1
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Li X, Wang C, Wang Y, Chen X, Li Z, Wang J, Liu Y. Integrated analysis of the role of PR/SET domain 14 in gastric cancer. BMC Cancer 2024; 24:685. [PMID: 38840106 PMCID: PMC11151633 DOI: 10.1186/s12885-024-12424-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Gastric cancer is one of the most common tumors worldwide, and most patients are deprived of treatment options when diagnosed at advanced stages. PRDM14 has carcinogenic potential in breast and non-small cell lung cancer. however, its role in gastric cancer has not been elucidated. METHODS We aimed to elucidate the expression of PRDM14 using pan-cancer analysis. We monitored the expression of PRDM14 in cells and patients using quantitative polymerase chain reaction, western blotting, and immunohistochemistry. We observed that cell phenotypes and regulatory genes were influenced by PRDM14 by silencing PRDM14. We evaluated and validated the value of the PRDM14-derived prognostic model. Finally, we predicted the relationship between PRDM14 and small-molecule drug responses using the Connectivity Map and The Genomics of Drug Sensitivity in Cancer databases. RESULTS PRDM14 was significantly overexpressed in gastric cancer, which identified in cell lines and patients' tissues. Silencing the expression of PRDM14 resulted in apoptosis promotion, cell cycle arrest, and inhibition of the growth and migration of GC cells. Functional analysis revealed that PRDM14 acts in epigenetic regulation and modulates multiple DNA methyltransferases or transcription factors. The PRDM14-derived differentially expressed gene prognostic model was validated to reliably predict the patient prognosis. Nomograms (age, sex, and PRDM14-risk score) were used to quantify the probability of survival. PRDM14 was positively correlated with sensitivity to small-molecule drugs such as TPCA-1, PF-56,227, mirin, and linsitinib. CONCLUSIONS Collectively, our findings suggest that PRDM14 is a positive regulator of gastric cancer progression. Therefore, it may be a potential therapeutic target for gastric cancer.
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Affiliation(s)
- Xiao Li
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Cong Wang
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Youcai Wang
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xiaobing Chen
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Zhi Li
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jianwei Wang
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou, China.
| | - Yingjun Liu
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.
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2
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Gupta S, Heinrichs E, Novitch BG, Butler SJ. Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses. Development 2024; 151:dev202209. [PMID: 38804879 PMCID: PMC11166460 DOI: 10.1242/dev.202209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/29/2024]
Abstract
Dorsal interneurons (dIs) in the spinal cord encode the perception of touch, pain, heat, itchiness and proprioception. Previous studies using genetic strategies in animal models have revealed important insights into dI development, but the molecular details of how dIs arise as distinct populations of neurons remain incomplete. We have developed a resource to investigate dI fate specification by combining a single-cell RNA-Seq atlas of mouse embryonic stem cell-derived dIs with pseudotime analyses. To validate this in silico resource as a useful tool, we used it to first identify genes that are candidates for directing the transition states that lead to distinct dI lineage trajectories, and then validated them using in situ hybridization analyses in the developing mouse spinal cord in vivo. We have also identified an endpoint of the dI5 lineage trajectory and found that dIs become more transcriptionally homogeneous during terminal differentiation. This study introduces a valuable tool for further discovery about the timing of gene expression during dI differentiation and demonstrates its utility in clarifying dI lineage relationships.
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Affiliation(s)
- Sandeep Gupta
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Heinrichs
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Genetics and Genomics Graduate Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bennett G. Novitch
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samantha J. Butler
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
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3
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Gupta S, Heinrichs E, Novitch BG, Butler SJ. Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.24.550380. [PMID: 37546781 PMCID: PMC10402035 DOI: 10.1101/2023.07.24.550380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Dorsal interneurons (dIs) in the spinal cord encode the perception of touch, pain, heat, itch, and proprioception. While previous studies using genetic strategies in animal models have revealed important insights into dI development, the molecular details by which dIs arise as distinct populations of neurons remain incomplete. We have developed a resource to investigate dI fate specification by combining a single-cell RNA-Seq atlas of mouse ESC-derived dIs with pseudotime analyses. To validate this in silico resource as a useful tool, we used it to first identify novel genes that are candidates for directing the transition states that lead to distinct dI lineage trajectories, and then validated them using in situ hybridization analyses in the developing mouse spinal cord in vivo . We have also identified a novel endpoint of the dI5 lineage trajectory and found that dIs become more transcriptionally homogenous during terminal differentiation. Together, this study introduces a valuable tool for further discovery about the timing of gene expression during dI differentiation and demonstrates its utility clarifying dI lineage relationships. Summary statement Pseudotime analyses of embryonic stem cell-derived dorsal spinal interneurons reveals both novel regulators and lineage relationships between different interneuron populations.
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4
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Matsui S, Granitto M, Buckley M, Ludwig K, Koigi S, Shiley J, Zacharias WJ, Mayhew CN, Lim HW, Iwafuchi M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Mol Cell 2024; 84:476-489.e10. [PMID: 38211589 PMCID: PMC10872272 DOI: 10.1016/j.molcel.2023.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Katie Ludwig
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sandra Koigi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joseph Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - William J Zacharias
- Division of Pulmonary Biology and Pulmonary and Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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5
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Zhang H, Liu Z, Wang J, Zeng T, Ai X, Wu K. An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs. Int J Mol Sci 2023; 24:14812. [PMID: 37834260 PMCID: PMC10573446 DOI: 10.3390/ijms241914812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Meishan pigs are a well-known indigenous pig breed in China characterized by a high fertility. Notably, the number of endometrial grands is significantly higher in Meishan pigs than Duroc pigs. The characteristics of the endometrial tissue are related to litter size. Therefore, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-sequencing (RNA-seq) to analyze the mechanisms underlying the differences in fecundity between the breeds. We detected the key transcription factors, including Double homeobox (Dux), Ladybird-like homeobox gene 2 (LBX2), and LIM homeobox 8 (Lhx8), with potentially pivotal roles in the regulation of the genes related to endometrial development. We identified the differentially expressed genes between the breeds, including SOX17, ANXA4, DLX3, DMRT1, FLNB, IRF6, CBFA2T2, TFCP2L1, EFNA5, SLIT2, and CYFIP2, with roles in epithelial cell differentiation, fertility, and ovulation. Interestingly, ANXA4, CBFA2T2, and TFCP2L1, which were upregulated in the Meishan pigs in the RNA-seq analysis, were identified again by the integration of the ATAC-seq and RNA-seq data. Moreover, we identified genes in the cancer or immune pathways, FoxO signaling, Wnt signaling, and phospholipase D signaling pathways. These ATAC-seq and RNA-seq analyses revealed the accessible chromatin and potential mechanisms underlying the differences in the endometrial tissues between the two types of pigs.
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Affiliation(s)
| | | | | | | | | | - Keliang Wu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.Z.); (Z.L.); (J.W.); (T.Z.); (X.A.)
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6
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Cortical interneuron specification and diversification in the era of big data. Curr Opin Neurobiol 2023; 80:102703. [PMID: 36933450 DOI: 10.1016/j.conb.2023.102703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Inhibition in the mammalian cerebral cortex is mediated by a small population of highly diverse GABAergic interneurons. These largely local neurons are interspersed among excitatory projection neurons and exert pivotal regulation on the formation and function of cortical circuits. We are beginning to understand the extent of GABAergic neuron diversity and how this is generated and shaped during brain development in mice and humans. In this review, we summarise recent findings and discuss how new technologies are being used to further advance our knowledge. Understanding how inhibitory neurons are generated in the embryo is an essential pre-requisite of stem cell therapy, an evolving area of research, aimed at correcting human disorders that result in inhibitory dysfunction.
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7
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Asgarian Z, Oliveira MG, Stryjewska A, Maragkos I, Rubin AN, Magno L, Pachnis V, Ghorbani M, Hiebert SW, Denaxa M, Kessaris N. MTG8 interacts with LHX6 to specify cortical interneuron subtype identity. Nat Commun 2022; 13:5217. [PMID: 36064547 PMCID: PMC9445035 DOI: 10.1038/s41467-022-32898-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/23/2022] [Indexed: 11/09/2022] Open
Abstract
Cortical interneurons originating in the embryonic medial ganglionic eminence (MGE) diverge into a range of different subtypes found in the adult mouse cerebral cortex. The mechanisms underlying this divergence and the timing when subtype identity is set up remain unclear. We identify the highly conserved transcriptional co-factor MTG8 as being pivotal in the development of a large subset of MGE cortical interneurons that co-expresses Somatostatin (SST) and Neuropeptide Y (NPY). MTG8 interacts with the pan-MGE transcription factor LHX6 and together the two factors are sufficient to promote expression of critical cortical interneuron subtype identity genes. The SST-NPY cortical interneuron fate is initiated early, well before interneurons migrate into the cortex, demonstrating an early onset specification program. Our findings suggest that transcriptional co-factors and modifiers of generic lineage specification programs may hold the key to the emergence of cortical interneuron heterogeneity from the embryonic telencephalic germinal zones. There is a large diversity of inhibitory interneurons in the mammalian cerebral cortex. How this emerges during embryogenesis remains unclear. Here, the authors identify MTG8 as a co-factor of LHX6 and a new regulator of cortical interneuron development.
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Affiliation(s)
- Zeinab Asgarian
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Marcio Guiomar Oliveira
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Agata Stryjewska
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Ioannis Maragkos
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Anna Noren Rubin
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | - Lorenza Magno
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Mohammadmersad Ghorbani
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.,Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Scott Wayne Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Myrto Denaxa
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Nicoletta Kessaris
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, UK.
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8
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Hendrikse LD, Haldipur P, Saulnier O, Millman J, Sjoboen AH, Erickson AW, Ong W, Gordon V, Coudière-Morrison L, Mercier AL, Shokouhian M, Suárez RA, Ly M, Borlase S, Scott DS, Vladoiu MC, Farooq H, Sirbu O, Nakashima T, Nambu S, Funakoshi Y, Bahcheli A, Diaz-Mejia JJ, Golser J, Bach K, Phuong-Bao T, Skowron P, Wang EY, Kumar SA, Balin P, Visvanathan A, Lee JJY, Ayoub R, Chen X, Chen X, Mungall KL, Luu B, Bérubé P, Wang YC, Pfister SM, Kim SK, Delattre O, Bourdeaut F, Doz F, Masliah-Planchon J, Grajkowska WA, Loukides J, Dirks P, Fèvre-Montange M, Jouvet A, French PJ, Kros JM, Zitterbart K, Bailey SD, Eberhart CG, Rao AAN, Giannini C, Olson JM, Garami M, Hauser P, Phillips JJ, Ra YS, de Torres C, Mora J, Li KKW, Ng HK, Poon WS, Pollack IF, López-Aguilar E, Gillespie GY, Van Meter TE, Shofuda T, Vibhakar R, Thompson RC, Cooper MK, Rubin JB, Kumabe T, Jung S, Lach B, Iolascon A, Ferrucci V, de Antonellis P, Zollo M, Cinalli G, Robinson S, Stearns DS, Van Meir EG, Porrati P, Finocchiaro G, Massimino M, Carlotti CG, Faria CC, Roussel MF, Boop F, Chan JA, Aldinger KA, Razavi F, Silvestri E, McLendon RE, Thompson EM, Ansari M, Garre ML, Chico F, Eguía P, Pérezpeña M, Morrissy AS, Cavalli FMG, Wu X, Daniels C, Rich JN, Jones SJM, Moore RA, Marra MA, Huang X, Reimand J, Sorensen PH, Wechsler-Reya RJ, Weiss WA, Pugh TJ, Garzia L, Kleinman CL, Stein LD, Jabado N, Malkin D, Ayrault O, Golden JA, Ellison DW, Doble B, Ramaswamy V, Werbowetski-Ogilvie TE, Suzuki H, Millen KJ, Taylor MD. Failure of human rhombic lip differentiation underlies medulloblastoma formation. Nature 2022; 609:1021-1028. [PMID: 36131014 PMCID: PMC10026724 DOI: 10.1038/s41586-022-05215-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/09/2022] [Indexed: 02/08/2023]
Abstract
Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain1-4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage5-8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTX and OTX2. CBFA2T2 is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2 in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES+KI67+ unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.
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Affiliation(s)
- Liam D Hendrikse
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jake Millman
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Alexandria H Sjoboen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Anders W Erickson
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Winnie Ong
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Victor Gordon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Audrey L Mercier
- PSL Research University, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Institut Curie, Orsay, France
| | - Mohammad Shokouhian
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Raúl A Suárez
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Ly
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Borlase
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David S Scott
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria C Vladoiu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Hamza Farooq
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Olga Sirbu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Takuma Nakashima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Shohei Nambu
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Yusuke Funakoshi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Alec Bahcheli
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - J Javier Diaz-Mejia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Joseph Golser
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kathleen Bach
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Tram Phuong-Bao
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Patryk Skowron
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Evan Y Wang
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sachin A Kumar
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Polina Balin
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Abhirami Visvanathan
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ramy Ayoub
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Xin Chen
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaodi Chen
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Betty Luu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pierre Bérubé
- McGill University Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Yu C Wang
- McGill University Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Seung-Ki Kim
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Olivier Delattre
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- INSERM U830, Institut Curie, Paris, France
| | - Franck Bourdeaut
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- INSERM U830, Institut Curie, Paris, France
| | - François Doz
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- Université Paris Cité, Paris, France
| | | | | | - James Loukides
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Dirks
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Fèvre-Montange
- INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences, Université de Lyon, Lyon, France
- Centre de Pathologie EST, Groupement Hospitalier EST, Université de Lyon, Bron, France
| | - Anne Jouvet
- Centre de Pathologie EST, Groupement Hospitalier EST, Université de Lyon, Bron, France
| | - Pim J French
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Karel Zitterbart
- Department of Pediatric Oncology, Masaryk University School of Medicine, Brno, Czech Republic
| | - Swneke D Bailey
- Department of Surgery, Division of Thoracic and Upper Gastrointestinal Surgery, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Charles G Eberhart
- Departments of Pathology, Ophthalmology and Oncology, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amulya A N Rao
- Division of Pediatric Hematology/Oncology, Mayo Clinic, Rochester, MN, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Miklós Garami
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Peter Hauser
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Young S Ra
- Department of Neurosurgery, University of Ulsan, Asan Medical Center, Seoul, South Korea
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Kay K W Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wai S Poon
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Enrique López-Aguilar
- Division of Pediatric Hematology/Oncology, Hospital Pediatría Centro Médico Nacional century XXI, Mexico City, Mexico
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Timothy E Van Meter
- Pediatrics, Virginia Commonwealthy University, School of Medicine, Richmond, VA, USA
| | - Tomoko Shofuda
- Division of Stem Cell Research, Institute for Clinical Research, Osaka National Hospital, Osaka, Japan
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Reid C Thompson
- Department of Neurological Surgery, Vanderbilt Medical Center, Nashville, TN, USA
| | - Michael K Cooper
- Department of Neurology, Vanderbilt Medical Center, Nashville, TN, USA
| | - Joshua B Rubin
- Departments of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Toshihiro Kumabe
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Shin Jung
- Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun-gun, South Korea
| | - Boleslaw Lach
- Department of Pathology and Molecular Medicine, Division of Anatomical Pathology, McMaster University, Hamilton, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Hamilton General Hospital, Hamilton, Ontario, Canada
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Veronica Ferrucci
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Pasqualino de Antonellis
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Massimo Zollo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Giuseppe Cinalli
- Department of Pediatric Neurosurgery, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Shenandoah Robinson
- Division of Pediatric Neurosurgery, Case Western Reserve, Cleveland, OH, USA
| | - Duncan S Stearns
- Department of Pediatrics-Hematology and Oncology, Case Western Reserve, Cleveland, OH, USA
| | - Erwin G Van Meir
- Department of Hematology and Medical Oncology, Emory University School of Medicine and Winship Cancer Institute, Atlanta, GA, USA
| | - Paola Porrati
- Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | | | - Carlos G Carlotti
- Department of Surgery and Anatomy, Faculty of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Claudia C Faria
- Division of Neurosurgery, Centro Hospitalar Lisboa Norte (CHULN), Hospital de Santa Maria, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Martine F Roussel
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Frederick Boop
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer A Chan
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ferechte Razavi
- Assistance Publique Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - Evelina Silvestri
- Surgical Pathology Unit, San Camillo Forlanini Hospital, Rome, Italy
| | - Roger E McLendon
- Department of Pathology, Duke University, Durham, NC, USA
- Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Marc Ansari
- Cansearch Research Platform for Pediatric Oncology and Hematology, Faculty of Medicine, Department of Pediatrics, Gynecology and Obstetrics, University of Geneva, Geneva, Switzerland
- Division of Pediatric Oncology and Hematology, Department of Women, Child and Adolescent, University Geneva Hospitals, Geneva, Switzerland
| | - Maria L Garre
- U.O. Neurochirurgia, Istituto Giannina Gaslini, Genova, Italy
| | - Fernando Chico
- Department of Neurosurgery, Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | - Pilar Eguía
- Department of Neurosurgery, Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | - Mario Pérezpeña
- Instituto Nacional De Pediatría de México, Mexico City, Mexico
| | - A Sorana Morrissy
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Florence M G Cavalli
- INSERM U900, Institut Curie, Paris, France
- PSL Research University, Institut Curie, Paris, France
- CBIO-Centre for Computational Biology, PSL Research University, MINES ParisTech, Paris, France
| | - Xiaochong Wu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Craig Daniels
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xi Huang
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jüri Reimand
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - William A Weiss
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Livia Garzia
- Cancer Research Program, McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Adaptive Oncology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nada Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Quebec, Canada
- The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olivier Ayrault
- PSL Research University, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Institut Curie, Orsay, France
| | - Jeffrey A Golden
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brad Doble
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tamra E Werbowetski-Ogilvie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.
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9
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Ito J, Seita Y, Kojima S, Parrish NF, Sasaki K, Sato K. A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells. PLoS Genet 2022; 18:e1009846. [PMID: 35551519 PMCID: PMC9128956 DOI: 10.1371/journal.pgen.1009846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/24/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
Mammalian germ cells stem from primordial germ cells (PGCs). Although the gene regulatory network controlling the development of germ cells such as PGCs is critical for ensuring gamete integrity, substantial differences exist in this network among mammalian species, suggesting that this network has been modified during mammalian evolution. Here, we show that a hominoid-specific group of endogenous retroviruses, LTR5_Hs, discloses enhancer-like signatures in human in vitro-induced PGCs, PGC-like cells (PGCLCs). Human PGCLCs exhibit a transcriptome signature similar to that of naïve-state pluripotent cells. LTR5_Hs are epigenetically activated in both PGCLCs and naïve pluripotent cells, and the expression of genes in the vicinity of LTR5_Hs is coordinately upregulated in these cell types, contributing to the establishment of the transcriptome similarity between these cell types. LTR5_Hs are preferentially bound by transcription factors that are highly expressed in both PGCLCs and naïve pluripotent cells (KLF4, TFAP2C, NANOG, and CBFA2T2), suggesting that these transcription factors contribute to the epigenetic activation of LTR5_Hs in these cells. Comparative transcriptome analysis between humans and macaques suggests that the expression of many genes in PGCLCs and naïve pluripotent cells is upregulated by LTR5_Hs insertions in the hominoid lineage. Together, this study suggests that LTR5_Hs insertions may have finetuned the gene regulatory network shared between PGCLCs and naïve pluripotent cells and coordinately altered the gene expression in these cells during hominoid evolution. To ensure the health of the next generation and the continuation of a species, the development of germ cells, including primordial germ cells (PGCs), is strictly controlled by a complex gene regulatory network. Nevertheless, the gene regulatory network controlling the germ cell development has been substantially diversified during mammalian or even primate evolution. Here, our integrated analyses using multiomics and comparative genomics resources suggest that hominoid-specific insertions of endogenous retroviruses are epigenetically activated in both in vitro-induced PGCs and naïve pluripotent cells and may have coordinately altered the expression of the adjacent genes in these cells. This study provides evidence suggesting that the gene regulatory network shared between PGCs and naïve pluripotent cells may have been rewired by ERV insertions during hominoid evolution.
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Affiliation(s)
- Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasunari Seita
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Bell Research Center for Reproductive Health and Cancer, Nagoya, Aichi, Japan
| | - Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Kotaro Sasaki
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (KS); (KS)
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- * E-mail: (KS); (KS)
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10
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Sequential enhancer state remodelling defines human germline competence and specification. Nat Cell Biol 2022; 24:448-460. [PMID: 35411086 PMCID: PMC7612729 DOI: 10.1038/s41556-022-00878-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/28/2022] [Indexed: 12/26/2022]
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11
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Dinsmore CJ, Ke CY, Soriano P. The Wnt1-Cre2 transgene is active in the male germline. Genesis 2022; 60:e23468. [PMID: 35180326 PMCID: PMC8940701 DOI: 10.1002/dvg.23468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022]
Abstract
The Wnt1-Cre transgenic mouse line is widely used to express the CRE recombinase in neural crest lineages, but it overexpresses WNT1 itself, which can cause undesired phenotypes. To address this, we and others previously developed a Wnt1-Cre2 line based on the same regulatory elements as Wnt1-Cre but without ectopic Wnt1 expression. However, while Wnt1-Cre2 exhibits normal activity when transmitted from female mice, it exhibits unexpected activity in the male germline. The Wnt1-Cre2 transgene was previously mapped to the E2f1 locus. Several genes in this genomic region exhibit significant expression in spermatogonia or spermatocytes, suggesting that local regulatory elements may be driving ectopic transgene expression. The Wnt1-Cre2 line can therefore be used both as a neural crest specific and a general deleter, and care should be taken when setting up genetic crosses.
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12
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Ortabozkoyun H, Huang PY, Cho H, Narendra V, LeRoy G, Gonzalez-Buendia E, Skok JA, Tsirigos A, Mazzoni EO, Reinberg D. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nat Genet 2022; 54:202-212. [PMID: 35145304 PMCID: PMC8837555 DOI: 10.1038/s41588-021-01008-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022]
Abstract
CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.
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Affiliation(s)
- Havva Ortabozkoyun
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Pin-Yao Huang
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hyunwoo Cho
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA
| | - Varun Narendra
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Edgar Gonzalez-Buendia
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jane A Skok
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Danny Reinberg
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA. .,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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13
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Kim M, Ly SH, Xie Y, Duronio GN, Ford-Roshon D, Hwang JH, Sulahian R, Rennhack JP, So J, Gjoerup O, Talamas JA, Grandclaudon M, Long HW, Doench JG, Sethi NS, Giannakis M, Hahn WC. YAP1 and PRDM14 converge to promote cell survival and tumorigenesis. Dev Cell 2022; 57:212-227.e8. [PMID: 34990589 PMCID: PMC8827663 DOI: 10.1016/j.devcel.2021.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/15/2021] [Accepted: 12/03/2021] [Indexed: 01/26/2023]
Abstract
The transcriptional co-activator YAP1 oncogene is the downstream effector of the Hippo pathway, which regulates tissue homeostasis, organ size, regeneration, and tumorigenesis. Multiple cancers are dependent on sustained expression of YAP1 for cell proliferation, survival, and tumorigenesis, but the molecular basis of this oncogene dependency is not well understood. To identify genes that can functionally substitute for YAP1, we performed a genome-scale genetic rescue screen in YAP1-dependent colon cancer cells expressing an inducible YAP1-specific shRNA. We found that the transcription factor PRDM14 rescued cell proliferation and tumorigenesis upon YAP1 suppression in YAP1-dependent cells, xenografts, and colon cancer organoids. YAP1 and PRDM14 individually activated the transcription of calmodulin 2 (CALM2) and a glucose transporter SLC2A1 upon YAP1 suppression, and CALM2 or SLC2A1 expression was required for the rescue of YAP1 suppression. Together, these findings implicate PRDM14-mediated transcriptional upregulation of CALM2 and SLC2A1 as key components of oncogenic YAP1 signaling and dependency.
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Affiliation(s)
- Miju Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Seav Huong Ly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Gina N Duronio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dane Ford-Roshon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Justin H Hwang
- Masonic Cancer Center and Department of Medicine, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Rita Sulahian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan P Rennhack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan So
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ole Gjoerup
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jessica A Talamas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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14
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Gjaltema RAF, Schwämmle T, Kautz P, Robson M, Schöpflin R, Ravid Lustig L, Brandenburg L, Dunkel I, Vechiatto C, Ntini E, Mutzel V, Schmiedel V, Marsico A, Mundlos S, Schulz EG. Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Mol Cell 2022; 82:190-208.e17. [PMID: 34932975 DOI: 10.1016/j.molcel.2021.11.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
Developmental genes such as Xist, which initiates X chromosome inactivation, are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatiotemporal expression patterns. Xist integrates information on X chromosome dosage and developmental stage to trigger X inactivation in the epiblast specifically in female embryos. Through a pooled CRISPR screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist at the onset of random X inactivation. Chromatin profiling reveals that X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. The strongest distal element lies in an enhancer cluster associated with a previously unannotated Xist-enhancing regulatory transcript, which we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. With this study, we start to disentangle how multiple, functionally distinct regulatory elements interact to generate complex expression patterns in mammals.
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Affiliation(s)
- Rutger A F Gjaltema
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Pauline Kautz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Michael Robson
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, Edinburgh, UK
| | - Robert Schöpflin
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Liat Ravid Lustig
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lennart Brandenburg
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ilona Dunkel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Carolina Vechiatto
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Evgenia Ntini
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vera Schmiedel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center München, 85764 Neuherberg, Germany
| | - Stefan Mundlos
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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15
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IMAI K, TANIGUCHI H. Therapeutic siRNA targeting the cancer cell stemness regulator PRDI-BF1 and RIZ domain zinc finger protein 14. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:325-335. [PMID: 35908955 PMCID: PMC9363597 DOI: 10.2183/pjab.98.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
PRDI-BF1 and RIZ (PR) domain zinc finger protein 14 (PRDM14), first reported in 2007 to be overexpressed in breast cancer, plays an important role in breast cancer proliferation. Subsequent studies reported that PRDM14 is expressed in embryonic stem cells, primordial germ cells, and various cancers. PRDM14 was reported to confer stemness properties to cancer cells. These properties induce cancer initiation, cancer progression, therapeutic resistance, distant metastasis, and recurrence in refractory tumors. Therefore, PRDM14 may be an ideal therapeutic target for various types of tumors. Silencing PRDM14 expression using PRDM14-specific siRNA delivered through an innovative intravenous drug delivery system reduced the size of inoculated tumors, incidence of distant metastases, and increased overall survival in nude mice without causing adverse effects. Therapeutic siRNA targeting PRDM14 is now being evaluated in a human phase I clinical trial for patients with refractory breast cancer, including triple-negative breast cancer.
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Affiliation(s)
- Kohzoh IMAI
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroaki TANIGUCHI
- Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
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16
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X-chromosome reactivation: a concise review. Biochem Soc Trans 2021; 49:2797-2805. [PMID: 34821360 DOI: 10.1042/bst20210777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Mammalian females (XX) silence transcription on one of the two X chromosomes to compensate the expression dosage with males (XY). This process - named X-chromosome inactivation - entails a variety of epigenetic modifications that act synergistically to maintain silencing and make it heritable through cell divisions. Genes along the inactive X chromosome are, indeed, refractory to reactivation. Nonetheless, X-chromosome reactivation can occur alongside with epigenome reprogramming or by perturbing multiple silencing pathways. Here we review the events associated with X-chromosome reactivation during in vivo and in vitro reprogramming and highlight recent efforts in inducing Xi reactivation by molecular perturbations. This provides us with a first understanding of the mechanisms underlying X-chromosome reactivation, which could be tackled for therapeutic purposes.
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17
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Rafiee MR, Zagalak JA, Sidorov S, Steinhauser S, Davey K, Ule J, Luscombe NM. Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. Nucleic Acids Res 2021; 49:13092-13107. [PMID: 34871434 PMCID: PMC8682780 DOI: 10.1093/nar/gkab1180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play diverse roles in regulating co-transcriptional RNA-processing and chromatin functions, but our knowledge of the repertoire of chromatin-associated RBPs (caRBPs) and their interactions with chromatin remains limited. Here, we developed SPACE (Silica Particle Assisted Chromatin Enrichment) to isolate global and regional chromatin components with high specificity and sensitivity, and SPACEmap to identify the chromatin-contact regions in proteins. Applied to mouse embryonic stem cells, SPACE identified 1459 chromatin-associated proteins, ∼48% of which are annotated as RBPs, indicating their dual roles in chromatin and RNA-binding. Additionally, SPACEmap stringently verified chromatin-binding of 403 RBPs and identified their chromatin-contact regions. Notably, SPACEmap showed that about 40% of the caRBPs bind chromatin by intrinsically disordered regions (IDRs). Studying SPACE and total proteome dynamics from mES cells grown in 2iL and serum medium indicates significant correlation (R = 0.62). One of the most dynamic caRBPs is Dazl, which we find co-localized with PRC2 at transcription start sites of genes that are distinct from Dazl mRNA binding. Dazl and other PRC2-colocalised caRBPs are rich in intrinsically disordered regions (IDRs), which could contribute to the formation and regulation of phase-separated PRC condensates. Together, our approach provides an unprecedented insight into IDR-mediated interactions and caRBPs with moonlighting functions in native chromatin.
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Affiliation(s)
| | - Julian A Zagalak
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | | | | | - Karen Davey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
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18
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Borkiewicz L. Histone 3 Lysine 27 Trimethylation Signature in Breast Cancer. Int J Mol Sci 2021; 22:12853. [PMID: 34884658 PMCID: PMC8657745 DOI: 10.3390/ijms222312853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer development and progression rely on complicated genetic and also epigenetic changes which regulate gene expression without altering the DNA sequence. Epigenetic mechanisms such as DNA methylation, histone modifications, and regulation by lncRNAs alter protein expression by either promoting gene transcription or repressing it. The presence of so-called chromatin modification marks at various gene promoters and gene bodies is associated with normal cell development but also with tumorigenesis and progression of different types of cancer, including the most frequently diagnosed breast cancer. This review is focused on the significance of one of the abundant post-translational modifications of histone 3- trimethylation of lysine 27 (H3K27me3), which was shown to participate in tumour suppressor genes' silencing. Unlike other reviews in the field, here the overview of existing evidence linking H3K27me3 status with breast cancer biology and the tumour outcome is presented especially in the context of diverse breast cancer subtypes. Moreover, the potential of agents that target H3K27me3 for the treatment of this complex disease as well as H3K27 methylation in cross-talk with other chromatin modifications and lncRNAs are discussed.
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Affiliation(s)
- Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-059 Lublin, Poland
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19
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Papathanasiou M, Tsiftsoglou SA, Polyzos AP, Papadopoulou D, Valakos D, Klagkou E, Karagianni P, Pliatska M, Talianidis I, Agelopoulos M, Thanos D. Identification of a dynamic gene regulatory network required for pluripotency factor-induced reprogramming of mouse fibroblasts and hepatocytes. EMBO J 2021; 40:e102236. [PMID: 33034061 PMCID: PMC7780151 DOI: 10.15252/embj.2019102236] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/27/2020] [Accepted: 09/07/2020] [Indexed: 01/04/2023] Open
Abstract
The generation of induced pluripotent stem cells (iPSCs) from somatic cells provides an excellent model to study mechanisms of transcription factor-induced global alterations of the epigenome and genome function. Here, we have investigated the early transcriptional events of cellular reprogramming triggered by the co-expression of Oct4, Sox2, Klf4, and c-Myc (OSKM) in mouse embryonic fibroblasts (MEFs) and mouse hepatocytes (mHeps). In this analysis, we identified a gene regulatory network composed of nine transcriptional regulators (9TR; Cbfa2t3, Gli2, Irf6, Nanog, Ovol1, Rcan1, Taf1c, Tead4, and Tfap4), which are directly targeted by OSKM, in vivo. Functional studies using single and double shRNA knockdowns of any of these factors caused disruption of the network and dramatic reductions in reprogramming efficiency, indicating that this network is essential for the induction and establishment of pluripotency. We demonstrate that the stochastic co-expression of 9TR network components occurs in a remarkably small number of cells, approximating the percentage of terminally reprogrammed cells as a result of dynamic molecular events. Thus, the early DNA-binding patterns of OSKM and the subsequent probabilistic co-expression of essential 9TR components in subpopulations of cells undergoing reprogramming steer the reconstruction of a gene regulatory network marking the transition to pluripotency.
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Affiliation(s)
| | | | | | | | | | | | | | - Maria Pliatska
- Biomedical Research Foundation Academy of AthensAthensGreece
| | | | | | - Dimitris Thanos
- Biomedical Research Foundation Academy of AthensAthensGreece
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20
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Carlini V, Gretarsson KH, Hackett JA. Genome-Scale CRISPR Screening for Regulators of Cell Fate Transitions. Methods Mol Biol 2021; 2214:91-108. [PMID: 32944905 DOI: 10.1007/978-1-0716-0958-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Knockout CRISPR screening enables the unbiased discovery of genes with a functional role in almost any cellular or molecular process of interest. The approach couples a genome-scale library of guide RNA (gRNA), the Cas9 endonuclease, and a faithful phenotypic read-out to systematically identify candidate genes via their loss-of-function effect. Here we provide a detailed description of the CRISPR screen protocol and outline how to apply it to decipher the gene networks that underlie developmental cell fate decisions. As a paradigm we use the in vitro model of cell state transition(s) from naive pluripotency to primordial germ cell (PGC) fate, exploiting the Stella-GFP:Esg1-tdTomato (SGET) mouse ESC line. The principles in this protocol can be readily adapted to characterize lineage regulators for other cell fate models and/or for other species.
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Affiliation(s)
- Valentina Carlini
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Kristjan H Gretarsson
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Jamie A Hackett
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy.
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21
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Luo J, Dou L, Yang Z, Zhou Z, Huang H. CBFA2T2 promotes adipogenic differentiation of mesenchymal stem cells by regulating CEBPA. Biochem Biophys Res Commun 2020; 529:133-139. [PMID: 32703401 DOI: 10.1016/j.bbrc.2020.05.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/16/2020] [Indexed: 12/28/2022]
Abstract
The unique metabolic characteristics and diverse functions of marrow adipose tissue (MAT) have drawn more attention recently. Previously, we have reported that CBFA2T2 is required for BMP2-induced osteogenic differentiation of mesenchymal stem/stromal cells (MSCs). In the present study, we further investigated the role of CBFA2T2 in regulation of adipogenic differentiation in mouse bone marrow-derived MSCs (mBMSCs) and human dental pulp stem cells (hDPSCs). We found CBFA2T2 expression was dramatically upregulated during adipogenesis of mBMSCs and hDPSCs. More importantly, knockdown of CBFA2T2 in mBMSCs and hDPSCs significantly inhibited the process of adipogenic differentiation, as revealed by the expression of adipogenic markers and Oil Red O staining. Mechanistically, we found knockdown of CBFA2T2 led to an increase in H3K9me2 and H3K9me3 levels at promoter of CEBPA, an essential transcription factor of adipogenesis. Taken together, these findings suggest CBFA2T2 is key regulator of adipogenic differentiation of MSCs, and it may represent a therapeutic target for conditions with excessive MAT.
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Affiliation(s)
- Jun Luo
- Stomatological Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China; Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Lei Dou
- Stomatological Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China; Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Zhengyan Yang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China; Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Zhi Zhou
- Stomatological Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China; Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Hong Huang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China; Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China.
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22
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Yamamoto M, Suwa Y, Sugiyama K, Okashita N, Kawaguchi M, Tani N, Matsubara K, Nakamura A, Seki Y. The PRDM14-CtBP1/2-PRC2 complex regulates transcriptional repression during the transition from primed to naïve pluripotency. J Cell Sci 2020; 133:jcs240176. [PMID: 32661086 DOI: 10.1242/jcs.240176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/25/2020] [Indexed: 12/17/2022] Open
Abstract
The pluripotency-associated transcriptional network is regulated by a core circuitry of transcription factors. The PR domain-containing protein PRDM14 maintains pluripotency by activating and repressing transcription in a target gene-dependent manner. However, the mechanisms underlying dichotomic switching of PRDM14-mediated transcriptional control remain elusive. Here, we identified C-terminal binding protein 1 and 2 (CtBP1 and CtBP2; generically referred to as CtBP1/2) as components of the PRDM14-mediated repressive complex. CtBP1/2 binding to PRDM14 depends on CBFA2T2, a core component of the PRDM14 complex. The loss of Ctbp1/2 impaired the PRDM14-mediated transcriptional repression required for pluripotency maintenance and transition from primed to naïve pluripotency. Furthermore, CtBP1/2 interacted with the PRC2 complexes, and the loss of Ctbp1/2 impaired Polycomb repressive complex 2 (PRC2) and H3K27me3 enrichment at target genes after Prdm14 induction. These results provide evidence that the target gene-dependent transcriptional activity of PRDM14 is regulated by partner switching to ensure the transition from primed to naïve pluripotency.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Maiko Yamamoto
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Yoshiaki Suwa
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Kohta Sugiyama
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Naoki Okashita
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Masanori Kawaguchi
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Naoki Tani
- Liaison Laboratory Research Promotion Center, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Kazumi Matsubara
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Akira Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Yoshiyuki Seki
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
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23
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Xie H, Liu S, Zhang Z, Chen P, Tao Y. A novel seven-gene signature as Prognostic Biomarker in Hepatocellular Carcinoma. J Cancer 2020; 11:5768-5781. [PMID: 32913470 PMCID: PMC7477431 DOI: 10.7150/jca.44573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/29/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose: Our study is designed to develop and certify a promising prognostic signature for hepatocellular carcinoma (HCC). Materials and methods: We retrospectively analyzed mRNA expression profiles and clinicopathological data fetched from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. We formulated a prognostic seven-gene signature composed of differentially expressed mRNAs (DEmRNAs) between HCC and nonneoplastic tissues through univariate Cox regression analysis. The receiver operating characteristic (ROC) curve, survival analysis and multivariate Cox regression analysis as well as nomograms were utilized to assess the prognostic performance of the seven-gene signature. Results: The risk score based on a seven-gene signature categorized HCC subjects into a high- and low-risk group. There was significantly discrepant overall survival (OS) between patients in both groups and the corresponding ROC curve revealed a satisfactory predictive performance in HCC survival in both TCGA and GSE76427 cohort. Multivariate Cox regression analysis demonstrated that a seven-gene signature was an independently prognostic factor for HCC. Nomograms combining this prognostic signature with significant clinical characteristics conferred a crucial reference to predict the 1-,3- and 5 years OS. Conclusions: Our study defined a promising seven-gene signature and nomogram model to forecast the OS of HCC patients, which is instrumental in clinical decision and personalized therapy.
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Affiliation(s)
- Hui Xie
- Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078 China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, 410078 China.,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Shouping Liu
- Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078 China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, 410078 China
| | - Ziying Zhang
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Peng Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yongguang Tao
- Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan, 410078 China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, 410078 China.,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China.,Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
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24
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Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development. Nat Struct Mol Biol 2020; 27:706-716. [DOI: 10.1038/s41594-020-0445-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
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25
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Shanak S, Helms V. DNA methylation and the core pluripotency network. Dev Biol 2020; 464:145-160. [PMID: 32562758 DOI: 10.1016/j.ydbio.2020.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/01/2020] [Accepted: 06/04/2020] [Indexed: 01/06/2023]
Abstract
From the onset of fertilization, the genome undergoes cell division and differentiation. All of these developmental transitions and differentiation processes include cell-specific signatures and gradual changes of the epigenome. Understanding what keeps stem cells in the pluripotent state and what leads to differentiation are fascinating and biomedically highly important issues. Numerous studies have identified genes, proteins, microRNAs and small molecules that exert essential effects. Notably, there exists a core pluripotency network that consists of several transcription factors and accessory proteins. Three eminent transcription factors, OCT4, SOX2 and NANOG, serve as hubs in this core pluripotency network. They bind to the enhancer regions of their target genes and modulate, among others, the expression levels of genes that are associated with Gene Ontology terms related to differentiation and self-renewal. Also, much has been learned about the epigenetic rewiring processes during these changes of cell fate. For example, DNA methylation dynamics is pivotal during embryonic development. The main goal of this review is to highlight an intricate interplay of (a) DNA methyltransferases controlling the expression levels of core pluripotency factors by modulation of the DNA methylation levels in their enhancer regions, and of (b) the core pluripotency factors controlling the transcriptional regulation of DNA methyltransferases. We discuss these processes both at the global level and in atomistic detail based on information from structural studies and from computer simulations.
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Affiliation(s)
- Siba Shanak
- Faculty of Science, Arab-American University, Jenin, Palestine; Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
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26
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Yadu N, Kumar PG. Retinoic acid signaling in regulation of meiosis during embryonic development in mice. Genesis 2019; 57:e23327. [PMID: 31313882 DOI: 10.1002/dvg.23327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 06/23/2019] [Accepted: 07/04/2019] [Indexed: 12/12/2022]
Abstract
In the embryonic gonads of mice, the genetic and epigenetic regulatory programs for germ cell sex specification and meiosis induction or suppression are intertwined. The quest for garnering comprehensive understanding of these programs has led to the emergence of retinoic acid (RA) as an important extrinsic factor, which regulates initiation of meiosis in female fetal germ cells that have attained a permissive epigenetic ground state. In contrast, germ cells in fetal testis are protected from the exposure to RA due to the activity of CYP26B1, an RA metabolizing enzyme, which is highly expressed in fetal testis. In this review, we provide an overview of the molecular mechanisms operating in fetal gonads of mice, which enable regulation of meiosis via RA signaling.
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Affiliation(s)
- Nomesh Yadu
- Division of Molecular Reproduction, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Pradeep G Kumar
- Division of Molecular Reproduction, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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PRDM14 controls X-chromosomal and global epigenetic reprogramming of H3K27me3 in migrating mouse primordial germ cells. Epigenetics Chromatin 2019; 12:38. [PMID: 31221220 PMCID: PMC6585054 DOI: 10.1186/s13072-019-0284-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/12/2019] [Indexed: 01/18/2023] Open
Abstract
Background In order to prepare the genome for gametogenesis, primordial germ cells (PGCs) undergo extensive epigenetic reprogramming during migration toward the gonads in mammalian embryos. This includes changes on a genome-wide scale and additionally in females the remodeling of the inactive X-chromosome to enable X-chromosome reactivation (XCR). However, if global remodeling and X-chromosomal remodeling are related, how they occur in PGCs in vivo in relation to their migration progress and which factors are important are unknown. Results Here we identify the germ cell determinant PR-domain containing protein 14 (PRDM14) as the first known factor that is instrumental for both global reprogramming and X-chromosomal reprogramming in migrating mouse PGCs. We find that global upregulation of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark is PRDM14 dosage dependent in PGCs of both sexes. When focusing on XCR, we observed that PRDM14 is required for removal of H3K27me3 from the inactive X-chromosome, which, in contrast to global upregulation, takes place progressively along the PGC migration path. Furthermore, we show that global and X-chromosomal reprogramming of H3K27me3 are functionally separable, despite their common regulation by PRDM14. Conclusions In summary, here we provide new insight and spatiotemporal resolution to the progression and regulation of epigenome remodeling along mouse PGC migration in vivo and link epigenetic reprogramming to its developmental context. Electronic supplementary material The online version of this article (10.1186/s13072-019-0284-7) contains supplementary material, which is available to authorized users.
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Tracey LJ, Justice MJ. Off to a Bad Start: Cancer Initiation by Pluripotency Regulator PRDM14. Trends Genet 2019; 35:489-500. [PMID: 31130394 DOI: 10.1016/j.tig.2019.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 04/23/2019] [Indexed: 12/16/2022]
Abstract
Despite advances in chemotherapies that improve cancer survival, most patients who relapse succumb to the disease due to the presence of cancer stem cells (CSCs), which are highly chemoresistant. The pluripotency factor PR domain 14 (PRDM14) has a key role in initiating many types of cancer. Normally, PRDM14 uses epigenetic mechanisms to establish and maintain the pluripotency of embryonic cells, and its role in cancer is similar. This important link between cancer and induced pluripotency is a key revelation for how CSCs may form: pluripotency genes, such as PRDM14, can expand stem-like cells as they promote ongoing DNA damage. PRDM14 and its protein-binding partners, the ETO/CBFA2T family, are ideal candidates for eliminating CSCs from relevant cancers, preventing relapse and improving long-term survival.
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Affiliation(s)
- Lauren J Tracey
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ONT, M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ONT, M5S 1A8, Canada
| | - Monica J Justice
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ONT, M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ONT, M5S 1A8, Canada.
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Sybirna A, Wong FCK, Surani MA. Genetic basis for primordial germ cells specification in mouse and human: Conserved and divergent roles of PRDM and SOX transcription factors. Curr Top Dev Biol 2019; 135:35-89. [PMID: 31155363 DOI: 10.1016/bs.ctdb.2019.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Primordial germ cells (PGCs) are embryonic precursors of sperm and egg that pass on genetic and epigenetic information from one generation to the next. In mammals, they are induced from a subset of cells in peri-implantation epiblast by BMP signaling from the surrounding tissues. PGCs then initiate a unique developmental program that involves comprehensive epigenetic resetting and repression of somatic genes. This is orchestrated by a set of signaling molecules and transcription factors that promote germ cell identity. Here we review significant findings on mammalian PGC biology, in particular, the genetic basis for PGC specification in mice and human, which has revealed an evolutionary divergence between the two species. We discuss the importance and potential basis for these differences and focus on several examples to illustrate the conserved and divergent roles of critical transcription factors in mouse and human germline.
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Affiliation(s)
- Anastasiya Sybirna
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
| | - Frederick C K Wong
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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30
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Abstract
Germ cells undergo epigenome reprogramming for proper development of the next generation. The achievement of in vitro germ cell derivation from human and mouse pluripotent stem cells and further differentiation in a plane culture and in aggregation with gonadal somatic cells offers unprecedented opportunities for investigation of the germ cell development. Moreover, advances in low-input/single-cell genomics have enabled detailed investigation of epigenome dynamics during germ cell development. These technologies have advanced our knowledge of epigenome reprogramming during the specification and development of primordial germ cells, their sex differentiation, and gametogenesis. Key findings include details of chromatin remodeling and transcriptional regulation, progressive and comprehensive DNA demethylation, and tight links between DNA demethylation and histone marks during the development of primordial germ cells, acquisition of unique totipotent epigenome during oogenesis (e.g., broad H3K4me3 domains and low-level three-dimensional genomic organization), and unexpected organization of the sperm genome. Moreover, these studies suggest the importance of epigenome analyses for in-depth evaluations of in vitro gametogenesis.
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Affiliation(s)
- Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan.
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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31
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Tracey LJ, Brooke-Bisschop T, Jansen PWTC, Campos EI, Vermeulen M, Justice MJ. The Pluripotency Regulator PRDM14 Requires Hematopoietic Regulator CBFA2T3 to Initiate Leukemia in Mice. Mol Cancer Res 2019; 17:1468-1479. [PMID: 31015254 DOI: 10.1158/1541-7786.mcr-18-1327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/07/2019] [Accepted: 04/19/2019] [Indexed: 12/20/2022]
Abstract
PR domain-containing 14 (Prdm14) is a pluripotency regulator central to embryonic stem cell identity and primordial germ cell specification. Genomic regions containing PRDM14 are often amplified leading to misexpression in human cancer. Prdm14 expression in mouse hematopoietic stem cells (HSC) leads to progenitor cell expansion prior to the development of T-cell acute lymphoblastic leukemia (T-ALL), consistent with PRDM14's role in cancer initiation. Here, we demonstrate mechanistic insight into PRDM14-driven leukemias in vivo. Mass spectrometry revealed novel PRDM14-protein interactions including histone H1, RNA-binding proteins, and the master hematopoietic regulator CBFA2T3. In mouse leukemic cells, CBFA2T3 and PRDM14 associate independently of the related ETO family member CBFA2T2, PRDM14's primary protein partner in pluripotent cells. CBFA2T3 plays crucial roles in HSC self-renewal and lineage commitment, and participates in oncogenic translocations in acute myeloid leukemia. These results suggest a model whereby PRDM14 recruits CBFA2T3 to DNA, leading to gene misregulation causing progenitor cell expansion and lineage perturbations preceding T-ALL development. Strikingly, Prdm14-induced T-ALL does not occur in mice deficient for Cbfa2t3, demonstrating that Cbfa2t3 is required for leukemogenesis. Moreover, T-ALL develops in Cbfa2t3 heterozygotes with a significantly longer latency, suggesting that PRDM14-associated T-ALL is sensitive to Cbfa2t3 levels. Our study highlights how an oncogenic protein uses a native protein in progenitor cells to initiate leukemia, providing insight into PRDM14-driven oncogenesis in other cell types. IMPLICATIONS: The pluripotency regulator PRDM14 requires the master hematopoietic regulator CBFA2T3 to initiate leukemia in progenitor cells, demonstrating an oncogenic role for CBFA2T3 and providing an avenue for targeting cancer-initiating cells.
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Affiliation(s)
- Lauren J Tracey
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Travis Brooke-Bisschop
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pascal W T C Jansen
- Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Eric I Campos
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michiel Vermeulen
- Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Monica J Justice
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
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32
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Rajderkar S, Mann JM, Panaretos C, Yumoto K, Li HD, Mishina Y, Ralston B, Kaartinen V. Trim33 is required for appropriate development of pre-cardiogenic mesoderm. Dev Biol 2019; 450:101-114. [PMID: 30940539 DOI: 10.1016/j.ydbio.2019.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 11/25/2022]
Abstract
Congenital cardiac malformations are among the most common birth defects in humans. Here we show that Trim33, a member of the Tif1 subfamily of tripartite domain containing transcriptional cofactors, is required for appropriate differentiation of the pre-cardiogenic mesoderm during a narrow time window in late gastrulation. While mesoderm-specific Trim33 mutants did not display noticeable phenotypes, epiblast-specific Trim33 mutant embryos developed ventricular septal defects, showed sparse trabeculation and abnormally thin compact myocardium, and died as a result of cardiac failure during late gestation. Differentiating embryoid bodies deficient in Trim33 showed an enrichment of gene sets associated with cardiac differentiation and contractility, while the total number of cardiac precursor cells was reduced. Concordantly, cardiac progenitor cell proliferation was reduced in Trim33-deficient embryos. ChIP-Seq performed using antibodies against Trim33 in differentiating embryoid bodies revealed more than 4000 peaks, which were significantly enriched close to genes implicated in stem cell maintenance and mesoderm development. Nearly half of the Trim33 peaks overlapped with binding sites of the Ctcf insulator protein. Our results suggest that Trim33 is required for appropriate differentiation of precardiogenic mesoderm during late gastrulation and that it will likely mediate some of its functions via multi-protein complexes, many of which include the chromatin architectural and insulator protein Ctcf.
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Affiliation(s)
- Sudha Rajderkar
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey M Mann
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christopher Panaretos
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kenji Yumoto
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hong-Dong Li
- Center for Bioinformatics, School of Information Science and Engineering, Central South University, Changsha, Hunan, 410083, PR China
| | - Yuji Mishina
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Benjamin Ralston
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vesa Kaartinen
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, 48109, USA.
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Wei X, Guo J, Li Q, Jia Q, Jing Q, Li Y, Zhou B, Chen J, Gao S, Zhang X, Jia M, Niu C, Yang W, Zhi X, Wang X, Yu D, Bai L, Wang L, Na J, Zou Y, Zhang J, Zhang S, Meng D. Bach1 regulates self-renewal and impedes mesendodermal differentiation of human embryonic stem cells. SCIENCE ADVANCES 2019; 5:eaau7887. [PMID: 30891497 PMCID: PMC6415956 DOI: 10.1126/sciadv.aau7887] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/30/2019] [Indexed: 05/03/2023]
Abstract
The transcription factor BTB and CNC homology 1 (Bach1) is expressed in the embryos of mice, but whether Bach1 regulates the self-renewal and early differentiation of human embryonic stem cells (hESCs) is unknown. We report that the deubiquitinase ubiquitin-specific processing protease 7 (Usp7) is a direct target of Bach1, that Bach1 interacts with Nanog, Sox2, and Oct4, and that Bach1 facilitates their deubiquitination and stabilization via the recruitment of Usp7, thereby maintaining stem cell identity and self-renewal. Bach1 also interacts with polycomb repressive complex 2 (PRC2) and represses mesendodermal gene expression by recruiting PRC2 to the genes' promoters. The loss of Bach1 in hESCs promotes differentiation toward the mesendodermal germ layers by reducing the occupancy of EZH2 and H3K27me3 in mesendodermal gene promoters and by activating the Wnt/β-catenin and Nodal/Smad2/3 signaling pathways. Our study shows that Bach1 is a key determinant of pluripotency, self-renewal, and lineage specification in hESCs.
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Affiliation(s)
- Xiangxiang Wei
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jieyu Guo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qinhan Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qianqian Jia
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Qing Jing
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Li
- The State Key Laboratory of Cell Biology, CAS Center for Excellence on Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence on Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xinyue Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Mengping Jia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Cong Niu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenlong Yang
- Department of Cardiology, Zhongshan Hospital, Shanghai Cardiovascular Medical Center, Shanghai Institute of Cardiovascular Diseases, Institute of Pan-vascular Medicine, Fudan University, Shanghai 200032, China
| | - Xiuling Zhi
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xinhong Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dian Yu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lufeng Bai
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lin Wang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jie Na
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yunzeng Zou
- Department of Cardiology, Zhongshan Hospital, Shanghai Cardiovascular Medical Center, Shanghai Institute of Cardiovascular Diseases, Institute of Pan-vascular Medicine, Fudan University, Shanghai 200032, China
| | - Jianyi Zhang
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shuning Zhang
- Department of Cardiology, Zhongshan Hospital, Shanghai Cardiovascular Medical Center, Shanghai Institute of Cardiovascular Diseases, Institute of Pan-vascular Medicine, Fudan University, Shanghai 200032, China
- Corresponding author. (D.M.); (S.Z.)
| | - Dan Meng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Corresponding author. (D.M.); (S.Z.)
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Gasiūnienė M, Zentelytė A, Wojtas B, Baronaitė S, Krasovskaja N, Savickienė J, Gielniewski B, Kaminska B, Utkus A, Navakauskienė R. DNA methyltransferases inhibitors effectively induce gene expression changes suggestive of cardiomyogenic differentiation of human amniotic fluid-derived mesenchymal stem cells via chromatin remodeling. J Tissue Eng Regen Med 2019; 13:469-481. [PMID: 30637987 DOI: 10.1002/term.2800] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/31/2018] [Accepted: 01/09/2019] [Indexed: 12/17/2022]
Abstract
Human amniotic fluid-derived mesenchymal stem cells (AF-MSCs) are a new potential stem cell source for cell therapy and regenerative medicine. These are fetal mesenchymal stem cells with multilineage differentiation potential found in amniotic fluid. The aim of the present study was to evaluate in vitro differentiation initiation of AF-MSCs into cardiac progenitors upon application of inhibitors of DNA methyltransferases (DNMT), such as Decitabine (DEC; 5-aza-2'-deoxycytidine) and Zebularine (ZEB). We assessed epigenetic changes and explored patterns of genes, enriched in association with hyperacetylated H4 after induced differentiation. Upregulation of cardiomyogenesis-related genes (TNNT2, MYH6, ACTN2, and DES) and cardiac ion channels genes, downregulation of pluripotency genes markers as well as increase in Connexin43 expression indicated cardiomyogenic commitment. Evaluation of global epigenetic changes showed that levels of chromatin modifying enzymes, such as Polycomb repressive complex 2 proteins (EZH2, SUZ12), DNMT1, histone deacetylases 1 and 2 were reduced to the similar extent by both differentiation agents. Levels of specific histone marks keeping active state of chromatin (H3K4me3, H3K9Ac, and H4hyperAc) increased and marks of repressed chromatin state (H3K27me3 and H3K9me3) decreased after DEC or ZEB treatment. Chip-Seq analysis after chromatin immunoprecipitation with H4hyperAc demonstrated enrichment of around 100 functionally annotated genes, related to chromatin reorganization and cardiomyogenesis and confirmed relation between H4 hyperacetylation and gene expression. Our results demonstrate that both DEC and ZEB can be potentially used as cardiomyogenic differentiation inducers in AF-MSCs, and they cause various genetic and epigenetic changes resulting in global chromatin remodeling.
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Affiliation(s)
- Monika Gasiūnienė
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Aistė Zentelytė
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Sandra Baronaitė
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Jūratė Savickienė
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Algirdas Utkus
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Rūta Navakauskienė
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Kawaguchi M, Sugiyama K, Matsubara K, Lin CY, Kuraku S, Hashimoto S, Suwa Y, Yong LW, Takino K, Higashida S, Kawamura D, Yu JK, Seki Y. Co-option of the PRDM14–CBFA2T complex from motor neurons to pluripotent cells during vertebrate evolution. Development 2019; 146:dev.168633. [DOI: 10.1242/dev.168633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/20/2018] [Indexed: 11/20/2022]
Abstract
Gene regulatory networks underlying cellular pluripotency are controlled by a core circuitry of transcription factors in mammals, including POU5F1. However, the evolutionary origin and transformation of pluripotency-related transcriptional networks have not been elucidated in deuterostomes. PR domain-containing protein 14 (PRDM14) is specifically expressed in pluripotent cells and germ cells, and required for establishing embryonic stem cells (ESCs) and primordial germ cells in mice. Here, we compared the functions and expression patterns of PRDM14 orthologues within deuterostomes. Amphioxus PRDM14 and zebrafish PRDM14, but not sea urchin PRDM14, compensated for mouse PRDM14 function in maintaining mouse ESC pluripotency. Interestingly, sea urchin PRDM14 together with sea urchin CBFA2T, an essential partner of PRDM14 in mouse ESCs, complemented the self-renewal defect in mouse Prdm14 KO ESCs. Contrary to the Prdm14-expression pattern in mouse embryos, Prdm14 was expressed in motor neurons of amphioxus embryos as observed in zebrafish embryos. Thus, Prdm14 expression in motor neurons was conserved in non-tetrapod deuterostomes and the co-option of the PRDM14-CBFA2T complex from motor neurons into pluripotent cells may have maintained the transcriptional network for pluripotency during vertebrate evolution.
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Affiliation(s)
- Masanori Kawaguchi
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
| | - Kota Sugiyama
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
| | - Kazumi Matsubara
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
| | - Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minami, Kobe, 650-0047, Japan
| | - Shota Hashimoto
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
| | - Yoshiaki Suwa
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
| | - Luok Wen Yong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Koji Takino
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
| | - Shota Higashida
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
| | - Daisuke Kawamura
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yoshiyuki Seki
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin Univerisity, Japan
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36
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Lebedeva LA, Yakovlev KV, Kozlov EN, Schedl P, Deshpande G, Shidlovskii YV. Transcriptional quiescence in primordial germ cells. Crit Rev Biochem Mol Biol 2018; 53:579-595. [PMID: 30280955 PMCID: PMC8729227 DOI: 10.1080/10409238.2018.1506733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/09/2018] [Accepted: 07/27/2018] [Indexed: 12/31/2022]
Abstract
In most animal species, newly formed primordial germ cells (PGCs) acquire the special characteristics that distinguish them from the surrounding somatic cells. Proper fate specification of the PGCs is coupled with transcriptional quiescence, whether they are segregated by determinative or inductive mechanisms. Inappropriate differentiation of PGCs into somatic cells is thought to be prevented due to repression of RNA polymerase (Pol) II-dependent transcription. In the case of a determinative mode of PGC formation (Drosophila, Caenorhabditis elegans, etc.), there is a broad downregulation of Pol II activity. By contrast, PGCs display only gene-specific repression in organisms that rely on inductive signaling-based mechanism (e.g., mice). In addition to the global block of Pol II activity in PGCs, gene expression can be suppressed in other ways, such as chromatin remodeling and Piwi-mediated RNAi. Here, we discuss the mechanisms responsible for the transcriptionally silent state of PGCs in common experimental animals, such as Drosophila, C. elegans, Danio rerio, Xenopus, and mouse. While a PGC-specific downregulation of transcription is a common feature among these organisms, the diverse nature of underlying mechanisms suggests that this functional trait likely evolved independently on several instances. We discuss the possible biological relevance of these silencing mechanisms vis-a-vis fate determination of PGCs.
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Affiliation(s)
| | - Konstantin V. Yakovlev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Eugene N. Kozlov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Paul Schedl
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, USA
| | - Girish Deshpande
- Department of Molecular Biology, Princeton University, Princeton, USA
| | - Yulii V. Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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37
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Hackett JA, Huang Y, Günesdogan U, Gretarsson KA, Kobayashi T, Surani MA. Tracing the transitions from pluripotency to germ cell fate with CRISPR screening. Nat Commun 2018; 9:4292. [PMID: 30327475 PMCID: PMC6191455 DOI: 10.1038/s41467-018-06230-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/08/2018] [Indexed: 12/26/2022] Open
Abstract
Early mammalian development entails transit through naive pluripotency towards post-implantation epiblast, which subsequently gives rise to primordial germ cells (PGC), the founding germline population. To investigate these cell fate transitions, we developed a compound-reporter to track cellular identity in a model of PGC specification (PGC-like cells; PGCLC), and coupled it with genome-wide CRISPR screening. We identify key genes both for exit from pluripotency and for acquisition of PGC fate, and characterise a central role for the transcription regulators Nr5a2 and Zfp296 in germline ontogeny. Abrogation of these genes results in widespread activation (Nr5a2−/−) or inhibition (Zfp296−/−) of WNT pathway factors in PGCLC. This leads to aberrant upregulation of the somatic programme or failure to activate germline genes, respectively, and consequently loss of germ cell identity. Our study places Zfp296 and Nr5a2 as key components of an expanded PGC gene regulatory network, and outlines a transferable strategy for identifying critical regulators of complex cell fate decisions. Primordial Germ Cell-Like Cells (PGCLCs) are an in vitro model for primordial germ cell development. Here, the authors couple a novel compound reporter with CRISPR screening to identify key genes for exit from pluripotency and acquisition of PGCLC fate; specifically identifying Nr5a2 and Zfp296.
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Affiliation(s)
- Jamie A Hackett
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK. .,Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), via Ramarini 32, 00015, Rome, Italy. .,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.
| | - Yun Huang
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Ufuk Günesdogan
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.,Department of Developmental Biology, University of Göttingen, Göttingen Center for Molecular Biosciences, Justus-von-Liebig Weg 11, 37077, Göttingen, Germany
| | - Kristjan A Gretarsson
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), via Ramarini 32, 00015, Rome, Italy
| | - Toshihiro Kobayashi
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.,Center for Genetic Analysis of Behaviour, National Institute for Physiological Sciences, 5-1 Higashiyama Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK. .,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.
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38
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Nikopoulou C, Panagopoulos G, Sianidis G, Psarra E, Ford E, Thanos D. The Transcription Factor ThPOK Orchestrates Stochastic Interchromosomal Interactions Required for IFNB1 Virus-Inducible Gene Expression. Mol Cell 2018; 71:352-361.e5. [PMID: 30017585 DOI: 10.1016/j.molcel.2018.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/30/2018] [Accepted: 06/07/2018] [Indexed: 02/01/2023]
Abstract
Virus infection induces stochastic activation of the interferon-β gene. Three previously identified Alu-like DNA elements called NRCs (NF-κB reception centers) function by capturing and delivering NF-κB to the IFNB1 enhancer via stochastic interchromosomal interactions. We show that the transcription factor ThPOK binds cooperatively with NF-κB to NRCs and mediates their physical proximity with the IFNB1 gene via its ability to oligomerize when bound to DNA. ThPOK knockdown significantly decreased the frequency of interchromosomal interactions, NF-κB DNA binding to the IFNB1 enhancer, and virus-induced IFNB1 gene activation. We also demonstrate that cooperative DNA binding between ThPOK and NF-κB on the same face of the double DNA helix is required for interchromosomal interactions and distinguishes NRCs from various other Alu elements bearing κB sites. These studies show how DNA binding cooperativity of stereospecifically aligned transcription factors provides the necessary ultrasensitivity for the all-or-none stochastic cell responses to virus infection.
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Affiliation(s)
- Chrysa Nikopoulou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Giorgos Panagopoulos
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Georgios Sianidis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Eleni Psarra
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Ethan Ford
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece.
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39
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Ma X, Li P, Sun X, Sun Y, Hu R, Yuan P. Differentiation of female Oct4-GFP embryonic stem cells into germ lineage cells. Cell Biol Int 2018; 42:488-494. [PMID: 29271529 DOI: 10.1002/cbin.10918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 12/17/2017] [Indexed: 02/05/2023]
Abstract
Due to high infertility ratio nowadays, it is essential to explore efficient ways of enhancing mammalian reproductivity, in particular female reproductivity. Using female Oct4-GFP embryonic stem cells, we mimic the in vivo development procedure to induce ES cells into epiblast cell-like cells (EpiLCs) and then primordial germ cell-like cells (PGCLCs). GFP positive PGCLCs that showed typical PGC markers and epigenetic modification were efficiently obtained. Further transplantation of the GFP positive PGCLC and native ovary cell mixture into ovary of infertile mice revealed that both MVH and GFP positive cells could be developed in ovary, but no later developmental stage germ cells were observed. This study suggested that Oct4-GFP ES cells may be only suitable for tracing early germ cell development.
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Affiliation(s)
- Xin Ma
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Shenzhen Futian Hospital for Rheumatic Disease, No.22 Nonglin Road, Shenzhen, China
| | - Peng Li
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiang Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yifeng Sun
- Sing Loong Limited, Hong Kong SAR, China
| | - Rong Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
| | - Ping Yuan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong, 510655, China
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40
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Seki Y. PRDM14 Is a Unique Epigenetic Regulator Stabilizing Transcriptional Networks for Pluripotency. Front Cell Dev Biol 2018; 6:12. [PMID: 29487849 PMCID: PMC5816753 DOI: 10.3389/fcell.2018.00012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
PR-domain containing protein 14 (PRDM14) is a site-specific DNA-binding protein and is required for establishment of pluripotency in embryonic stem cells (ESCs) and primordial germ cells (PGCs) in mice. DNA methylation status is regulated by the balance between de novo methylation and passive/active demethylation, and global DNA hypomethylation is closely associated with cellular pluripotency and totipotency. PRDM14 ensures hypomethylation in mouse ESCs and PGCs through two distinct layers, transcriptional repression of the DNA methyltransferases Dnmt3a/b/l and active demethylation by recruitment of TET proteins. However, the function of PRDM14 remains unclear in other species including humans. Hence, here we focus on the unique characteristics of mouse PRDM14 in the epigenetic regulation of pluripotent cells and primordial germ cells. In addition, we discuss the expression regulation and function of PRDM14 in other species compared with those in mice.
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Affiliation(s)
- Yoshiyuki Seki
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Hyogo, Japan
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41
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Huang H, Dou L, Song J, Luo J. CBFA2T2 is required for BMP-2-induced osteogenic differentiation of mesenchymal stem cells. Biochem Biophys Res Commun 2018; 496:1095-1101. [DOI: 10.1016/j.bbrc.2018.01.144] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/23/2018] [Indexed: 01/06/2023]
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42
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The smallest de novo 20q11.2 microdeletion causing intellectual disability and dysmorphic features. Hum Genome Var 2017; 4:17050. [PMID: 29214040 PMCID: PMC5707190 DOI: 10.1038/hgv.2017.50] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/08/2017] [Accepted: 09/15/2017] [Indexed: 11/23/2022] Open
Abstract
The 20q11.2 microdeletion is a rare chromosomal aberration characterized by intellectual disability (ID), motor developmental delay, neonatal feeding problems, and facial dysmorphism. Here, a 2-year- and 6-month-old Japanese girl with a 1.2 Mb microdeletion of 20q11.2 showed ID, motor developmental delay, and distinctive facial features without feeding problems. The deleted region was identified by array-based comparative genomic hybridization and is the smallest reported for a 20q11.2 microdeletion.
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43
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Chen DC, Liang YD, Peng L, Wang YZ, Ai CZ, Zhu XX, Yan YW, Saeed Y, Yu B, Huang J, Gao Y, Liu J, Jiang YZ, Liu M, Chen D. CBFA2T2 is associated with a cancer stem cell state in renal cell carcinoma. Cancer Cell Int 2017; 17:103. [PMID: 29162985 PMCID: PMC5686942 DOI: 10.1186/s12935-017-0473-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 11/06/2017] [Indexed: 12/13/2022] Open
Abstract
Background Renal cell carcinoma (RCC) is the most common kidney cancer, accounting for approximately 80–90% of all primary kidney cancer. Treatment for patients with advanced RCC remains unsatisfactory. Rare cancer stem cells (CSCs) are proposed to be responsible for failure of current treatment. Methods OncoLnc was used as a tool for interactively exploring survival correlations. Gene manipulation and expression analysis were carried out using siRNA, RT-PCR and Western blotting. Wound healing and invasion assays were used for phenotypical characterization. Aldefluor assay and FACS sorting Sphere culture were used to determine the “stemness” of CSCs. Co-Immunoprecipitation (Co-IP) was used to examine the interaction between OCT4 and CBFA2T2. Student’s t-test and Chi square test was used to analyze statistical significance. Results CBFA2T2 expression can significantly predict the survival of RCC patients. Knocking-down of CBFA2T2 can inhibit cell migration and invasion in RCC cells in vitro, and reduce ALDHhigh CSCs populations. CBFA2T2 expression is necessary for sphere-forming ability and cancer stem cells marker expression in RCC cell lines. Conclusions Our data suggest that CBFA2T2 expression correlates with aggressive characteristics of RCC and CBFA2T2 is required for maintenance of “stemness” through regulation of stem cells factors, thereby highlighting CBFA2T2 as a potential therapeutic target for RCC treatment. Electronic supplementary material The online version of this article (10.1186/s12935-017-0473-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Du-Chu Chen
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 Fujian China.,Department of Oncology, Chinese PLA General Hospital, Beijing, 100853 China
| | - You-De Liang
- Department of Stomatology, Nanshan Affiliated Hospital of Guangdong Medical College, Shenzhen, 518060 Guangdong China
| | - Liang Peng
- Department of Oncology, Chinese PLA General Hospital, Beijing, 100853 China
| | - Yi-Ze Wang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Chun-Zhi Ai
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Xin-Xing Zhu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Ya-Wei Yan
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Yasmeen Saeed
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Bin Yu
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 Fujian China
| | - Jingying Huang
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 Fujian China
| | - Yuxin Gao
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 Fujian China
| | - Jiaqi Liu
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 Fujian China
| | - Yi-Zhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Min Liu
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 Fujian China
| | - Demeng Chen
- The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510275 Guangdong People's Republic of China
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44
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Mzoughi S, Zhang J, Hequet D, Teo SX, Fang H, Xing QR, Bezzi M, Seah MKY, Ong SLM, Shin EM, Wollmann H, Wong ESM, Al-Haddawi M, Stewart CL, Tergaonkar V, Loh YH, Dunn NR, Messerschmidt DM, Guccione E. PRDM15 safeguards naive pluripotency by transcriptionally regulating WNT and MAPK-ERK signaling. Nat Genet 2017; 49:1354-1363. [PMID: 28740264 DOI: 10.1038/ng.3922] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 06/30/2017] [Indexed: 12/11/2022]
Abstract
The transcriptional network acting downstream of LIF, WNT and MAPK-ERK to stabilize mouse embryonic stem cells (ESCs) in their naive state has been extensively characterized. However, the upstream factors regulating these three signaling pathways remain largely uncharted. PR-domain-containing proteins (PRDMs) are zinc-finger sequence-specific chromatin factors that have essential roles in embryonic development and cell fate decisions. Here we characterize the transcriptional regulator PRDM15, which acts independently of PRDM14 to regulate the naive state of mouse ESCs. Mechanistically, PRDM15 modulates WNT and MAPK-ERK signaling by directly promoting the expression of Rspo1 (R-spondin1) and Spry1 (Sprouty1). Consistent with these findings, CRISPR-Cas9-mediated disruption of PRDM15-binding sites in the Rspo1 and Spry1 promoters recapitulates PRDM15 depletion, both in terms of local chromatin organization and the transcriptional modulation of these genes. Collectively, our findings uncover an essential role for PRDM15 as a chromatin factor that modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency.
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Affiliation(s)
- Slim Mzoughi
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jingxian Zhang
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Delphine Hequet
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Shun Xie Teo
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Haitong Fang
- Epigenetics and Cell Fates Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Qiao Rui Xing
- Epigenetics and Cell Fates Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Marco Bezzi
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Michelle Kay Yi Seah
- Developmental Epigenetics and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Sheena L M Ong
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Eun Myoung Shin
- Cancer Science Institute of Singapore (CSI), National University of Singapore, Singapore.,NF-κB Signaling in Human Ailments, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Heike Wollmann
- DNA Sequencing Facility NGS Unit, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Esther S M Wong
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Colin L Stewart
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Vinay Tergaonkar
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NF-κB Signaling in Human Ailments, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,National Cancer Centre Singapore, Singapore.,Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - N Ray Dunn
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Daniel M Messerschmidt
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Developmental Epigenetics and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ernesto Guccione
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer Science Institute of Singapore (CSI), National University of Singapore, Singapore.,National Cancer Centre Singapore, Singapore.,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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45
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Abstract
The tripartite network of Prdm14, Blimp1, and AP2γ is essential for the important process of germ cell specification, but their precise molecular mechanisms of action remain lacking. Tu and colleagues (2016) report in Nature that the transcriptional co-repressor CBFA2T2 is an essential interactor protein regulating PRDM14 function, shedding light into the mechanisms directing germline formation and pluripotency.
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Affiliation(s)
- Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany.
| | - Maria-Elena Torres-Padilla
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964, 67404 Illkirch, CU de Strasbourg, France; Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany
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46
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Kumar DL, DeFalco T. Of Mice and Men: In Vivo and In Vitro Studies of Primordial Germ Cell Specification. Semin Reprod Med 2017; 35:139-146. [PMID: 28278531 DOI: 10.1055/s-0037-1599085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Specification of mouse primordial germ cells (PGCs), the precursors of sperm and eggs, involves three major molecular events: repression of the somatic program, reacquisition of pluripotency, and reprogramming to a unique epigenetic ground state. Gene knockout studies in mouse models, along with global transcriptome analyses, have revealed the key signaling pathways and transcription factors essential for PGC specification. Knowledge obtained from these studies has been utilized extensively to develop robust in vitro PGC induction models not only in mice but also in humans. These models have, in turn, formed the basis for a detailed understanding of the signaling pathways and epigenetic dynamics during in vivo PGC specification and development. Recapitulation of human PGC specification in culture is of tremendous significance for understanding the mechanisms of human germ cell development in normal and disease states and has implications for addressing germ-cell-based causes of infertility.
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Affiliation(s)
- Deepti Lava Kumar
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Tony DeFalco
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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47
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Abstract
Pluripotency is a state that exists transiently in the early embryo and, remarkably, can be recapitulated in vitro by deriving embryonic stem cells or by reprogramming somatic cells to become induced pluripotent stem cells. The state of pluripotency, which is stabilized by an interconnected network of pluripotency-associated genes, integrates external signals and exerts control over the decision between self-renewal and differentiation at the transcriptional, post-transcriptional and epigenetic levels. Recent evidence of alternative pluripotency states indicates the regulatory flexibility of this network. Insights into the underlying principles of the pluripotency network may provide unprecedented opportunities for studying development and for regenerative medicine.
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48
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Abstract
In an effort to identify a chromatin-associated pluripotent network, Rafiee et al., (2016) developed a powerful ChIP-MS technique and discovered a novel protein, TRIM24, enriched on OCT4-, SOX2-, and NANOG-associated chromatin, paving the way for future proteomic studies on chromatin.
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Affiliation(s)
- Shengjiang Tu
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
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49
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Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J. Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins. Mol Cell 2016; 64:624-635. [PMID: 27773674 PMCID: PMC5101186 DOI: 10.1016/j.molcel.2016.09.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/11/2016] [Accepted: 09/14/2016] [Indexed: 12/13/2022]
Abstract
Maintenance of pluripotency is regulated by a network of transcription factors coordinated by Oct4, Sox2, and Nanog (OSN), yet a systematic investigation of the composition and dynamics of the OSN protein network specifically on chromatin is still missing. Here we have developed a method combining ChIP with selective isolation of chromatin-associated proteins (SICAP) followed by mass spectrometry to identify chromatin-bound partners of a protein of interest. ChIP-SICAP in mouse embryonic stem cells (ESCs) identified over 400 proteins associating with OSN, including several whose interaction depends on the pluripotent state. Trim24, a previously unrecognized protein in the network, converges with OSN on multiple enhancers and suppresses the expression of developmental genes while activating cell cycle genes. Consistently, Trim24 significantly improved efficiency of cellular reprogramming, demonstrating its direct functionality in establishing pluripotency. Collectively, ChIP-SICAP provides a powerful tool to decode chromatin protein composition, further enhanced by its integrative capacity to perform ChIP-seq. ChIP-SICAP isolates and identifies proteins that colocalize on chromatin Chromatin composition around Oct4, Sox2, and Nanog depends on the pluripotent state Trim24 is part of the pluripotency network and promotes reprogramming ChIP-SICAP allows recovery of DNA for sequencing with ChIP-seq quality
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Affiliation(s)
- Mahmoud-Reza Rafiee
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gianluca Sigismondo
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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50
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Leitch HG, Surani MA, Hajkova P. DNA (De)Methylation: The Passive Route to Naïvety? Trends Genet 2016; 32:592-595. [DOI: 10.1016/j.tig.2016.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/08/2016] [Indexed: 11/27/2022]
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