medicine, University of British Columbia, The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Wei Wei
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Fanny Chu
- Department of Pathology and Laboratory Medicine, University of British Columbia, The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Decheng Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
- * E-mail:
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24
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Xiang P, Wei W, Lo C, Rosten P, Hou J, Hoodless PA, Bilenky M, Bonifer C, Cockerill PN, Kirkpatrick A, Gottgens B, Hirst M, Humphries KR. Delineating MEIS1 cis-regulatory elements active in hematopoietic cells. Leukemia 2013; 28:433-6. [PMID: 24097337 DOI: 10.1038/leu.2013.287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- P Xiang
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - W Wei
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - C Lo
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - P Rosten
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - J Hou
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - P A Hoodless
- 1] Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada [2] University of British Columbia, Medical Genetics, Vancouver, British Columbia, Canada
| | - M Bilenky
- BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - C Bonifer
- School of Cancer Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - P N Cockerill
- School of Immunity and Infection, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - A Kirkpatrick
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - B Gottgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - M Hirst
- BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - K R Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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25
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Swanson L, Robertson G, Mungall KL, Butterfield YS, Chiu R, Corbett RD, Docking TR, Hogge D, Jackman SD, Moore RA, Mungall AJ, Nip KM, Parker JDK, Qian JQ, Raymond A, Sung S, Tam A, Thiessen N, Varhol R, Wang S, Yorukoglu D, Zhao Y, Hoodless PA, Sahinalp SC, Karsan A, Birol I. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. BMC Genomics 2013; 14:550. [PMID: 23941359 PMCID: PMC3751903 DOI: 10.1186/1471-2164-14-550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 08/06/2013] [Indexed: 11/24/2022] Open
Abstract
Background Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers. Results We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets. Conclusions Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases.
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Affiliation(s)
- Lucas Swanson
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
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26
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Wei W, Hou J, Alder O, Ye X, Lee S, Cullum R, Chu A, Zhao Y, Warner SM, Knight DA, Yang D, Jones SJM, Marra MA, Hoodless PA. Genome-wide microRNA and messenger RNA profiling in rodent liver development implicates mir302b and mir20a in repressing transforming growth factor-beta signaling. Hepatology 2013; 57:2491-501. [PMID: 23315977 DOI: 10.1002/hep.26252] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 12/19/2012] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are recently discovered small RNA molecules that regulate developmental processes, such as proliferation, differentiation, and apoptosis; however, the identity of miRNAs and their functions during liver development are largely unknown. Here we investigated the miRNA and gene expression profiles for embryonic day (E)8.5 endoderm, E14.5 Dlk1(+) liver cells (hepatoblasts), and adult liver by employing Illumina sequencing. We found that miRNAs were abundantly expressed at all three stages. Using K-means clustering analysis, 13 miRNA clusters with distinct temporal expression patterns were identified. mir302b, an endoderm-enriched miRNA, was identified as an miRNA whose predicted targets are expressed highly in E14.5 hepatoblasts but low in the endoderm. We validated the expression of mir302b in the endoderm by whole-mount in situ hybridization. Interestingly, mir20a, the most highly expressed miRNA in the endoderm library, was also predicted to regulate some of the same targets as mir302b. We found that through targeting Tgfbr2, mir302b and mir20a are able to regulate transforming growth factor beta (TGFβ) signal transduction. Moreover, mir302b can repress liver markers in an embryonic stem cell differentiation model. Collectively, we uncovered dynamic patterns of individual miRNAs during liver development, as well as miRNA networks that could be essential for the specification and differentiation of liver progenitors. (HEPATOLOGY 2013).
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Affiliation(s)
- Wei Wei
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, B.C., Canada
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27
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Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XYC, Dickman CTD, Fulton DL, Lim JS, Schnabl JM, Ramos OHP, Vasseur-Cognet M, de Leeuw CN, Simpson EM, Ryffel GU, Lam EWF, Kist R, Wilson MSC, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HDC, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli MM, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperrière D, Leprince D, de Cristofaro T, Prince KL, Putker M, del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SWZ, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW. The transcription factor encyclopedia. Genome Biol 2012; 13:R24. [PMID: 22458515 PMCID: PMC3439975 DOI: 10.1186/gb-2012-13-3-r24] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/19/2012] [Accepted: 03/29/2012] [Indexed: 12/20/2022] Open
Abstract
Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.
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Affiliation(s)
- Dimas Yusuf
- Department of Medical Genetics, Faculty of Medicine, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
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Hneino M, François A, Buard V, Tarlet G, Abderrahmani R, Blirando K, Hoodless PA, Benderitter M, Milliat F. The TGF-β/Smad repressor TG-interacting factor 1 (TGIF1) plays a role in radiation-induced intestinal injury independently of a Smad signaling pathway. PLoS One 2012; 7:e35672. [PMID: 22567107 PMCID: PMC3342305 DOI: 10.1371/journal.pone.0035672] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 03/22/2012] [Indexed: 01/17/2023] Open
Abstract
Despite advances in radiation delivery protocols, exposure of normal tissues during the course of radiation therapy remains a limiting factor of cancer treatment. If the canonical TGF-β/Smad pathway has been extensively studied and implicated in the development of radiation damage in various organs, the precise modalities of its activation following radiation exposure remain elusive. In the present study, we hypothesized that TGF-β1 signaling and target genes expression may depend on radiation-induced modifications in Smad transcriptional co-repressors/inhibitors expressions (TGIF1, SnoN, Ski and Smad7). In endothelial cells (HUVECs) and in a model of experimental radiation enteropathy in mice, radiation exposure increases expression of TGF-β/Smad pathway and of its target gene PAI-1, together with the overexpression of Smad co-repressor TGIF1. In mice, TGIF1 deficiency is not associated with changes in the expression of radiation-induced TGF-β pathway-related transcripts following localized small intestinal irradiation. In HUVECs, TGIF1 overexpression or silencing has no influence either on the radiation-induced Smad activation or the Smad3-dependent PAI-1 overexpression. However, TGIF1 genetic deficiency sensitizes mice to radiation-induced intestinal damage after total body or localized small intestinal radiation exposure, demonstrating that TGIF1 plays a role in radiation-induced intestinal injury. In conclusion, the TGF-β/Smad co-repressor TGIF1 plays a role in radiation-induced normal tissue damage by a Smad-independent mechanism.
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Affiliation(s)
- Mohammad Hneino
- Laboratory of Radiopathology and Experimental Therapies, Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
| | - Agnes François
- Laboratory of Radiopathology and Experimental Therapies, Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
| | - Valerie Buard
- Laboratory of Radiopathology and Experimental Therapies, Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
| | - Georges Tarlet
- Laboratory of Radiopathology and Experimental Therapies, Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
| | - Rym Abderrahmani
- Laboratory of Radiopathology and Experimental Therapies, Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
| | - Karl Blirando
- Laboratory of Radiopathology and Experimental Therapies, Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
| | - Pamela A. Hoodless
- Terry Fox Laboratory, British Columbia Cancer Agency and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc Benderitter
- Laboratory of Radiopathology and Experimental Therapies, Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
| | - Fabien Milliat
- Laboratory of Radiopathology and Experimental Therapies, Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
- * E-mail:
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29
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Chang ACY, Fu Y, Garside VC, Niessen K, Chang L, Fuller M, Setiadi A, Smrz J, Kyle A, Minchinton A, Marra M, Hoodless PA, Karsan A. Notch initiates the endothelial-to-mesenchymal transition in the atrioventricular canal through autocrine activation of soluble guanylyl cyclase. Dev Cell 2011; 21:288-300. [PMID: 21839921 DOI: 10.1016/j.devcel.2011.06.022] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 04/20/2011] [Accepted: 06/17/2011] [Indexed: 01/08/2023]
Abstract
The heart is the most common site of congenital defects, and valvuloseptal defects are the most common of the cardiac anomalies seen in the newborn. The process of endothelial-to-mesenchymal transition (EndMT) in the cardiac cushions is a required step during early valve development, and Notch signaling is required for this process. Here we show that Notch activation induces the transcription of both subunits of the soluble guanylyl cyclase (sGC) heterodimer, GUCY1A3 and GUCY1B3, which form the nitric oxide receptor. In parallel, Notch also promotes nitric oxide (NO) production by inducing Activin A, thereby activating a PI3-kinase/Akt pathway to phosphorylate eNOS. We thus show that the activation of sGC by NO through a Notch-dependent autocrine loop is necessary to drive early EndMT in the developing atrioventricular canal (AVC).
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Affiliation(s)
- Alex C Y Chang
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver BC V5Z 1L3, Canada
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30
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Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nat Methods 2010; 7:909-12. [PMID: 20935650 DOI: 10.1038/nmeth.1517] [Citation(s) in RCA: 595] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 09/13/2010] [Indexed: 12/20/2022]
Abstract
We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.
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Affiliation(s)
- Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
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31
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Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao Y, Hirst M, Verchere CB, Helgason CD, Marra MA, Jones SJM, Hoodless PA. Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res 2010; 20:1037-51. [PMID: 20551221 DOI: 10.1101/gr.104356.109] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The liver and pancreas share a common origin and coexpress several transcription factors. To gain insight into the transcriptional networks regulating the function of these tissues, we globally identify binding sites for FOXA2 in adult mouse islets and liver, PDX1 in islets, and HNF4A in liver. Because most eukaryotic transcription factors bind thousands of loci, many of which are thought to be inactive, methods that can discriminate functionally active binding events are essential for the interpretation of genome-wide transcription factor binding data. To develop such a method, we also generated genome-wide H3K4me1 and H3K4me3 localization data in these tissues. By analyzing our binding and histone methylation data in combination with comprehensive gene expression data, we show that H3K4me1 enrichment profiles discriminate transcription factor occupied loci into three classes: those that are functionally active, those that are poised for activation, and those that reflect pioneer-like transcription factor activity. Furthermore, we demonstrate that the regulated presence of H3K4me1-marked nucleosomes at transcription factor occupied promoters and enhancers controls their activity, implicating both tissue-specific transcription factor binding and nucleosome remodeling complex recruitment in determining tissue-specific gene expression. Finally, we apply these approaches to generate novel insights into how FOXA2, PDX1, and HNF4A cooperate to drive islet- and liver-specific gene expression.
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Affiliation(s)
- Brad G Hoffman
- Department of Cancer Endocrinology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.
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32
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Hassan AS, Hou J, Wei W, Hoodless PA. Expression of two novel transcripts in the mouse definitive endoderm. Gene Expr Patterns 2010; 10:127-34. [PMID: 20153842 DOI: 10.1016/j.gep.2010.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 02/03/2010] [Accepted: 02/05/2010] [Indexed: 12/19/2022]
Abstract
Here we describe the expression of two novel transcripts, Ende (AK014119) and Npe (AK084355), during early mouse embryogenesis. Ende mRNA was first detected at embryonic day (E) 7.0 in a small population of epiblast cells in the distal half of the embryo. At E7.5, Ende was expressed by newly formed definitive endoderm cells in the proximal half of the embryo, and was not expressed in extra-embryonic endoderm. This expression pattern then changed to the ventral aspect of the developing foregut pocket and the entire hindgut pocket at E8.0-8.5, before becoming restricted to the foregut overlying the heart and the posterior-most hindgut. By E9.25 Ende expression was also observed in the posterior half of the ventral neural tube. Thus, Ende was expressed dynamically and in specific populations of the definitive endoderm from E7.0 to E8.5. We found Npe expression to be restricted to the node/posterior notochord region at the distal tip of the embryo between E7.0 and E8.0. By E9.5, Npe expression was observed in the posterior-most population of dorsal hindgut cells and notochord cells. Given their expression in mouse definitive endoderm populations, Ende and Npe will be valuable tools to study formation and development of this tissue.
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Affiliation(s)
- Ali S Hassan
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
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McKnight KD, Hou J, Hoodless PA. Foxh1 and Foxa2 are not required for formation of the midgut and hindgut definitive endoderm. Dev Biol 2010; 337:471-81. [DOI: 10.1016/j.ydbio.2009.10.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 10/29/2009] [Accepted: 10/29/2009] [Indexed: 11/16/2022]
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Vrljicak P, Chang ACY, Morozova O, Wederell ED, Niessen K, Marra MA, Karsan A, Hoodless PA. Genomic analysis distinguishes phases of early development of the mouse atrio-ventricular canal. Physiol Genomics 2009; 40:150-7. [PMID: 19952280 DOI: 10.1152/physiolgenomics.00142.2009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Valve formation during embryonic heart development involves a complex interplay of regional specification, cell transformations, and remodeling events. While many studies have addressed the role of specific genes during this process, a global understanding of the genetic basis for the regional specification and development of the heart valves is incomplete. We have undertaken genome-wide transcriptional profiling of the developing heart valves in the mouse. Four Serial Analysis of Gene Expression libraries were generated and analyzed from the mouse atrio-ventricular canal (AVC) at embryonic days 9.5-12.5, covering the stages from initiation of endothelial to mesenchymal transition (EMT) through to the beginning of endocardial cushion remodeling. We identified 14 distinct temporal patterns of gene expression during AVC development. These were associated with specific functions and signaling pathway members. We defined the temporal distribution of mesenchyme genes during the EMT process and of specific Notch and transforming growth factor-beta targets. This work provides the first comprehensive temporal dataset during the formation of heart valves. These results identify molecular signatures that distinguish different phases of early heart valve formation allowing gene expression and function to be further investigated.
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Affiliation(s)
- Pavle Vrljicak
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 1L3
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35
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Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJM. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res 2008; 18:1906-17. [PMID: 18787082 DOI: 10.1101/gr.078519.108] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different transcription factors: STAT1 in the immortalized HeLa S3 cell line, with and without interferon-gamma (IFNG) stimulation; and FOXA2 in mouse adult liver tissue. In unstimulated and stimulated HeLa cells, respectively, we determined approximately 270,000 and approximately 301,000 H3K4me1-enriched regions, and approximately 54,500 and approximately 76,100 H3K4me3-enriched regions. In mouse adult liver, we determined approximately 227,000 and approximately 34,800 H3K4me1 and H3K4me3 regions. Seventy-five percent of the approximately 70,300 STAT1 binding sites in stimulated HeLa cells and 87% of the approximately 11,000 FOXA2 sites in mouse liver were distal to known gene TSS; in both cell types, approximately 83% of these distal sites were associated with at least one of the two histone modifications, and H3K4me1 was associated with over 96% of marked distal sites. After filtering against predicted transcription start sites, 50% of approximately 26,800 marked distal IFNG-stimulated STAT1 binding sites, but 95% of approximately 5800 marked distal FOXA2 sites, were associated with H3K4me1 only. Results for HeLa cells generated additional insights into transcriptional regulation involving STAT1. STAT1 binding was associated with 25% of all H3K4me1 regions in stimulated HeLa cells, suggesting that a single transcription factor can interact with an unexpectedly large fraction of regulatory regions. Strikingly, for a large majority of the locations of stimulated STAT1 binding, the dominant H3K4me1/me3 combinations were established before activation, suggesting mechanisms independent of IFNG stimulation and high-affinity STAT1 binding.
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36
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Niessen K, Fu Y, Chang L, Hoodless PA, McFadden D, Karsan A. Slug is a direct Notch target required for initiation of cardiac cushion cellularization. ACTA ACUST UNITED AC 2008; 182:315-25. [PMID: 18663143 PMCID: PMC2483533 DOI: 10.1083/jcb.200710067] [Citation(s) in RCA: 255] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Snail family proteins are key regulators of epithelial-mesenchymal transition, but their role in endothelial-to-mesenchymal transition (EMT) is less well studied. We show that Slug, a Snail family member, is expressed by a subset of endothelial cells as well as mesenchymal cells of the atrioventricular canal and outflow tract during cardiac cushion morphogenesis. Slug deficiency results in impaired cellularization of the cardiac cushion at embryonic day (E)–9.5 but is compensated by increased Snail expression at E10.5, which restores cardiac cushion EMT. We further demonstrate that Slug, but not Snail, is directly up-regulated by Notch in endothelial cells and that Slug expression is required for Notch-mediated repression of the vascular endothelial cadherin promoter and for promoting migration of transformed endothelial cells. In contrast, transforming growth factor β (TGF-β) induces Snail but not Slug. Interestingly, activation of Notch in the context of TGF-β stimulation results in synergistic up-regulation of Snail in endothelial cells. Collectively, our data suggest that combined expression of Slug and Snail is required for EMT in cardiac cushion morphogenesis.
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Affiliation(s)
- Kyle Niessen
- Department of Medical Biophysics, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada
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37
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Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res 2008; 36:4549-64. [PMID: 18611952 PMCID: PMC2504304 DOI: 10.1093/nar/gkn382] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Foxa2 (HNF3β) is a one of three, closely related transcription factors that are critical to the development and function of the mouse liver. We have used chromatin immunoprecipitation and massively parallel Illumina 1G sequencing (ChIP–Seq) to create a genome-wide profile of in vivo Foxa2-binding sites in the adult liver. More than 65% of the ∼11.5 k genomic sites associated with Foxa2 binding, mapped to extended gene regions of annotated genes, while more than 30% of intragenic sites were located within first introns. 20.5% of all sites were further than 50 kb from any annotated gene, suggesting an association with novel gene regions. QPCR analysis demonstrated a strong positive correlation between peak height and fold enrichment for Foxa2-binding sites. We measured the relationship between Foxa2 and liver gene expression by overlapping Foxa2-binding sites with a SAGE transcriptome profile, and found that 43.5% of genes expressed in the liver were also associated with Foxa2 binding. We also identified potential Foxa2-interacting transcription factors whose motifs were enriched near Foxa2-binding sites. Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function.
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38
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Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones SJM, Marra MA, Helgason CD. Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol 2008; 9:R99. [PMID: 18554416 PMCID: PMC2481431 DOI: 10.1186/gb-2008-9-6-r99] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 05/13/2008] [Accepted: 06/14/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite recent advances, the transcriptional hierarchy driving pancreas organogenesis remains largely unknown, in part due to the paucity of comprehensive analyses. To address this deficit we generated ten SAGE libraries from the developing murine pancreas spanning Theiler stages 17-26, making use of available Pdx1 enhanced green fluorescent protein (EGFP) and Neurog3 EGFP reporter strains, as well as tissue from adult islets and ducts. RESULTS We used a specificity metric to identify 2,536 tags with pancreas-enriched expression compared to 195 other mouse SAGE libraries. We subsequently grouped co-expressed transcripts with differential expression during pancreas development using K-means clustering. We validated the clusters first using quantitative real time PCR and then by analyzing the Theiler stage 22 pancreas in situ hybridization staining patterns of over 600 of the identified genes using the GenePaint database. These were then categorized into one of the five expression domains within the developing pancreas. Based on these results we identified a cascade of transcriptional regulators expressed in the endocrine pancreas lineage and, from this, we developed a predictive regulatory network describing beta-cell development. CONCLUSION Taken together, this work provides evidence that the SAGE libraries generated here are a valuable resource for continuing to elucidate the molecular mechanisms regulating pancreas development. Furthermore, our studies provide a comprehensive analysis of pancreas development, and insights into the regulatory networks driving this process are revealed.
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Affiliation(s)
- Brad G Hoffman
- Department of Cancer Endocrinology, BC Cancer Research Center, West 10th Ave, Vancouver, BC V5Z 1L3, Canada.
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Abstract
Thyrotropin-releasing hormone (TRH) is a well-characterized regulator of the hypothalamic-pituitary-thyroid endocrine axis. Here, we describe the expression of Trh during early embryonic development in the mouse. We find Trh to be highly expressed during postimplantation stages in the mouse embryo, with expression first observed in the epiblast at embryonic day (E) 6.5. During gastrulation, Trh is expressed in the newly formed definitive endoderm cells, and at embryonic day (E) 7.75, marks the entire definitive endoderm. Subsequently, Trh mRNA levels rapidly decrease such that, by E9.0, expression in the definitive endoderm is no longer detected, after which neural expression predominates. Thus, Trh is expressed dynamically and specifically in the developing mouse definitive endoderm from E7.0 to E8.5. Trh is unique among definitive endoderm markers as it transiently marks the entire definitive endoderm population and is not expressed in the extraembryonic endoderm. Trh will be a valuable tool to study definitive endoderm formation in the mouse embryo.
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Affiliation(s)
- Kristen D McKnight
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
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40
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Hoffman B, Kok D, Witzsche J, Hirst M, Robertson G, Hoodless PA, Jones, Marra M. Genome-wide analysis of Nkx2.2 binding sites using ChIP-tag sequencing (ChIP-TS). Dev Biol 2007. [DOI: 10.1016/j.ydbio.2007.03.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Bowie MB, Kent DG, Dykstra B, McKnight KD, McCaffrey L, Hoodless PA, Eaves CJ. Identification of a new intrinsically timed developmental checkpoint that reprograms key hematopoietic stem cell properties. Proc Natl Acad Sci U S A 2007; 104:5878-82. [PMID: 17379664 PMCID: PMC1829493 DOI: 10.1073/pnas.0700460104] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Indexed: 01/07/2023] Open
Abstract
Hematopoietic stem cells (HSCs) execute self-renewal divisions throughout fetal and adult life, although some of their properties do alter. Here we analyzed the magnitude and timing of changes in the self-renewal properties and differentiated cell outputs of transplanted HSCs obtained from different sources during development. We also assessed the expression of several "stem cell" genes in corresponding populations of highly purified HSCs. Fetal and adult HSCs displayed marked differences in their self-renewal, differentiated cell output, and gene expression properties, with persistence of a fetal phenotype until 3 weeks after birth. Then, 1 week later, the HSCs became functionally indistinguishable from adult HSCs. The same schedule of changes in HSC properties occurred when HSCs from fetal or 3-week-old donors were transplanted into adult recipients. These findings point to the existence of a previously unrecognized, intrinsically regulated master switch that effects a developmental change in key HSC properties.
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Affiliation(s)
- Michelle B. Bowie
- *Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3; and
| | - David G. Kent
- *Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3; and
| | - Brad Dykstra
- *Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3; and
| | - Kristen D. McKnight
- *Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3; and
| | - Lindsay McCaffrey
- *Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3; and
| | - Pamela A. Hoodless
- *Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3; and
| | - Connie J. Eaves
- *Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3; and
- University of British Columbia, Vancouver, BC, Canada V5Z 1L3
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42
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McKnight KD, Hoodless PA. WITHDRAWN: Thyrotropin-releasing hormone precursor—A novel marker of the mouse definitive endoderm. Dev Biol 2007. [DOI: 10.1016/j.ydbio.2007.03.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bowie MB, McKnight KD, Kent DG, McCaffrey L, Hoodless PA, Eaves CJ. Hematopoietic stem cells proliferate until after birth and show a reversible phase-specific engraftment defect. J Clin Invest 2007; 116:2808-16. [PMID: 17016561 PMCID: PMC1578623 DOI: 10.1172/jci28310] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 07/11/2006] [Indexed: 01/18/2023] Open
Abstract
The regulation of HSC proliferation and engraftment of the BM is an important but poorly understood process, particularly during ontogeny. Here we show that in mice, all HSCs are cycling until 3 weeks after birth. Then, within 1 week, most became quiescent. Prior to 4 weeks of age, the proliferating HSCs with long-term multilineage repopulating activity displayed an engraftment defect when transiting S/G2/M. During these cell cycle phases, their expression of CXC chemokine ligand 12 (CXCL12; also referred to as stromal cell-derived factor 1 [SDF-1]) transiently increased. The defective engrafting activity of HSCs in S/G2/M was reversed when cells were allowed to progress into G1 prior to injection or when the hosts (but not the cells) were pretreated with a CXCL12 antagonist. Interestingly, the enhancing effect of CXCL12 antagonist pretreatment was exclusive to transplants of long-term multilineage repopulating HSCs in S/G2/M. These results demonstrate what we believe to be a new HSC regulatory checkpoint during development. They also suggest an ability of HSCs to express CXCL12 in a fashion that changes with cell cycle progression and is associated with a defective engraftment that can be overcome by in vivo administration of a CXCL12 antagonist.
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Affiliation(s)
- Michelle B. Bowie
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kristen D. McKnight
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David G. Kent
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsay McCaffrey
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Connie J. Eaves
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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44
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Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Eaves C, Jones S, Holt R, Hirst M, Hoodless PA, Marra MA. Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res 2006; 17:108-16. [PMID: 17135571 PMCID: PMC1716260 DOI: 10.1101/gr.5488207] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We describe the details of a serial analysis of gene expression (SAGE) library construction and analysis platform that has enabled the generation of >298 high-quality SAGE libraries and >30 million SAGE tags primarily from sub-microgram amounts of total RNA purified from samples acquired by microdissection. Several RNA isolation methods were used to handle the diversity of samples processed, and various measures were applied to minimize ditag PCR carryover contamination. Modifications in the SAGE protocol resulted in improved cloning and DNA sequencing efficiencies. Bioinformatic measures to automatically assess DNA sequencing results were implemented to analyze the integrity of ditag structure, linker or cross-species ditag contamination, and yield of high-quality tags per sequence read. Our analysis of singleton tag errors resulted in a method for correcting such errors to statistically determine tag accuracy. From the libraries generated, we produced an essentially complete mapping of reliable 21-base-pair tags to the mouse reference genome sequence for a meta-library of approximately 5 million tags. Our analyses led us to reject the commonly held notion that duplicate ditags are artifacts. Rather than the usual practice of discarding such tags, we conclude that they should be retained to avoid introducing bias into the results and thereby maintain the quantitative nature of the data, which is a major theoretical advantage of SAGE as a tool for global transcriptional profiling.
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Affiliation(s)
- Jaswinder Khattra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Allen D. Delaney
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Asim Siddiqui
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Jennifer Asano
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Helen McDonald
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Noreen Dhalla
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Anna-liisa Prabhu
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Kevin Ma
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Stephanie Lee
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Adrian Ally
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Angela Tam
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Danne Sa
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Sean Rogers
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - David Charest
- Genome British Columbia, Vancouver, British Columbia V5Z 1C6, Canada
| | - Jeff Stott
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Scott Zuyderduyn
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Richard Varhol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Connie Eaves
- Terry Fox Laboratory, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Steven Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Robert Holt
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Martin Hirst
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
- Corresponding author.E-mail ; fax (604) 877-6085
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45
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Houde C, Dickinson RJ, Houtzager VM, Cullum R, Montpetit R, Metzler M, Simpson EM, Roy S, Hayden MR, Hoodless PA, Nicholson DW. Hippi is essential for node cilia assembly and Sonic hedgehog signaling. Dev Biol 2006; 300:523-33. [PMID: 17027958 PMCID: PMC5053816 DOI: 10.1016/j.ydbio.2006.09.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 08/30/2006] [Accepted: 09/05/2006] [Indexed: 11/28/2022]
Abstract
Hippi functions as an adapter protein that mediates pro-apoptotic signaling from poly-glutamine-expanded huntingtin, an established cause of Huntington disease, to the extrinsic cell death pathway. To explore other functions of Hippi we generated Hippi knock-out mice. This deletion causes randomization of the embryo turning process and heart looping, which are hallmarks of defective left-right (LR) axis patterning. We report that motile monocilia normally present at the surface of the embryonic node, and proposed to initiate the break in LR symmetry, are absent on Hippi-/- embryos. Furthermore, defects in central nervous system development are observed. The Sonic hedgehog (Shh) pathway is downregulated in the neural tube in the absence of Hippi, which results in failure to establish ventral neural cell fate. Together, these findings demonstrate a dual role for Hippi in cilia assembly and Shh signaling during development, in addition to its proposed role in apoptosis signal transduction in the adult brain under pathogenically stressful conditions.
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Affiliation(s)
- Caroline Houde
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
| | - Robin J. Dickinson
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | | | - Rebecca Cullum
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Rachel Montpetit
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Martina Metzler
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Sophie Roy
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
- Merck Research Laboratories, Rahway, New Jersey 07065, USA
| | - Michael R. Hayden
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Pamela A. Hoodless
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Donald W. Nicholson
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
- Merck Research Laboratories, Rahway, New Jersey 07065, USA
- Corresponding author. D.N. Merck Research Laboratories, Merck and Co. Inc., RY80Y-370, 126 East Lincoln Avenue, P.O. Box 2000, Rahway, NJ 07065-0900, USA. Fax: +1 732 594 3910. (D.W. Nicholson)
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46
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Abstract
Holoprosencephaly (HPE) is the most common structural anomaly of the human brain, resulting from incomplete cleavage of the developing forebrain during embryogenesis. Haploinsufficient mutations in the TG-interacting factor (TGIF) gene were previously identified in a subset of HPE families and sporadic patients, and this gene is located within a region of chromosome 18 that is associated with nonrandom chromosomal aberrations in HPE patients. TGIF is a three-amino-acid loop extension (TALE) homeodomain-containing transcription factor that functions both as a corepressor of the transforming growth factor beta (TGF-beta) pathway and as a competitor of the retinoic acid pathway. Here we describe mice deficient in Tgif that exhibited laterality defects and growth retardation and developed kinked tails. Cellular analysis of mutant mouse embryonic fibroblasts (MEFs) demonstrated for the first time that Tgif regulates proliferation and progression through the G1 cell cycle phase. Additionally, wild-type human TGIF was able to rescue this proliferative defect in MEFs. In contrast, a subset of human Tgif mutations detected in HPE patients was unable to rescue the proliferative defect. However, an absence of Tgif did not alter the normal inhibition of proliferation caused by treatment with TGF-beta or retinoic acid. Developmental control of proliferation by Tgif may play a role in the pathogenesis of HPE.
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Affiliation(s)
- Lynn Mar
- Terry Fox Laboratory, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada, V5Z 1L3
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47
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Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BYL, Lee LLC, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJM, Helgason CD, Simpson EM, Hoodless PA, Marra MA. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A 2005; 102:18485-90. [PMID: 16352711 PMCID: PMC1311911 DOI: 10.1073/pnas.0509455102] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of approximately 24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci.
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Affiliation(s)
- Asim S Siddiqui
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4S6
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48
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Noseda M, McLean G, Niessen K, Chang L, Pollet I, Montpetit R, Shahidi R, Dorovini-Zis K, Li L, Beckstead B, Durand RE, Hoodless PA, Karsan A. Notch activation results in phenotypic and functional changes consistent with endothelial-to-mesenchymal transformation. Circ Res 2004; 94:910-7. [PMID: 14988227 DOI: 10.1161/01.res.0000124300.76171.c9] [Citation(s) in RCA: 225] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Various studies have identified a critical role for Notch signaling in cardiovascular development. In this and other systems, Notch receptors and ligands are expressed in regions that undergo epithelial-to-mesenchymal transformation. However, there is no direct evidence that Notch activation can induce mesenchymal transdifferentiation. In this study we show that Notch activation in endothelial cells results in morphological, phenotypic, and functional changes consistent with mesenchymal transformation. These changes include downregulation of endothelial markers (vascular endothelial [VE]-cadherin, Tie1, Tie2, platelet-endothelial cell adhesion molecule-1, and endothelial NO synthase), upregulation of mesenchymal markers (alpha-smooth muscle actin, fibronectin, and platelet-derived growth factor receptors), and migration toward platelet-derived growth factor-BB. Notch-induced endothelial-to-mesenchymal transformation does not seem to require external regulation and is restricted to cells expressing activated Notch. Jagged1 stimulation of endothelial cells induces a similar mesenchymal transformation, and Jagged1, Notch1, and Notch4 are expressed in the ventricular outflow tract during stages of endocardial cushion formation. This is the first evidence that Jagged1-Notch interactions induce endothelial-to-mesenchymal transformation, and our findings suggest that Notch signaling may be required for proper endocardial cushion differentiation and/or vascular smooth muscle cell development.
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MESH Headings
- Actins/biosynthesis
- Actins/genetics
- Animals
- Antigens, CD
- Becaplermin
- Cadherins/metabolism
- Calcium-Binding Proteins
- Cell Differentiation
- Cell Line
- Endocardium/cytology
- Endothelium, Vascular/cytology
- Endothelium, Vascular/metabolism
- Fetal Heart/metabolism
- Fetal Heart/ultrastructure
- Gene Expression Regulation, Developmental
- Heart Septum/embryology
- Humans
- Intercellular Signaling Peptides and Proteins
- Jagged-1 Protein
- Membrane Proteins
- Mesoderm/cytology
- Mice
- Muscle, Smooth, Vascular/cytology
- Phenotype
- Platelet Endothelial Cell Adhesion Molecule-1/metabolism
- Platelet-Derived Growth Factor/pharmacology
- Protein Biosynthesis
- Proteins/genetics
- Proteins/physiology
- Proto-Oncogene Proteins/biosynthesis
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/physiology
- Proto-Oncogene Proteins c-sis
- Receptor, Notch1
- Receptor, Notch4
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/physiology
- Receptors, Notch
- Recombinant Fusion Proteins/physiology
- Serrate-Jagged Proteins
- Sheep
- Signal Transduction/physiology
- Transcription Factors
- Transduction, Genetic
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Affiliation(s)
- Michela Noseda
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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49
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Hoodless PA, Pye M, Chazaud C, Labbé E, Attisano L, Rossant J, Wrana JL. FoxH1 (Fast) functions to specify the anterior primitive streak in the mouse. Genes Dev 2001; 15:1257-71. [PMID: 11358869 PMCID: PMC313796 DOI: 10.1101/gad.881501] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The node and the anterior visceral endoderm (AVE) are important organizing centers that pattern the mouse embryo by establishing the anterior-posterior (A-P), dorsal-ventral (D-V), and left-right (L-R) axes. Activin/nodal signaling through the Smad2 pathway has been implicated in AVE formation and in morphogenesis of the primitive streak, the anterior end of which gives rise to the node. The forkhead DNA-binding protein, FoxH1 (or Fast), functions as a Smad DNA-binding partner to regulate transcription in response to activin signaling. Here, we show that deletion of FoxH1 in mice results in failure to pattern the anterior primitive streak (APS) and form node, prechordal mesoderm, notochord, and definitive endoderm. In contrast, formation of the AVE can occur in the absence of FoxH1. The FoxH1 mutant phenotype is remarkably similar to that of mice deficient in the forkhead protein Foxa2 (HNF3beta), and we show that Foxa2 expression is dependent on FoxH1 function. These results show that FoxH1 functions in an activin/nodal-Smad signaling pathway that acts upstream of Foxa2 and is required specifically for patterning the APS and node in the mouse.
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Affiliation(s)
- P A Hoodless
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
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50
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Abstract
TGFbeta growth factors specify cell fate and establish the body plan during early vertebrate development. Diverse cellular responses are elicited via interactions with specific cell surface receptor kinases that in turn activate Smad effector proteins. Smad2-dependent signals arising in the extraembryonic tissues of early mouse embryos serve to restrict the site of primitive streak formation and establish anteroposterior identity in the epiblast. Here we have generated chimeric embryos using lacZ-marked Smad2-deficient ES cells. Smad2 mutant cells extensively colonize ectodermal and mesodermal populations without disturbing normal development, but are not recruited into the definitive endoderm lineage during gastrulation. These experiments provide the first evidence that TGFbeta signaling pathways are required for specification of the definitive endoderm lineage in mammals and identify Smad2 as a key mediator that directs epiblast derivatives towards an endodermal as opposed to a mesodermal fate. In largely Smad2-deficient chimeras, asymmetric nodal gene expression is maintained and expression of pitx2, a nodal target, is also unaffected. These results strongly suggest that other Smad(s) act downstream of Nodal signals in mesodermal populations. We found Smad2 and Smad3 transcripts both broadly expressed in derivatives of the epiblast. However, Smad2 and not Smad3 mRNA is expressed in the visceral endoderm, potentially explaining why the primary defect in Smad2 mutant embryos originates in this cell population.
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Affiliation(s)
- K D Tremblay
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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