1
|
Huber PB, Rao A, LaBonne C. BET activity plays an essential role in control of stem cell attributes in Xenopus. Development 2024; 151:dev202990. [PMID: 38884356 PMCID: PMC11266789 DOI: 10.1242/dev.202990] [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: 04/26/2024] [Accepted: 05/31/2024] [Indexed: 06/18/2024]
Abstract
Neural crest cells are a stem cell population unique to vertebrate embryos that retains broad multi-germ layer developmental potential through neurulation. Much remains to be learned about the genetic and epigenetic mechanisms that control the potency of neural crest cells. Here, we examine the role that epigenetic readers of the BET (bromodomain and extra terminal) family play in controlling the potential of pluripotent blastula and neural crest cells. We find that inhibiting BET activity leads to loss of pluripotency at blastula stages and a loss of neural crest at neurula stages. We compare the effects of HDAC (an eraser of acetylation marks) and BET (a reader of acetylation) inhibition and find that they lead to similar cellular outcomes through distinct effects on the transcriptome. Interestingly, loss of BET activity in cells undergoing lineage restriction is coupled to increased expression of genes linked to pluripotency and prolongs the competence of initially pluripotent cells to transit to a neural progenitor state. Together these findings advance our understanding of the epigenetic control of pluripotency and the formation of the vertebrate neural crest.
Collapse
Affiliation(s)
- Paul B. Huber
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University, Evanston, IL 60208, USA
| | - Anjali Rao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
2
|
Yoneyama Y, Zhang RR, Kimura M, Cai Y, Adam M, Parameswaran S, Masaki H, Mizuno N, Bhadury J, Maezawa S, Ochiai H, Nakauchi H, Potter SS, Weirauch MT, Takebe T. Inter-cellular mRNA Transfer Alters Human Pluripotent Stem Cell State. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600209. [PMID: 38979277 PMCID: PMC11230441 DOI: 10.1101/2024.06.27.600209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Inter-cellular transmission of mRNA is being explored in mammalian species using immortal cell lines (1-3). Here, we uncover an inter-cellular mRNA transfer phenomenon that allows for the adaptation and reprogramming of human primed pluripotent stem cells (hPSCs). This process is induced by the direct cell contact-mediated coculture with mouse embryonic stem cells (mESCs) under the condition impermissible for human primed PSC culture. Mouse-derived mRNA contents are transmitted into adapted hPSCs only in the coculture. Transfer-specific mRNA analysis show the enrichment for divergent biological pathways involving transcription/translational machinery and stress-coping mechanisms, wherein such transfer is diminished when direct cell contacts are lost. After 5 days of mESC culture, surface marker analysis, and global gene profiling confirmed that mRNA transfer-prone hPSC efficiently gains a naïve-like state. Furthermore, transfer-specific knockdown experiments targeting mouse-specific transcription factor-coding mRNAs in hPSC show that mouse-derived Tfcp2l1, Tfap2c, and Klf4 are indispensable for human naïve-like conversion. Thus, inter-species mRNA transfer triggers cellular reprogramming in mammalian cells. Our results support that episodic mRNA transfer can occur in cell cooperative and competitive processes(4), which provides a fresh perspective on understanding the roles of mRNA mobility for intra- and inter-species cellular communications.
Collapse
Affiliation(s)
- Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ran-Ran Zhang
- Divisions of Gastroenterology, Hepatology & Nutrition, Developmental Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Masaki Kimura
- Divisions of Gastroenterology, Hepatology & Nutrition, Developmental Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Yuqi Cai
- Divisions of Gastroenterology, Hepatology & Nutrition, Developmental Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Mike Adam
- Divisions of Gastroenterology, Hepatology & Nutrition, Developmental Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Hideki Masaki
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Naoaki Mizuno
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Joydeep Bhadury
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - So Maezawa
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Chiba, 278-8510, Japan
| | - Hiroshi Ochiai
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - S. Steven Potter
- Divisions of Gastroenterology, Hepatology & Nutrition, Developmental Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Matthew T. Weirauch
- Divisions of Gastroenterology, Hepatology & Nutrition, Developmental Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Takanori Takebe
- Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Divisions of Gastroenterology, Hepatology & Nutrition, Developmental Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
3
|
Zhu M, Meglicki M, Lamba A, Wang P, Royer C, Turner K, Jauhar MA, Jones C, Child T, Coward K, Na J, Zernicka-Goetz M. Tead4 and Tfap2c generate bipotency and a bistable switch in totipotent embryos to promote robust lineage diversification. Nat Struct Mol Biol 2024; 31:964-976. [PMID: 38789684 PMCID: PMC11189297 DOI: 10.1038/s41594-024-01311-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
The mouse and human embryo gradually loses totipotency before diversifying into the inner cell mass (ICM, future organism) and trophectoderm (TE, future placenta). The transcription factors TFAP2C and TEAD4 with activated RHOA accelerate embryo polarization. Here we show that these factors also accelerate the loss of totipotency. TFAP2C and TEAD4 paradoxically promote and inhibit Hippo signaling before lineage diversification: they drive expression of multiple Hippo regulators while also promoting apical domain formation, which inactivates Hippo. Each factor activates TE specifiers in bipotent cells, while TFAP2C also activates specifiers of the ICM fate. Asymmetric segregation of the apical domain reconciles the opposing regulation of Hippo signaling into Hippo OFF and the TE fate, or Hippo ON and the ICM fate. We propose that the bistable switch established by TFAP2C and TEAD4 is exploited to trigger robust lineage diversification in the developing embryo.
Collapse
Affiliation(s)
- Meng Zhu
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maciej Meglicki
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Adiyant Lamba
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Peizhe Wang
- Centre for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Christophe Royer
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Karen Turner
- Oxford Fertility, Institute of Reproductive Sciences, Oxford, UK
| | - Muhammad Abdullah Jauhar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Celine Jones
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Tim Child
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Kevin Coward
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jie Na
- Centre for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
4
|
Wang L, Yi S, Cui X, Guo Z, Wang M, Kou X, Zhao Y, Wang H, Jiang C, Gao S, Yang G, Chen J, Gao R. Chromatin landscape instructs precise transcription factor regulome during embryonic lineage specification. Cell Rep 2024; 43:114136. [PMID: 38643480 DOI: 10.1016/j.celrep.2024.114136] [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] [Received: 11/29/2023] [Revised: 03/10/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
Embryos, originating from fertilized eggs, undergo continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Chromatin regulators, including transcription factors (TFs), play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was identified as crucial in initiating early cell fate decisions. However, Tfap2c transcripts persist in both the inner cell mass and trophectoderm of blastocysts, prompting inquiry into Tfap2c's function in post-lineage establishment. In this study, we delineate the dynamics of TFAP2C during the mouse peri-implantation stage and elucidate its collaboration with the key lineage regulators CDX2 and NANOG. Importantly, we propose that de novo formation of H3K9me3 in the extraembryonic ectoderm during implantation antagonizes TFAP2C binding to crucial developmental genes, thereby maintaining its lineage identity. Together, these results highlight the plasticity of the chromatin environment in designating the genomic binding of highly adaptable lineage-specific TFs and regulating embryonic cell fates.
Collapse
Affiliation(s)
- Liping Wang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mengting Wang
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai 200120, China.
| | - Guang Yang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Rui 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| |
Collapse
|
5
|
Zhu Z, Dong S, Qin S, Gu K, Zhou Y. ANOS1 accelerates the progression of esophageal cancer identified by multi-omic approaches. Am J Cancer Res 2024; 14:2343-2370. [PMID: 38859828 PMCID: PMC11162658 DOI: 10.62347/spcp3536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/27/2024] [Indexed: 06/12/2024] Open
Abstract
To assess the role of ANOS1 in esophageal cancer (ESCA) progression, multi-omic analysis and experimental validation were employed. It was revealed that ANOS1 expression is significantly enhanced in ESCA patients and cell lines. The expression level of ANOS1 in ESCA patients can distinguish the malignancy from normal tissue with an area under curve (AUC) >0.75. Moreover, increased expression of ANOS1 is associated with advanced T stage and worse disease-free survival of ESCA patients. Therefore, a clinically applicable nomogram with ANOS1 was established with strong predictive power. Furthermore, high expression of ANOS1 in ESCA is correlated with (i) the enrichment of epithelial-mesenchymal transition by gene set enrichment analysis, (ii) the involvement in hypoxia, angiogenesis, WNT signaling pathway, and TGFβ signaling pathway by gene set variation analysis, (iii) the presence of the small insertion and deletion mutational signature ID9, associated with chromothripsis, in the single-nucleotide polymorphism analysis, (iv) the amplification of 11q13.3 in the copy number variants analysis, (v) the enrichment of cancer-associated fibroblasts and mesenchymal stromal cells in the tumor microenvironment. All the results from multi-omic analysis indicate that ANOS1 plays a pivotal role in accelerating the progression of ESCA. Results from in vivo and in vitro experiments show that the knockdown of ANOS1 hampers the proliferation of ESCA cells, further validating the oncogenic role of ANOS1 in ESCA. Additionally, potential chemotherapeutics with sensitivity were identified in the high-ANOS1 group. In conclusion, ANOS1 accelerates the progression of ESCA.
Collapse
Affiliation(s)
- Zuoquan Zhu
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Shikun Dong
- Department of Otorhinolaryngology, Zhongda Hospital, Southeast UniversityNanjing 210009, Jiangsu, China
| | - Shaolei Qin
- Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Ke Gu
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Yanjun Zhou
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| |
Collapse
|
6
|
Li N, Jin K, Liu B, Yang M, Shi P, Heng D, Wang J, Liu L. Single-cell 3D genome structure reveals distinct human pluripotent states. Genome Biol 2024; 25:122. [PMID: 38741214 PMCID: PMC11089717 DOI: 10.1186/s13059-024-03268-w] [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: 05/23/2023] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Pluripotent states of embryonic stem cells (ESCs) with distinct transcriptional profiles affect ESC differentiative capacity and therapeutic potential. Although single-cell RNA sequencing has revealed additional subpopulations and specific features of naive and primed human pluripotent stem cells (hPSCs), the underlying mechanisms that regulate their specific transcription and that control their pluripotent states remain elusive. RESULTS By single-cell analysis of high-resolution, three-dimensional (3D) genomic structure, we herein demonstrate that remodeling of genomic structure is highly associated with the pluripotent states of human ESCs (hESCs). The naive pluripotent state is featured with specialized 3D genomic structures and clear chromatin compartmentalization that is distinct from the primed state. The naive pluripotent state is achieved by remodeling the active euchromatin compartment and reducing chromatin interactions at the nuclear center. This unique genomic organization is linked to enhanced chromatin accessibility on enhancers and elevated expression levels of naive pluripotent genes localized to this region. In contradistinction, the primed state exhibits intermingled genomic organization. Moreover, active euchromatin and primed pluripotent genes are distributed at the nuclear periphery, while repressive heterochromatin is densely concentrated at the nuclear center, reducing chromatin accessibility and the transcription of naive genes. CONCLUSIONS Our data provide insights into the chromatin structure of ESCs in their naive and primed states, and we identify specific patterns of modifications in transcription and chromatin structure that might explain the genes that are differentially expressed between naive and primed hESCs. Thus, the inversion or relocation of heterochromatin to euchromatin via compartmentalization is related to the regulation of chromatin accessibility, thereby defining pluripotent states and cellular identity.
Collapse
Affiliation(s)
- Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Weifang People's Hospital, Shandong, 261041, China
| | - Kairang Jin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Bin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Weifang People's Hospital, Shandong, 261041, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
| | - Mingzhu Yang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - PanPan Shi
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Dai Heng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jichang Wang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China.
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
| |
Collapse
|
7
|
Gao R, Yang G, Wang M, Xiao J, Yi S, Huang Y, Guo Z, Kang Y, Fu Q, Wang M, Xu B, Shen S, Zhu Q, Liu M, Wang L, Cui X, Yi S, Kou X, Zhao Y, Gu L, Wang H, Gao S, Jiang C, Chen J. Defining a TFAP2C-centered transcription factor network during murine peri-implantation. Dev Cell 2024; 59:1146-1158.e6. [PMID: 38574734 DOI: 10.1016/j.devcel.2024.03.015] [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] [Received: 05/24/2023] [Revised: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 04/06/2024]
Abstract
Transcription factors (TFs) play important roles in early embryonic development, but factors regulating TF action, relationships in signaling cascade, genome-wide localizations, and impacts on cell fate transitions during this process have not been clearly elucidated. In this study, we used uliCUT&RUN-seq to delineate a TFAP2C-centered regulatory network, showing that it involves promoter-enhancer interactions and regulates TEAD4 and KLF5 function to mediate cell polarization. Notably, we found that maternal retinoic acid metabolism regulates TFAP2C expression and function by inducing the active demethylation of SINEs, indicating that the RARG-TFAP2C-TEAD4/KLF5 axis connects the maternal-to-zygotic transition to polarization. Moreover, we found that both genomic imprinting and SNP-transferred genetic information can influence TF positioning to regulate parental gene expressions in a sophisticated manner. In summary, we propose a ternary model of TF regulation in murine embryonic development with TFAP2C as the core element and metabolic, epigenetic, and genetic information as nodes connecting the pathways.
Collapse
Affiliation(s)
- Rui 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Guang Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Mengting Wang
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jing Xiao
- 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; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanxin Huang
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yunzhe Kang
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianzheng Fu
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mingzhu Wang
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Ben Xu
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shijun Shen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Meng Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanshan Yi
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- 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; Frontier Science Center for Stem Cell Research, 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai 200120, China.
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, 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; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| |
Collapse
|
8
|
Abeywardana T, Wu X, Huang ST, Aldana Masangkay G, Rodin AS, Branciamore S, Gogoshin G, Li A, Du L, Tharuka N, Tomaino R, Chen Y. Regulation of Enhancers by SUMOylation Through TFAP2C Binding and Recruitment of HDAC Complex to the Chromatin. RESEARCH SQUARE 2024:rs.3.rs-4201913. [PMID: 38645262 PMCID: PMC11030540 DOI: 10.21203/rs.3.rs-4201913/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Enhancers are fundamental to gene regulation. Post-translational modifications by the small ubiquitin-like modifiers (SUMO) modify chromatin regulation enzymes, including histone acetylases and deacetylases. However, it remains unclear whether SUMOylation regulates enhancer marks, acetylation at the 27th lysine residue of the histone H3 protein (H3K27Ac). To investigate whether SUMOylation regulates H3K27Ac, we performed genome-wide ChIP-seq analyses and discovered that knockdown (KD) of the SUMO activating enzyme catalytic subunit UBA2 reduced H3K27Ac at most enhancers. Bioinformatic analysis revealed that TFAP2C-binding sites are enriched in enhancers whose H3K27Ac was reduced by UBA2 KD. ChIP-seq analysis in combination with molecular biological methods showed that TFAP2C binding to enhancers increased upon UBA2 KD or inhibition of SUMOylation by a small molecule SUMOylation inhibitor. However, this is not due to the SUMOylation of TFAP2C itself. Proteomics analysis of TFAP2C interactome on the chromatin identified histone deacetylation (HDAC) and RNA splicing machineries that contain many SUMOylation targets. TFAP2C KD reduced HDAC1 binding to chromatin and increased H3K27Ac marks at enhancer regions, suggesting that TFAP2C is important in recruiting HDAC machinery. Taken together, our findings provide insights into the regulation of enhancer marks by SUMOylation and TFAP2C and suggest that SUMOylation of proteins in the HDAC machinery regulates their recruitments to enhancers.
Collapse
Affiliation(s)
| | - Xiwei Wu
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | | | | | - Andrei S Rodin
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | - Sergio Branciamore
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | - Grigoriy Gogoshin
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | - Arthur Li
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | - Li Du
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | | | - Ross Tomaino
- Harvard Medical School Taplin Mass Spectrometry Facility
| | | |
Collapse
|
9
|
Driscoll CS, Kim J, Ashry M, Knott JG. Does TFAP2C govern conflicting cell fates in mouse preimplantation embryos? Reproduction 2024; 167:e230440. [PMID: 38165360 PMCID: PMC10967010 DOI: 10.1530/rep-23-0440] [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: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 01/03/2024]
Abstract
Transcription factor AP2 gamma (TFAP2C) is a well-established regulator of the trophoblast lineage in mice and humans, but a handful of studies indicate that TFAP2C may play an important role in pluripotency. Here, we hypothesize and provide new evidence that TFAP2C functions as an activator of trophoblast and pluripotency genes during preimplantation embryo development.
Collapse
Affiliation(s)
| | | | - Mohamed Ashry
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | - Jason G. Knott
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
10
|
Okubo T, Rivron N, Kabata M, Masaki H, Kishimoto K, Semi K, Nakajima-Koyama M, Kunitomi H, Kaswandy B, Sato H, Nakauchi H, Woltjen K, Saitou M, Sasaki E, Yamamoto T, Takashima Y. Hypoblast from human pluripotent stem cells regulates epiblast development. Nature 2024; 626:357-366. [PMID: 38052228 PMCID: PMC10849967 DOI: 10.1038/s41586-023-06871-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Recently, several studies using cultures of human embryos together with single-cell RNA-seq analyses have revealed differences between humans and mice, necessitating the study of human embryos1-8. Despite the importance of human embryology, ethical and legal restrictions have limited post-implantation-stage studies. Thus, recent efforts have focused on developing in vitro self-organizing models using human stem cells9-17. Here, we report genetic and non-genetic approaches to generate authentic hypoblast cells (naive hPSC-derived hypoblast-like cells (nHyCs))-known to give rise to one of the two extraembryonic tissues essential for embryonic development-from naive human pluripotent stem cells (hPSCs). Our nHyCs spontaneously assemble with naive hPSCs to form a three-dimensional bilaminar structure (bilaminoids) with a pro-amniotic-like cavity. In the presence of additional naive hPSC-derived analogues of the second extraembryonic tissue, the trophectoderm, the efficiency of bilaminoid formation increases from 20% to 40%, and the epiblast within the bilaminoids continues to develop in response to trophectoderm-secreted IL-6. Furthermore, we show that bilaminoids robustly recapitulate the patterning of the anterior-posterior axis and the formation of cells reflecting the pregastrula stage, the emergence of which can be shaped by genetically manipulating the DKK1/OTX2 hypoblast-like domain. We have therefore successfully modelled and identified the mechanisms by which the two extraembryonic tissues efficiently guide the stage-specific growth and progression of the epiblast as it establishes the post-implantation landmarks of human embryogenesis.
Collapse
Affiliation(s)
- Takumi Okubo
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Nicolas Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Mio Kabata
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Hideki Masaki
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Advanced Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Katsunori Semi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - May Nakajima-Koyama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Haruko Kunitomi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Belinda Kaswandy
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Hideyuki Sato
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Advanced Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiromitsu Nakauchi
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Advanced Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Knut Woltjen
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Mitinori Saitou
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Erika Sasaki
- Central Institute for Experimental Animals, Kawasaki, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan.
| | - Yasuhiro Takashima
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.
| |
Collapse
|
11
|
Alanis-Lobato G, Bartlett TE, Huang Q, Simon CS, McCarthy A, Elder K, Snell P, Christie L, Niakan KK. MICA: a multi-omics method to predict gene regulatory networks in early human embryos. Life Sci Alliance 2024; 7:e202302415. [PMID: 37879938 PMCID: PMC10599980 DOI: 10.26508/lsa.202302415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
Recent advances in single-cell omics have transformed characterisation of cell types in challenging-to-study biological contexts. In contexts with limited single-cell samples, such as the early human embryo inference of transcription factor-gene regulatory network (GRN) interactions is especially difficult. Here, we assessed application of different linear or non-linear GRN predictions to single-cell simulated and human embryo transcriptome datasets. We also compared how expression normalisation impacts on GRN predictions, finding that transcripts per million reads outperformed alternative methods. GRN inferences were more reproducible using a non-linear method based on mutual information (MI) applied to single-cell transcriptome datasets refined with chromatin accessibility (CA) (called MICA), compared with alternative network prediction methods tested. MICA captures complex non-monotonic dependencies and feedback loops. Using MICA, we generated the first GRN inferences in early human development. MICA predicted co-localisation of the AP-1 transcription factor subunit proto-oncogene JUND and the TFAP2C transcription factor AP-2γ in early human embryos. Overall, our comparative analysis of GRN prediction methods defines a pipeline that can be applied to single-cell multi-omics datasets in especially challenging contexts to infer interactions between transcription factor expression and target gene regulation.
Collapse
Affiliation(s)
| | | | - Qiulin Huang
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
- https://ror.org/013meh722 Department of Physiology, Development and Neuroscience, The Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Claire S Simon
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | | | | | | | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, UK
- https://ror.org/013meh722 Department of Physiology, Development and Neuroscience, The Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- https://ror.org/013meh722 Wellcome - Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| |
Collapse
|
12
|
Li Q, Qin K, Tian Y, Chen B, Zhao G, Xu S, Wu L. Inhibition of demethylase by IOX1 modulates chromatin accessibility to enhance NSCLC radiation sensitivity through attenuated PIF1. Cell Death Dis 2023; 14:817. [PMID: 38086789 PMCID: PMC10716120 DOI: 10.1038/s41419-023-06346-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Chromatin accessibility is a critical determinant of gene transcriptional expression and regulated by histones modification. However, the potential for manipulating chromatin accessibility to regulate radiation sensitivity remains unclear. Our findings demonstrated that the histone demethylase inhibitor, 5-carboxy-8-hydroxyquinoline (IOX1), could enhance the radiosensitivity of non-small cell lung cancer (NSCLC) in vitro and in vivo. Mechanistically, IOX1 treatment reduced chromatin accessibility in the promoter region of DNA damage repair genes, leading to decreased DNA repair efficiency and elevated DNA damage induced by γ irradiation. Notably, IOX1 treatment significantly reduced both chromatin accessibility and the transcription of phytochrome interacting factor 1 (PIF1), a key player in telomere maintenance. Inhibition of PIF1 delayed radiation-induced DNA and telomeric DNA damage repair, as well as increased radiosensitivity of NSCLC in vitro and in vivo. Further study indicated that the above process was regulated by a reduction of transcription factor myc-associated zinc finger protein (MAZ) binding to the distal intergenic region of the PIF1. Taken together, IOX1-mediated demethylase inactivation reduced chromatin accessibility, leading to elevated telomere damage which is partly due to PIF1 inhibition, thereby enhancing NSCLC radiosensitivity.
Collapse
Affiliation(s)
- Qian Li
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Kexin Qin
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Yushan Tian
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, Henan, 450001, PR China
| | - Biao Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Guoping Zhao
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China.
| | - Lijun Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China.
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China.
| |
Collapse
|
13
|
Hwang YS, Seita Y, Blanco MA, Sasaki K. CRISPR loss of function screening to identify genes involved in human primordial germ cell-like cell development. PLoS Genet 2023; 19:e1011080. [PMID: 38091369 PMCID: PMC10752514 DOI: 10.1371/journal.pgen.1011080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/27/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023] Open
Abstract
Despite our increasing knowledge of molecular mechanisms guiding various aspects of human reproduction, those underlying human primordial germ cell (PGC) development remain largely unknown. Here, we conducted custom CRISPR screening in an in vitro system of human PGC-like cells (hPGCLCs) to identify genes required for acquisition and maintenance of PGC fate. Amongst our candidates, we identified TCL1A, an AKT coactivator. Functional assessment in our in vitro hPGCLCs system revealed that TCL1A played a critical role in later stages of hPGCLC development. Moreover, we found that TCL1A loss reduced AKT-mTOR signaling, downregulated expression of genes related to translational control, and subsequently led to a reduction in global protein synthesis and proliferation. Together, our study highlights the utility of CRISPR screening for human in vitro-derived germ cells and identifies novel translational regulators critical for hPGCLC development.
Collapse
Affiliation(s)
- Young Sun Hwang
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yasunari Seita
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - M. Andrés Blanco
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
14
|
Alberca CD, Papale LA, Madrid A, Alisch RS. Hippocampal and peripheral blood DNA methylation signatures correlate at the gene and pathway level in a mouse model of autism. Hum Mol Genet 2023; 32:3312-3322. [PMID: 37658766 DOI: 10.1093/hmg/ddad137] [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: 05/08/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Autism spectrum disorders (ASD) are polygenic multifactorial disorders influenced by environmental factors. ASD-related differential DNA methylation has been found in human peripheral tissues, such as placenta, paternal sperm, buccal epithelium, and blood. However, these data lack direct comparison of DNA methylation levels with brain tissue from the same individual to determine the extent that peripheral tissues are surrogates for behavior-related disorders. Here, whole genome methylation profiling at all the possible sites throughout the mouse genome (>25 million) from both brain and blood tissues revealed novel insights into the systemic contributions of DNA methylation to ASD. Sixty-six differentially methylated regions (DMRs) share the same genomic coordinates in these two tissues, many of which are linked to risk genes for neurodevelopmental disorders and intellectual disabilities (e.g. Prkch, Ptn, Hcfc1, Mid1, and Nfia). Gene ontological pathways revealed a significant number of common terms between brain and blood (N = 65 terms), and nearly half (30/65) were associated with brain/neuronal development. Furthermore, seven DMR-associated genes among these terms contain methyl-sensitive transcription factor sequence motifs within the DMRs of both tissues; four of them (Cux2, Kcnip2, Fgf13, and Mrtfa) contain the same methyl-sensitive transcription factor binding sequence motifs (HES1/2/5, TBX2 and TFAP2C), suggesting DNA methylation influences the binding of common transcription factors required for gene expression. Together, these findings suggest that peripheral blood is a good surrogate tissue for brain and support that DNA methylation contributes to altered gene regulation in the pathogenesis of ASD.
Collapse
Affiliation(s)
- Carolina D Alberca
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| |
Collapse
|
15
|
Pulver C, Grun D, Duc J, Sheppard S, Planet E, Coudray A, de Fondeville R, Pontis J, Trono D. Statistical learning quantifies transposable element-mediated cis-regulation. Genome Biol 2023; 24:258. [PMID: 37950299 PMCID: PMC10637000 DOI: 10.1186/s13059-023-03085-7] [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: 08/16/2022] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryogenesis to innate immune responses. Because of their repetitive nature, TEs have the potential to form CRE platforms enabling the coordinated and genome-wide regulation of protein-coding genes by only a handful of trans-acting transcription factors (TFs). RESULTS Here, we directly test this hypothesis through mathematical modeling and demonstrate that differences in expression at protein-coding genes alone are sufficient to estimate the magnitude and significance of TE-contributed cis-regulatory activities, even in contexts where TE-derived transcription fails to do so. We leverage hundreds of overexpression experiments and estimate that, overall, gene expression is influenced by TE-embedded CREs situated within approximately 500 kb of promoters. Focusing on the cis-regulatory potential of TEs within the gene regulatory network of human embryonic stem cells, we find that pluripotency-specific and evolutionarily young TE subfamilies can be reactivated by TFs involved in post-implantation embryogenesis. Finally, we show that TE subfamilies can be split into truly regulatorily active versus inactive fractions based on additional information such as matched epigenomic data, observing that TF binding may better predict TE cis-regulatory activity than differences in histone marks. CONCLUSION Our results suggest that TE-embedded CREs contribute to gene regulation during and beyond gastrulation. On a methodological level, we provide a statistical tool that infers TE-dependent cis-regulation from RNA-seq data alone, thus facilitating the study of TEs in the next-generation sequencing era.
Collapse
Affiliation(s)
- Cyril Pulver
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Delphine Grun
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Shaoline Sheppard
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Raphaël de Fondeville
- Swiss Data Science Center, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
| | - Julien Pontis
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- SOPHiA GENETICS SA, La Pièce 12, CH-1180, Rolle, Switzerland.
| | - Didier Trono
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
| |
Collapse
|
16
|
Tu Z, Bi Y, Mao T, Wang H, Gao S, Wang Y. Discordance between chromatin accessibility and transcriptional activity during the human primed-to-naïve pluripotency transition process. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:35. [PMID: 37938437 PMCID: PMC10632355 DOI: 10.1186/s13619-023-00179-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Naïve pluripotent state can be obtained by several strategies from various types of cells, in which the cell fate roadmap as well as key biological events involved in the journey have been described in detail. Here, we carefully explored the chromatin accessibility dynamics during the primed-to-naïve transition by adopting a dual fluorescent reporter system and the assay for transposase-accessible chromatin (ATAC)-seq. Our results revealed critical chromatin remodeling events and highlight the discordance between chromatin accessibility and transcriptional activity. We further demonstrate that the differential epigenetic modifications and transcription factor (TF) activities may play a critical role in regulating gene expression, and account for the observed variations in gene expression despite similar chromatin landscapes.
Collapse
Affiliation(s)
- Zhifen Tu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yan Bi
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Tengyan Mao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Hong Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| |
Collapse
|
17
|
Nair S, Ameen M, Sundaram L, Pampari A, Schreiber J, Balsubramani A, Wang YX, Burns D, Blau HM, Karakikes I, Wang KC, Kundaje A. Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560808. [PMID: 37873116 PMCID: PMC10592962 DOI: 10.1101/2023.10.04.560808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially during the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a densely sampled time course of human fibroblast reprogramming. Using neural networks that map DNA sequence to ATAC-seq profiles at base-resolution, we annotated cell-state-specific predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of Tn5-bias corrected TF footprints, linked peaks to putative target genes, and elucidated rewiring of TF-to-gene cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution, connect TF stoichiometry and motif syntax to diversification of cell fate trajectories, and provide new perspectives on the dynamics and role of transient regulatory elements in somatic silencing.
Collapse
Affiliation(s)
- Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Mohamed Ameen
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | | | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - David Burns
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| |
Collapse
|
18
|
Ermakova VV, Fokin NP, Aksenov ND, Bakhmet EI, Aleksandrova EV, Kuzmin AA, Tomilin AN. Regulatory Elements Outside Established Pou5f1 Gene Boundaries Are Required for Multilineage Differentiation of Embryonic Stem Cells. Int J Mol Sci 2023; 24:15434. [PMID: 37895112 PMCID: PMC10607089 DOI: 10.3390/ijms242015434] [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: 08/08/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The transcription factor Oct4 can rightfully be considered a pivotal element in maintaining pluripotency. In addition, its ability to function as a pioneer factor enables the reprogramming of somatic cells back into a pluripotent state. To better understand the regulation of the Oct4-encoding gene (Pou5f1), the main genetic elements that regulate its expression in different states of pluripotency ought to be identified. While some elements have been well characterized for their ability to drive Pou5f1 expression, others have yet to be determined. In this work, we show that translocation of the Pou5f1 gene fragment purported to span all essential cis-elements, including the well-known distal and proximal enhancers (DE and PE), into the Rosa26 locus impairs the self-renewal of mouse embryonic stem cells (ESCs) in the naïve pluripotency state, as well as their further advancement through the formative and primed pluripotency states, inducing overall differentiation failure. These results suggest that regulatory elements located outside the previously determined Pou5f1 boundaries are critical for the proper spatiotemporal regulation of this gene during development, indicating the need for their better characterization.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Alexey N. Tomilin
- Institute of Cytology, Russian Academy of Sciences, 194064 St.-Petersburg, Russia; (V.V.E.); (N.P.F.); (N.D.A.); (E.V.A.); (A.A.K.)
| |
Collapse
|
19
|
Maresca M, van den Brand T, Li H, Teunissen H, Davies J, de Wit E. Pioneer activity distinguishes activating from non-activating SOX2 binding sites. EMBO J 2023; 42:e113150. [PMID: 37691488 PMCID: PMC10577566 DOI: 10.15252/embj.2022113150] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 09/12/2023] Open
Abstract
Genome-wide transcriptional activity involves the binding of many transcription factors (TFs) to thousands of sites in the genome. Pioneer TFs are a class of TFs that maintain open chromatin and allow non-pioneer TFs access to their target sites. Determining which TF binding sites directly drive transcription remains a challenge. Here, we use acute protein depletion of the pioneer TF SOX2 to establish its functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of the pioneer factor. To understand the relationship with transcription, we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to all other SOX2 binding sites. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted mainly at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.
Collapse
Affiliation(s)
- Michela Maresca
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Teun van den Brand
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Hangpeng Li
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Hans Teunissen
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - James Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Elzo de Wit
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| |
Collapse
|
20
|
Agostinho de Sousa J, Wong CW, Dunkel I, Owens T, Voigt P, Hodgson A, Baker D, Schulz EG, Reik W, Smith A, Rostovskaya M, von Meyenn F. Epigenetic dynamics during capacitation of naïve human pluripotent stem cells. SCIENCE ADVANCES 2023; 9:eadg1936. [PMID: 37774033 PMCID: PMC10541016 DOI: 10.1126/sciadv.adg1936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are of fundamental relevance in regenerative medicine. Naïve hPSCs hold promise to overcome some of the limitations of conventional (primed) hPSCs, including recurrent epigenetic anomalies. Naïve-to-primed transition (capacitation) follows transcriptional dynamics of human embryonic epiblast and is necessary for somatic differentiation from naïve hPSCs. We found that capacitated hPSCs are transcriptionally closer to postimplantation epiblast than conventional hPSCs. This prompted us to comprehensively study epigenetic and related transcriptional changes during capacitation. Our results show that CpG islands, gene regulatory elements, and retrotransposons are hotspots of epigenetic dynamics during capacitation and indicate possible distinct roles of specific epigenetic modifications in gene expression control between naïve and primed hPSCs. Unexpectedly, PRC2 activity appeared to be dispensable for the capacitation. We find that capacitated hPSCs acquire an epigenetic state similar to conventional hPSCs. Significantly, however, the X chromosome erosion frequently observed in conventional female hPSCs is reversed by resetting and subsequent capacitation.
Collapse
Affiliation(s)
- João Agostinho de Sousa
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Chee-Wai Wong
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Ilona Dunkel
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thomas Owens
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Philipp Voigt
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Hodgson
- School of Biosciences, The Julia Garnham Centre, University of Sheffield, S10 2TN Sheffield, UK
| | - Duncan Baker
- Sheffield Diagnostic Genetics Services, Sheffield Children’s NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Edda G. Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1QR, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Altos Labs Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Austin Smith
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Living Systems Institute, University of Exeter, EX4 4QD Exeter, UK
| | - Maria Rostovskaya
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
- Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, SE1 9RT London, UK
| |
Collapse
|
21
|
Liu K, Xiao Y, Gan L, Li W, Zhang J, Min J. Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors. Nucleic Acids Res 2023; 51:8270-8282. [PMID: 37409559 PMCID: PMC10450164 DOI: 10.1093/nar/gkad583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
The TFAP2 family regulates gene expression during differentiation, development, and organogenesis, and includes five homologs in humans. They all possess a highly conserved DNA binding domain (DBD) followed by a helix-span-helix (HSH) domain. The DBD-HSH tandem domain specifically binds to a GCC(N3)GGC consensus sequence, but the precise recognition mechanisms remain unclear. Here, we found that TFAP2 preferred binding to the GCC(N3)GGC sequence, and the pseudo-palindromic GCC and GGC motifs and the length of the central spacer between the two motifs determined their binding specificity. Structural studies revealed that the two flat amphipathic α-helical HSH domains of TFAP2A stacked with each other to form a dimer via hydrophobic interactions, while the stabilized loops from both DBD domains inserted into two neighboring major grooves of the DNA duplex to form base-specific interactions. This specific DNA binding mechanism controlled the length of the central spacer and determined the DNA sequence specificity of TFAP2. Mutations of the TFAP2 proteins are implicated in various diseases. We illustrated that reduction or disruption of the DNA binding ability of the TFAP2 proteins is the primary cause of TFAP2 mutation-associated diseases. Thus, our findings also offer valuable insights into the pathogenesis of disease-associated mutations in TFAP2 proteins.
Collapse
Affiliation(s)
- Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yuqing Xiao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Linyao Gan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Weifang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jin Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| |
Collapse
|
22
|
Zhao Y, Liu J, Liu S, Yang P, Liang Y, Ma J, Mao S, Sun C, Yang Y. Fibroblast exosomal TFAP2C induced by chitosan oligosaccharides promotes peripheral axon regeneration via the miR-132-5p/CAMKK1 axis. Bioact Mater 2023; 26:249-263. [PMID: 36936807 PMCID: PMC10020534 DOI: 10.1016/j.bioactmat.2023.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Chitosan and its degradation product, oligosaccharides, have been shown to facilitate peripheral nerve regeneration. However, the underlying mechanisms are not well understood. In this study, we analyzed the protein expression profiles in sciatic nerves after injury using proteomics. A group of proteins related to exosome packaging and transport is up-regulated by chitosan oligosaccharides (COS), implying that exosomes are involved in COS-induced peripheral nerve regeneration. In fact, exosomes derived from fibroblasts (f-EXOs) treated with COS significantly promoted axon extension and regeneration. Exosomal protein identification and functional studies, revealed that TFAP2C is a key factor in neurite outgrowth induced by COS-f-EXOs. Furthermore, we showed that TFAP2C targets the pri-miRNA-132 gene and represses miR-132-5p expression in dorsal root ganglion neurons. Camkk1 is a downstream substrate of miR-132-5p that positively affects axon extension. In rats, miR-132-5p antagomir stimulates CAMKK1 expression and improves axon regeneration and functional recovery in sciatic nerves after injury. Our data reveal the mechanism for COS in axon regeneration, that is COS induce fibroblasts to produce TFAP2C-enriched EXOs, which are then transferred into axons to promote axon regeneration via miR-132-5p/CAMKK1. Moreover, these results show a new facet of fibroblasts in axon regeneration in peripheral nerves.
Collapse
Affiliation(s)
- Yahong Zhao
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
| | - Jina Liu
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
| | - Sha Liu
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
| | - Panpan Yang
- School of Medicine, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
| | - Yunyun Liang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
| | - Jinyu Ma
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
| | - Susu Mao
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
| | - Cheng Sun
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
- Corresponding author.
| | - Yumin Yang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, 19 Qixiu Road, Nantong, Jiangsu, 226001, China
- Corresponding author.
| |
Collapse
|
23
|
Hsu FM, Wu QY, Fabyanic EB, Wei A, Wu H, Clark AT. TET1 facilitates specification of early human lineages including germ cells. iScience 2023; 26:107191. [PMID: 37456839 PMCID: PMC10345126 DOI: 10.1016/j.isci.2023.107191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/07/2023] [Accepted: 06/18/2023] [Indexed: 07/18/2023] Open
Abstract
Ten Eleven Translocation 1 (TET1) is a regulator of localized DNA demethylation through the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). To examine DNA demethylation in human primordial germ cell-like cells (hPGCLCs) induced from human embryonic stem cells (hESCs), we performed bisulfite-assisted APOBEC coupled epigenetic sequencing (bACEseq) followed by integrated genomics analysis. Our data indicates that 5hmC enriches at hPGCLC-specific NANOG, SOX17 or TFAP2C binding sites on hPGCLC induction, and this is accompanied by localized DNA demethylation. Using CRISPR-Cas9, we show that deleting the catalytic domain of TET1 reduces hPGCLC competency when starting with hESC cultured on mouse embryonic fibroblasts, and this phenotype can be rescued after transitioning hESCs to defined media and a recombinant substrate. Taken together, our study demonstrates the importance of 5hmC in facilitating hPGCLC competency, and the role of hESC culture conditions in modulating this effect.
Collapse
Affiliation(s)
- Fei-Man Hsu
- Department of Molecular, Cell and Developmental Biology, 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
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Qiu Ya Wu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emily B. Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amander T. Clark
- Department of Molecular, Cell and Developmental Biology, 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
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
24
|
Li Z, Xu H, Li J, Xu X, Wang J, Wu D, Zhang J, Liu J, Xue Z, Zhan G, Tan BCP, Chen D, Chan YS, Ng HH, Liu W, Hsu CH, Zhang D, Shen Y, Liang H. Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network. Nat Commun 2023; 14:3646. [PMID: 37339952 DOI: 10.1038/s41467-023-39344-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Acquisition of new stem cell fates relies on the dissolution of the prior regulatory network sustaining the existing cell fates. Currently, extensive insights have been revealed for the totipotency regulatory network around the zygotic genome activation (ZGA) period. However, how the dissolution of the totipotency network is triggered to ensure the timely embryonic development following ZGA is largely unknown. In this study, we identify the unexpected role of a highly expressed 2-cell (2C) embryo specific transcription factor, ZFP352, in facilitating the dissolution of the totipotency network. We find that ZFP352 has selective binding towards two different retrotransposon sub-families. ZFP352 coordinates with DUX to bind the 2C specific MT2_Mm sub-family. On the other hand, without DUX, ZFP352 switches affinity to bind extensively onto SINE_B1/Alu sub-family. This leads to the activation of later developmental programs like ubiquitination pathways, to facilitate the dissolution of the 2C state. Correspondingly, depleting ZFP352 in mouse embryos delays the 2C to morula transition process. Thus, through a shift of binding from MT2_Mm to SINE_B1/Alu, ZFP352 can trigger spontaneous dissolution of the totipotency network. Our study highlights the importance of different retrotransposons sub-families in facilitating the timely and programmed cell fates transition during early embryogenesis.
Collapse
Affiliation(s)
- Zhengyi Li
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Haiyan Xu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Jiaqun Li
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
- Zhejiang Provincial Clinical Research Center for Child Health, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Xiao Xu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Junjiao Wang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
- Zhejiang Provincial Clinical Research Center for Child Health, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Danya Wu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Jiateng Zhang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Juan Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
- Zhejiang Provincial Clinical Research Center for Child Health, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Ziwei Xue
- Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Guankai Zhan
- Women's Hospital, Institute of Genetics, and Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Bobby Cheng Peow Tan
- Laboratory of Precision Disease Therapeutics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore, Singapore
| | - Di Chen
- Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Yun-Shen Chan
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China
| | - Huck Hui Ng
- Laboratory of Precision Disease Therapeutics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117597, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 639798, Singapore
| | - Wanlu Liu
- Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Chih-Hung Hsu
- Women's Hospital, Institute of Genetics, and Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
- Zhejiang Provincial Clinical Research Center for Child Health, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
| | - Yang Shen
- Laboratory of Precision Disease Therapeutics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore, Singapore.
- Vision Medicals Co., Ltd, G10 BLDG, Huaxin Park, 31 Kefeng Ave, Gaungzhou, 510000, China.
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
| |
Collapse
|
25
|
Zhou J, Hu J, Wang Y, Gao S. Induction and application of human naive pluripotency. Cell Rep 2023; 42:112379. [PMID: 37043354 DOI: 10.1016/j.celrep.2023.112379] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/18/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
Over the past few decades, many attempts have been made to capture different states of pluripotency in vitro. Naive and primed pluripotent stem cells, corresponding to the pluripotency states of pre- and post-implantation epiblasts, respectively, have been well characterized in mice and can be interconverted in vitro. Here, we summarize the recently reported strategies to generate human naive pluripotent stem cells in vitro. We discuss their applications in studies of regulatory mechanisms involved in early developmental processes, including identification of molecular features, X chromosome inactivation modeling, transposable elements regulation, metabolic characteristics, and cell fate regulation, as well as potential for extraembryonic differentiation and blastoid construction for embryogenesis modeling. We further discuss the naive pluripotency-related research, including 8C-like cell establishment and disease modeling. We also highlight limitations of current naive pluripotency studies, such as imperfect culture conditions and inadequate responsiveness to differentiation signals.
Collapse
Affiliation(s)
- Jianfeng Zhou
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jindian Hu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| |
Collapse
|
26
|
Markman S, Zada M, David E, Giladi A, Amit I, Zelzer E. A single-cell census of mouse limb development identifies complex spatiotemporal dynamics of skeleton formation. Dev Cell 2023; 58:565-581.e4. [PMID: 36931270 DOI: 10.1016/j.devcel.2023.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 10/20/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023]
Abstract
Limb development has long served as a model system for coordinated spatial patterning of progenitor cells. Here, we identify a population of naive limb progenitors and show that they differentiate progressively to form the skeleton in a complex, non-consecutive, three-dimensional pattern. Single-cell RNA sequencing of the developing mouse forelimb identified three progenitor states: naive, proximal, and autopodial, as well as Msx1 as a marker for the naive progenitors. In vivo lineage tracing confirmed this role and localized the naive progenitors to the outer margin of the limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that the progressive transition of Msx1+ naive progenitors into proximal and autopodial progenitors coincides with their differentiation to Sox9+ chondroprogenitors, which occurs along all the forming skeletal segments. Indeed, tracking the spatiotemporal sequence of differentiation showed that the skeleton forms progressively in a complex pattern. These findings suggest an alternative model for limb skeleton development.
Collapse
Affiliation(s)
- Svetlana Markman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mor Zada
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Elazar Zelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
27
|
Zorzan I, Betto RM, Rossignoli G, Arboit M, Drusin A, Corridori C, Martini P, Martello G. Chemical conversion of human conventional PSCs to TSCs following transient naive gene activation. EMBO Rep 2023; 24:e55235. [PMID: 36847616 PMCID: PMC10074076 DOI: 10.15252/embr.202255235] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
In human embryos, naive pluripotent cells of the inner cell mass (ICM) generate epiblast, primitive endoderm and trophectoderm (TE) lineages, whence trophoblast cells derive. In vitro, naive pluripotent stem cells (PSCs) retain this potential and efficiently generate trophoblast stem cells (TSCs), while conventional PSCs form TSCs at low efficiency. Transient histone deacetylase and MEK inhibition combined with LIF stimulation is used to chemically reset conventional to naive PSCs. Here, we report that chemical resetting induces the expression of both naive and TSC markers and of placental imprinted genes. A modified chemical resetting protocol allows for the fast and efficient conversion of conventional PSCs into TSCs, entailing shutdown of pluripotency genes and full activation of the trophoblast master regulators, without induction of amnion markers. Chemical resetting generates a plastic intermediate state, characterised by co-expression of naive and TSC markers, after which cells steer towards one of the two fates in response to the signalling environment. The efficiency and rapidity of our system will be useful to study cell fate transitions and to generate models of placental disorders.
Collapse
Affiliation(s)
- Irene Zorzan
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | | | | | - Mattia Arboit
- Department of Biology, University of Padua, Padua, Italy
| | - Andrea Drusin
- Department of Biology, University of Padua, Padua, Italy
| | | | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | |
Collapse
|
28
|
Maskalenka K, Alagöz G, Krueger F, Wright J, Rostovskaya M, Nakhuda A, Bendall A, Krueger C, Walker S, Scally A, Rugg-Gunn PJ. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells. Development 2023; 150:286291. [PMID: 36621005 PMCID: PMC10110494 DOI: 10.1242/dev.201155] [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: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023]
Abstract
Gene duplication events can drive evolution by providing genetic material for new gene functions, and they create opportunities for diverse developmental strategies to emerge between species. To study the contribution of duplicated genes to human early development, we examined the evolution and function of NANOGP1, a tandem duplicate of the transcription factor NANOG. We found that NANOGP1 and NANOG have overlapping but distinct expression profiles, with high NANOGP1 expression restricted to early epiblast cells and naïve-state pluripotent stem cells. Sequence analysis and epitope-tagging revealed that NANOGP1 is protein coding with an intact homeobox domain. The duplication that created NANOGP1 occurred earlier in primate evolution than previously thought and has been retained only in great apes, whereas Old World monkeys have disabled the gene in different ways, including homeodomain point mutations. NANOGP1 is a strong inducer of naïve pluripotency; however, unlike NANOG, it is not required to maintain the undifferentiated status of human naïve pluripotent cells. By retaining expression, sequence and partial functional conservation with its ancestral copy, NANOGP1 exemplifies how gene duplication and subfunctionalisation can contribute to transcription factor activity in human pluripotency and development.
Collapse
Affiliation(s)
| | - Gökberk Alagöz
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Joshua Wright
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Asif Nakhuda
- Gene Targeting Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Christel Krueger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| |
Collapse
|
29
|
Zhang H, Ren C, Liu Q, Wang Q, Wang D. TFAP2C exacerbates psoriasis-like inflammation by promoting Th17 and Th1 cells activation through regulating TEAD4 transcription. Allergol Immunopathol (Madr) 2023; 51:124-134. [PMID: 37169570 DOI: 10.15586/aei.v51i3.854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/20/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Psoriasis is one of the chronic and autoimmune skin diseases. It is important to uncover the mechanisms underlying the psoriasis. Transcription factor activator protein (TFAP-2) gamma, also known as AP2-gamma, is a protein encoded by the TFAP2C gene. Immune-mediated pathophysiological processes could be linked to psoriasis, but the mechanism is still unclear. Therefore, to date the cause of psoriasis has not been understood completely. MATERIALS AND METHODS Psoriasis is a complex disease triggered by genetic, immunological, and environmental stimuli. Keratinocytes play an important role in both initiation and maintenance phases of psoriasis. A psoriatic keratinocyte model was established by stimulating high sensitivity of human epidermal keratinocytes (HaCaT) to topoisomerase inhibitor cell lines using the accumulation of M5 cytokines comprising interleukin (IL)-17A, IL-22, oncostatin M, IL-1α, and tumor necrosis factor-α (TNF-α). The TFAP2C and transcriptional enhanced associate domain 4 (TEAD4) genes expression was evaluated by reverse transcription-quantitative polymerase chain reaction. Western blot analysis was used to examine protein expression. Cell viability (quantitative) of keratinocytes, including cytotoxicity, proliferation, and cell activation, was evaluated by the MTT assay. The relative percentage values of interleukin (IL)-17a, interferon gamma, and IL-4+ cells were measured by flow cytometry. Accordingly, chromatin immunoprecipitation and luciferase reporter assays were applied to evaluate the binding affinity of TFAP2C and TEAD4 promoter. RESULTS Level of the TFAP2C gene was elevated in the lesional skin of psoriasis patients. On the other hand, silencing of the TFAP2C gene suppressed the proliferation and inflammatory response in M5-induced keratinocytes. In addition, inhibition of TFAP2C alleviated imiquimod (IMQ)-induced skin injury in mice model. We also observed that suppression of TFAP2C inhibited the activation of T-helper 17 (Th17) and Th1 cells in IMQ-induced mice model. Mechanically, TFAP2C promoted TEAD4 transcriptional activation. CONCLUSION TFAP2C exacerbated psoriasis-like inflammation by increasing the activation of Th17 and Th1 cells by regulating TEAD4 transcription. This finding clearly indicated that TFAP2C could be considered a valuable biomarker for the prevention and treatment for psoriasis.
Collapse
Affiliation(s)
- Huanhuan Zhang
- Department of Dermatology, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Cuimin Ren
- Department of Dermatology, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Qiang Liu
- Department of Dermatology, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Qing Wang
- Department of Dermatology, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Dahu Wang
- Department of Dermatology, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China;
| |
Collapse
|
30
|
Waldhorn I, Turetsky T, Steiner D, Gil Y, Benyamini H, Gropp M, Reubinoff BE. Modeling sex differences in humans using isogenic induced pluripotent stem cells. Stem Cell Reports 2022; 17:2732-2744. [PMID: 36427492 PMCID: PMC9768579 DOI: 10.1016/j.stemcr.2022.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/27/2022] Open
Abstract
Biological sex is a fundamental trait influencing development, reproduction, pathogenesis, and medical treatment outcomes. Modeling sex differences is challenging because of the masking effect of genetic variability and the hurdle of differentiating chromosomal versus hormonal effects. In this work we developed a cellular model to study sex differences in humans. Somatic cells from a mosaic Klinefelter syndrome patient were reprogrammed to generate isogenic induced pluripotent stem cell (iPSC) lines with different sex chromosome complements: 47,XXY/46,XX/46,XY/45,X0. Transcriptional analysis of the hiPSCs revealed novel and known genes and pathways that are sexually dimorphic in the pluripotent state and during early neural development. Female hiPSCs more closely resembled the naive pluripotent state than their male counterparts. Moreover, the system enabled differentiation between the contributions of X versus Y chromosome to these differences. Taken together, isogenic hiPSCs present a novel platform for studying sex differences in humans and bear potential to promote gender-specific medicine in the future.
Collapse
Affiliation(s)
- Ithai Waldhorn
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Tikva Turetsky
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Debora Steiner
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Yaniv Gil
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Hadar Benyamini
- Bioinformatics Unit of the I-CORE at Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Michal Gropp
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Benjamin E. Reubinoff
- Hadassah Stem Cell Research Center, Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel,Department of Obstetrics and Gynecology, Ein Kerem, Hadassah Hebrew University Medical Center, Jerusalem, Israel,Corresponding author
| |
Collapse
|
31
|
Pontis J, Pulver C, Playfoot CJ, Planet E, Grun D, Offner S, Duc J, Manfrin A, Lutolf MP, Trono D. Primate-specific transposable elements shape transcriptional networks during human development. Nat Commun 2022; 13:7178. [PMID: 36418324 PMCID: PMC9684439 DOI: 10.1038/s41467-022-34800-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
The human genome contains more than 4.5 million inserts derived from transposable elements (TEs), the result of recurrent waves of invasion and internal propagation throughout evolution. For new TE copies to be inherited, they must become integrated in the genome of the germline or pre-implantation embryo, which requires that their source TE be expressed at these stages. Accordingly, many TEs harbor DNA binding sites for the pluripotency factors OCT4, NANOG, SOX2, and KLFs and are transiently expressed during embryonic genome activation. Here, we describe how many primate-restricted TEs have additional binding sites for lineage-specific transcription factors driving their expression during human gastrulation and later steps of fetal development. These TE integrants serve as lineage-specific enhancers fostering the transcription, amongst other targets, of KRAB-zinc finger proteins (KZFPs) of comparable evolutionary age, which in turn corral the activity of TE-embedded regulatory sequences in a similarly lineage-restricted fashion. Thus, TEs and their KZFP controllers play broad roles in shaping transcriptional networks during early human development.
Collapse
Affiliation(s)
- Julien Pontis
- grid.5333.60000000121839049Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Cyril Pulver
- grid.5333.60000000121839049Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Christopher J. Playfoot
- grid.5333.60000000121839049Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- grid.5333.60000000121839049Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Delphine Grun
- grid.5333.60000000121839049Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sandra Offner
- grid.5333.60000000121839049Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julien Duc
- grid.5333.60000000121839049Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andrea Manfrin
- grid.5333.60000000121839049Laboratory for Stem Cell Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matthias P. Lutolf
- grid.5333.60000000121839049Laboratory for Stem Cell Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Didier Trono
- grid.5333.60000000121839049Laboratory of Virology and Genetics, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| |
Collapse
|
32
|
Zhang W, Ji K, Min C, Zhang C, Yang L, Zhang Q, Tian Z, Zhang M, Wang X, Li X. Oncogenic LINC00857 recruits TFAP2C to elevate FAT1 expression in gastric cancer. Cancer Sci 2022; 114:63-74. [PMID: 35524544 PMCID: PMC9807510 DOI: 10.1111/cas.15394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/30/2022] [Accepted: 04/29/2022] [Indexed: 01/07/2023] Open
Abstract
FAT atypical cadherin 1 (FAT1) is a mutant gene frequently found in human cancers and mainly accumulates at the plasma membrane of cancer cells. Emerging evidence has implicated FAT1 in the progression of gastric cancer (GC). This study intended to identify a regulatory network related to FAT1 in GC development. Upregulated expression of FAT1 was confirmed in GC tissues, and silencing FAT1 was observed to result in suppression of GC cell oncogenic phenotypes. Mechanistic investigation results demonstrated that FAT1 upregulated AP-1 expression by phosphorylating c-JUN and c-FOS, whereas LINC00857 elevated the expression of FAT1 by recruiting a transcription factor TFAP2C. Functional experiments further suggested that LINC00857 enhanced the malignant biological characteristics of GC cells through TFAP2C-mediated promotion of FAT1. More importantly, LINC00857 silencing delayed the tumor growth and blocked epithelial-mesenchymal transition in tumor-bearing mice, which was associated with downregulated expression of TFAP2C/FAT1. To conclude, LINC00857 plays an oncogenic role in GC through regulating the TFAP2C/FAT1/AP-1 axis. Therefore, this study contributes to extended the understanding of gastric carcinogenesis and LINC00857 may serve as a therapeutic target for GC.
Collapse
Affiliation(s)
- Wenqing Zhang
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Kaiyue Ji
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | | | - Cuiping Zhang
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Lin Yang
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Qi Zhang
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Zibin Tian
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Mengyuan Zhang
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Xinyu Wang
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Xiaoyu Li
- Department of GastroenterologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| |
Collapse
|
33
|
Malik V, Zang R, Fuentes-Iglesias A, Huang X, Li D, Fidalgo M, Zhou H, Wang J. Comparative functional genomics identifies unique molecular features of EPSCs. Life Sci Alliance 2022; 5:5/11/e202201608. [PMID: 35961778 PMCID: PMC9378845 DOI: 10.26508/lsa.202201608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
The authors provide a comprehensive resource on proteomics, transcriptomic, and epigenetic level details of EPSCs to shed light on possible molecular pathways regulating their expanded pluripotency potential. Extended pluripotent or expanded potential stem cells (EPSCs) possess superior developmental potential to embryonic stem cells (ESCs). However, the molecular underpinning of EPSC maintenance in vitro is not well defined. We comparatively studied transcriptome, chromatin accessibility, active histone modification marks, and relative proteomes of ESCs and the two well-established EPSC lines to probe the molecular foundation underlying EPSC developmental potential. Despite some overlapping transcriptomic and chromatin accessibility features, we defined sets of molecular signatures that distinguish EPSCs from ESCs in transcriptional and translational regulation as well as metabolic control. Interestingly, EPSCs show similar reliance on pluripotency factors Oct4, Sox2, and Nanog for self-renewal as ESCs. Our study provides a rich resource for dissecting the regulatory network that governs the developmental potency of EPSCs and exploring alternative strategies to capture totipotent stem cells in culture.
Collapse
Affiliation(s)
- Vikas Malik
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Ruge Zang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandro Fuentes-Iglesias
- Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC)-Health Research Institute (IDIS), Santiago de Compostela, Spain
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Dan Li
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Miguel Fidalgo
- Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC)-Health Research Institute (IDIS), Santiago de Compostela, Spain
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| |
Collapse
|
34
|
Schuster J, Klar J, Khalfallah A, Laan L, Hoeber J, Fatima A, Sequeira VM, Jin Z, Korol SV, Huss M, Nordgren A, Anderlid BM, Gallant C, Birnir B, Dahl N. ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function. Front Mol Neurosci 2022; 15:988993. [PMID: 36353360 PMCID: PMC9637781 DOI: 10.3389/fnmol.2022.988993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 07/30/2023] Open
Abstract
Mowat-Wilson syndrome (MWS) is a severe neurodevelopmental disorder caused by heterozygous variants in the gene encoding transcription factor ZEB2. Affected individuals present with structural brain abnormalities, speech delay and epilepsy. In mice, conditional loss of Zeb2 causes hippocampal degeneration, altered migration and differentiation of GABAergic interneurons, a heterogeneous population of mainly inhibitory neurons of importance for maintaining normal excitability. To get insights into GABAergic development and function in MWS we investigated ZEB2 haploinsufficient induced pluripotent stem cells (iPSC) of MWS subjects together with iPSC of healthy donors. Analysis of RNA-sequencing data at two time points of GABAergic development revealed an attenuated interneuronal identity in MWS subject derived iPSC with enrichment of differentially expressed genes required for transcriptional regulation, cell fate transition and forebrain patterning. The ZEB2 haploinsufficient neural stem cells (NSCs) showed downregulation of genes required for ventral telencephalon specification, such as FOXG1, accompanied by an impaired migratory capacity. Further differentiation into GABAergic interneuronal cells uncovered upregulation of transcription factors promoting pallial and excitatory neurons whereas cortical markers were downregulated. The differentially expressed genes formed a neural protein-protein network with extensive connections to well-established epilepsy genes. Analysis of electrophysiological properties in ZEB2 haploinsufficient GABAergic cells revealed overt perturbations manifested as impaired firing of repeated action potentials. Our iPSC model of ZEB2 haploinsufficient GABAergic development thus uncovers a dysregulated gene network leading to immature interneurons with mixed identity and altered electrophysiological properties, suggesting mechanisms contributing to the neuropathogenesis and seizures in MWS.
Collapse
Affiliation(s)
- Jens Schuster
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Ayda Khalfallah
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Loora Laan
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Jan Hoeber
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Ambrin Fatima
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Velin Marita Sequeira
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Zhe Jin
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Sergiy V. Korol
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Mikael Huss
- Wallenberg Long-Term Bioinformatics Support, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Britt Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Gallant
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Bryndis Birnir
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| |
Collapse
|
35
|
Burn A, Roy F, Freeman M, Coffin JM. Widespread expression of the ancient HERV-K (HML-2) provirus group in normal human tissues. PLoS Biol 2022; 20:e3001826. [PMID: 36256614 PMCID: PMC9578601 DOI: 10.1371/journal.pbio.3001826] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/13/2022] [Indexed: 11/11/2022] Open
Abstract
Human endogenous retrovirus (HERV) transcripts are known to be highly expressed in cancers, yet their activity in nondiseased tissue is largely unknown. Using the GTEx RNA-seq dataset from normal tissue sampled at autopsy, we characterized individual expression of the recent HERV-K (HML-2) provirus group across 13,000 different samples of 54 different tissues from 948 individuals. HML-2 transcripts could be identified in every tissue sampled and were elevated in the cerebellum, pituitary, testis, and thyroid. A total of 37 different individual proviruses were expressed in 1 or more tissues, representing all 3 LTR5 subgroups. Nine proviruses were identified as having long terminal repeat (LTR)-driven transcription, 7 of which belonged to the most recent LTR5HS subgroup. Proviruses of different subgroups displayed a bias in tissue expression, which may be associated with differences in transcription factor binding sites in their LTRs. Provirus expression was greater in evolutionarily older proviruses with an earliest shared ancestor of gorilla or older. HML-2 expression was significantly affected by biological sex in 1 tissue, while age and timing of death (Hardy score) had little effect. Proviruses containing intact gag, pro, and env open reading frames (ORFs) were expressed in the dataset, with almost every tissue measured potentially expressing at least 1 intact ORF (gag). Human endogenous retrovirus (HERV) transcripts are known to be highly expressed in cancers, but what is their activity in normal tissue? This study uses unique patterns of HERV-K RNA expression in the large GEx dataset from non-diseased tissue sites to provide new insights into both the coevolution of HERV-K with our primate ancestors and their current role in human biology.
Collapse
Affiliation(s)
- Aidan Burn
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Farrah Roy
- Immuneering Corporation, Cambridge, Massachusetts, United States of America
| | - Michael Freeman
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - John M. Coffin
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
36
|
Cheng H, Shang D, Zhou R. Germline stem cells in human. Signal Transduct Target Ther 2022; 7:345. [PMID: 36184610 PMCID: PMC9527259 DOI: 10.1038/s41392-022-01197-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 12/02/2022] Open
Abstract
The germline cells are essential for the propagation of human beings, thus essential for the survival of mankind. The germline stem cells, as a unique cell type, generate various states of germ stem cells and then differentiate into specialized cells, spermatozoa and ova, for producing offspring, while self-renew to generate more stem cells. Abnormal development of germline stem cells often causes severe diseases in humans, including infertility and cancer. Primordial germ cells (PGCs) first emerge during early embryonic development, migrate into the gentile ridge, and then join in the formation of gonads. In males, they differentiate into spermatogonial stem cells, which give rise to spermatozoa via meiosis from the onset of puberty, while in females, the female germline stem cells (FGSCs) retain stemness in the ovary and initiate meiosis to generate oocytes. Primordial germ cell-like cells (PGCLCs) can be induced in vitro from embryonic stem cells or induced pluripotent stem cells. In this review, we focus on current advances in these embryonic and adult germline stem cells, and the induced PGCLCs in humans, provide an overview of molecular mechanisms underlying the development and differentiation of the germline stem cells and outline their physiological functions, pathological implications, and clinical applications.
Collapse
Affiliation(s)
- Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, 430072, Wuhan, China.
| | - Dantong Shang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, 430072, Wuhan, China
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, 430072, Wuhan, China.
| |
Collapse
|
37
|
Xing J, Chen W, Chen K, Zhu S, Lin F, Qi Y, Zhang Y, Han S, Rao T, Ruan Y, Zhao S, Yu W, Cheng F. TFAP2C Knockdown Sensitizes Bladder Cancer Cells to Cisplatin Treatment via Regulation of EGFR and NF-κB. Cancers (Basel) 2022; 14:cancers14194809. [PMID: 36230734 PMCID: PMC9562889 DOI: 10.3390/cancers14194809] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Bladder cancer (BCa) is considered one of the most common neoplasms of the urology system. Cisplatin-based chemotherapy has been the primary treatment for patients with advanced or metastatic BCa. Nevertheless, cisplatin resistance often limits the treatment of bladder cancer. We expect to find approaches to improve the therapeutic efficacy of cisplatin in bladder cancer. In recent years, many studies have shown that transcription factor AP-2 gamma (TFAP2C) acts as a key player in cancer development and and its expression level is closely related to the sensitivity of tumors to cisplatin. Our study investigated whether TFAP2C affects the sensitivity of BCa cells to cisplatin and the possible mechanisms. We found that TFAP2C expression was significantly upregulated in most BCa tissues compared to adjacent normal tissues. The present study confirmed that TFAP2C knockdown enhanced the anti-tumor effects of cisplatin by decreasing cisplatin-induced activation levels of epidermal growth factor receptor (EGFR) and nuclear factor kappaB (NF-κB). Specifically, this study provides a novel approach to improve the efficacy of cisplatin. Abstract Cisplatin is the first-line chemotherapy for advanced or metastatic bladder cancer. Nevertheless, approximately half of patients with BCa are insensitive to cisplatin therapy or develop cisplatin resistance during the treatment process. Therefore, it is especially crucial to investigate ways to enhance the sensitivity of tumor cells to cisplatin. Transcription factor AP-2 gamma (TFAP2C) is involved in cancer development and chemotherapy sensitivity. However, its relationship with chemotherapy has not been studied in BCa. In this study, we aimed to investigate the therapeutic potential of TFAP2C in human BCa. Results based on TCGA (The Cancer Genome Atlas), GTEx (The Genotype-Tissue Expression) and GEO (Gene Expression Omnibus) data showed that TFAP2C expression was upregulated in BCa tissues and that its high expression was associated with poor prognosis. Meanwhile, we demonstrated the overexpression of TFAP2C in BCa clinical specimens. Subsequently, in vitro, we knocked down TFAP2C in BCa cells and found that TFAP2C knockdown further increased cell cycle arrest and apoptosis caused by cisplatin. In addition, the inhibitory effect of cisplatin on BCa cell migration and invasion was enhanced by TFAP2C knockdown. Our data indicated that cisplatin increased epidermal growth factor receptor (EGFR) and nuclear factor-kappaB (NF-κB) activation levels, but TFAP2C knockdown suppressed this effect. Finally, in vivo data further validated these findings. Our study showed that TFAP2C knockdown affected the activation levels of EGFR and NF-κB and enhanced the anti-tumor effects of cisplatin in vivo and in vitro. This provides a new direction to improve the efficacy of traditional cisplatin chemotherapy.
Collapse
Affiliation(s)
- Ji Xing
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Wu Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Kang Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Shaoming Zhu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Fangyou Lin
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yucheng Qi
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yunlong Zhang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Shangting Han
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ting Rao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yuan Ruan
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Sheng Zhao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Weimin Yu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Correspondence: (W.Y.); (F.C.)
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Correspondence: (W.Y.); (F.C.)
| |
Collapse
|
38
|
Zhao Y, Vartak SV, Conte A, Wang X, Garcia DA, Stevens E, Kyoung Jung S, Kieffer-Kwon KR, Vian L, Stodola T, Moris F, Chopp L, Preite S, Schwartzberg PL, Kulinski JM, Olivera A, Harly C, Bhandoola A, Heuston EF, Bodine DM, Urrutia R, Upadhyaya A, Weirauch MT, Hager G, Casellas R. "Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes. Mol Cell 2022; 82:3398-3411.e11. [PMID: 35863348 PMCID: PMC9481673 DOI: 10.1016/j.molcel.2022.06.029] [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: 10/08/2021] [Revised: 04/06/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
Regulatory elements activate promoters by recruiting transcription factors (TFs) to specific motifs. Notably, TF-DNA interactions often depend on cooperativity with colocalized partners, suggesting an underlying cis-regulatory syntax. To explore TF cooperativity in mammals, we analyze ∼500 mouse and human primary cells by combining an atlas of TF motifs, footprints, ChIP-seq, transcriptomes, and accessibility. We uncover two TF groups that colocalize with most expressed factors, forming stripes in hierarchical clustering maps. The first group includes lineage-determining factors that occupy DNA elements broadly, consistent with their key role in tissue-specific transcription. The second one, dubbed universal stripe factors (USFs), comprises ∼30 SP, KLF, EGR, and ZBTB family members that recognize overlapping GC-rich sequences in all tissues analyzed. Knockouts and single-molecule tracking reveal that USFs impart accessibility to colocalized partners and increase their residence time. Mammalian cells have thus evolved a TF superfamily with overlapping DNA binding that facilitate chromatin accessibility.
Collapse
Affiliation(s)
- Yongbing Zhao
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA.
| | - Supriya V Vartak
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - Andrea Conte
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - Xiang Wang
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - David A Garcia
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Evan Stevens
- Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - Seol Kyoung Jung
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | | | - Laura Vian
- Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - Timothy Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Francisco Moris
- EntreChem S.L., Vivero Ciencias de la Salud, 33011 Oviedo, Spain
| | - Laura Chopp
- Laboratory of Immune Cell Biology, NCI, NIH, Bethesda, MD 20892, USA
| | - Silvia Preite
- Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Joseph M Kulinski
- Mast cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Ana Olivera
- Mast cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Christelle Harly
- Laboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - David M Bodine
- Genetics and Molecular Biology Branch, NHGRI, NIH, Bethesda, MD 20892, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Matthew T Weirauch
- Divisions of Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Gordon Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD 20893, USA
| | - Rafael Casellas
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
39
|
Ai Z, Xiang X, Xiang Y, Szczerbinska I, Qian Y, Xu X, Ma C, Su Y, Gao B, Shen H, Bin Ramli MN, Chen D, Liu Y, Hao JJ, Ng HH, Zhang D, Chan YS, Liu W, Liang H. Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency. Cell Rep 2022; 40:111240. [PMID: 36001968 DOI: 10.1016/j.celrep.2022.111240] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022] Open
Abstract
Endogenous retroviruses (ERVs) have been reported to participate in pre-implantation development of mammalian embryos. In early human embryogenesis, different ERV sub-families are activated in a highly stage-specific manner. How the specificity of ERV activation is achieved remains largely unknown. Here, we demonstrate the mechanism of how LTR7Ys, the human morula-blastocyst-specific HERVH long terminal repeats, are activated by the naive pluripotency transcription network. We find that KLF5 interacts with and rewires NANOG to bind and regulate LTR7Ys; in contrast, the primed-specific LTR7s are preferentially bound by NANOG in the absence of KLF5. The specific activation of LTR7Ys by KLF5 and NANOG in pluripotent stem cells contributes to human-specific naive pluripotency regulation. KLF5-LTR7Y axis also promotes the expression of trophectoderm genes and contributes to the expanded cell potential toward extra-embryonic lineage. Our study suggests that HERVs are activated by cell-state-specific transcription machinery and promote stage-specific transcription network and cell potency.
Collapse
Affiliation(s)
- Zhipeng Ai
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Yangquan Xiang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Iwona Szczerbinska
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yuli Qian
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Xiao Xu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Chenyang Ma
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yaqi Su
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Bing Gao
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Hao Shen
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Muhammad Nadzim Bin Ramli
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Di Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Yue Liu
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Jia-Jie Hao
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Huck Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117597, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.
| | - Yun-Shen Chan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China.
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China; Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310029, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China.
| |
Collapse
|
40
|
Cell fate roadmap of human primed-to-naive transition reveals preimplantation cell lineage signatures. Nat Commun 2022; 13:3147. [PMID: 35672317 PMCID: PMC9174176 DOI: 10.1038/s41467-022-30924-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human naive pluripotent stem cells offer a unique window into early embryogenesis studies. Recent studies have reported several strategies to obtain cells in the naive state. However, cell fate transitions and the underlying mechanisms remain poorly understood. Here, by a dual fluorescent reporter system, we depict the cell fate dynamics from primed state toward naive pluripotency with ALPG activation followed by the activation of OCT4-distal enhancer. Integration of transcription profiles and the chromatin accessibility landscape reveals the appearance of primitive endoderm and trophectoderm signatures in the transitioning subpopulations, with the capacities for derivation of extra-embryonic endoderm and trophoblast stem cell lines, respectively. Furthermore, despite different fluorescent dynamics, all transitioning intermediates are capable of reaching the naive state with prolonged induction, showing their developmental plasticity and potential. Overall, our study describes a global cell roadmap toward naive pluripotency and provides hints for embryo modeling-related studies. Cell fate dynamics during human naïve pluripotency establishment remain poorly understood. Here, Bi et al. depict a high-resolution cell roadmap of the primed-to-naïve pluripotency transition, providing hints for embryo modeling-related studies.
Collapse
|
41
|
Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction. Nat Cell Biol 2022; 24:858-871. [PMID: 35697783 PMCID: PMC9203278 DOI: 10.1038/s41556-022-00932-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
Abstract
Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here we define the chromatin-associated proteome, histone post-translational modifications and transcriptome of human naive and primed pluripotent stem cells. Our integrated analysis reveals differences in the relative abundance and activities of distinct chromatin modules. We identify a strong enrichment of polycomb repressive complex 2 (PRC2)-associated H3K27me3 in the chromatin of naive pluripotent stem cells and H3K27me3 enrichment at promoters of lineage-determining genes, including trophoblast regulators. PRC2 activity acts as a chromatin barrier restricting the differentiation of naive cells towards the trophoblast lineage, whereas inhibition of PRC2 promotes trophoblast-fate induction and cavity formation in human blastoids. Together, our results establish that human naive pluripotent stem cells are not epigenetically unrestricted, but instead possess chromatin mechanisms that oppose the induction of alternative cell fates. Two side-by-side papers report that H3K27me3 deposited by polycomb repressive complex 2 represents an epigenetic barrier that restricts naive human pluripotent cell differentiation into alternative lineages including trophoblasts.
Collapse
|
42
|
Abstract
POUV is a relatively newly emerged class of POU transcription factors present in jawed vertebrates (Gnathostomata). The function of POUV-class proteins is inextricably linked to zygotic genome activation (ZGA). A large body of evidence now extends the role of these proteins to subsequent developmental stages. While some functions resemble those of other POU-class proteins and are related to neuroectoderm development, others have emerged de novo. The most notable of the latter functions is pluripotency control by Oct4 in mammals. In this review, we focus on these de novo functions in the best-studied species harbouring POUV proteins-zebrafish, Xenopus (anamniotes) and mammals (amniotes). Despite the broad diversity of their biological functions in vertebrates, POUV proteins exert a common feature related to their role in safeguarding the undifferentiated state of cells. Here we summarize numerous pieces of evidence for these specific functions of the POUV-class proteins and recap available loss-of-function data.
Collapse
Affiliation(s)
- Evgeny I. Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Alexey N. Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| |
Collapse
|
43
|
Kumar B, Navarro C, Winblad N, Schell JP, Zhao C, Weltner J, Baqué-Vidal L, Salazar Mantero A, Petropoulos S, Lanner F, Elsässer SJ. Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation. Nat Cell Biol 2022; 24:845-857. [PMID: 35637409 PMCID: PMC9203276 DOI: 10.1038/s41556-022-00916-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
The first lineage choice in human embryo development separates trophectoderm from the inner cell mass. Naïve human embryonic stem cells are derived from the inner cell mass and offer possibilities to explore how lineage integrity is maintained. Here, we discover that polycomb repressive complex 2 (PRC2) maintains naïve pluripotency and restricts differentiation to trophectoderm and mesoderm lineages. Through quantitative epigenome profiling, we found that a broad gain of histone H3 lysine 27 trimethylation (H3K27me3) is a distinct feature of naïve pluripotency. We define shared and naïve-specific bivalent promoters featuring PRC2-mediated H3K27me3 concomitant with H3K4me3. Naïve bivalency maintains key trophectoderm and mesoderm transcription factors in a transcriptionally poised state. Inhibition of PRC2 forces naïve human embryonic stem cells into an 'activated' state, characterized by co-expression of pluripotency and lineage-specific transcription factors, followed by differentiation into either trophectoderm or mesoderm lineages. In summary, PRC2-mediated repression provides a highly adaptive mechanism to restrict lineage potential during early human development.
Collapse
Affiliation(s)
- Banushree Kumar
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Carmen Navarro
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Nerges Winblad
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - John P Schell
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Cheng Zhao
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Jere Weltner
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Laura Baqué-Vidal
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Angelo Salazar Mantero
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Sophie Petropoulos
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
- Département de Médecine, Université de Montréal, Montreal, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, Montreal, Canada
| | - Fredrik Lanner
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden.
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
44
|
Schock EN, York JR, LaBonne C. The developmental and evolutionary origins of cellular pluripotency in the vertebrate neural crest. Semin Cell Dev Biol 2022; 138:36-44. [PMID: 35534333 DOI: 10.1016/j.semcdb.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 11/30/2022]
Abstract
Neural crest cells are central to vertebrate development and evolution, endowing vertebrates with a "new head" that resulted in morphological, physiological, and behavioral features that allowed vertebrates to become active predators. One remarkable feature of neural crest cells is their multi-germ layer potential that allows for the formation of both ectodermal (pigmentation, peripheral glia, sensory neurons) and mesenchymal (connective tissue, cartilage/bone, dermis) cell types. Understanding the cellular and evolutionary origins of this broad cellular potential in the neural crest has been a long-standing focus for developmental biologists. Here, we review recent work that has demonstrated that neural crest cells share key features with pluripotent blastula stem cells, including expression of the Yamanaka stem cell factors (Oct3/4, Klf4, Sox2, c-Myc). These shared features suggest that pluripotency is either retained in the neural crest from blastula stages or subsequently reactivated as the neural crest forms. We highlight the cellular and molecular parallels between blastula stem cells and neural crest cells and discuss the work that has led to current models for the cellular origins of broad potential in the crest. Finally, we explore how these themes can provide new insights into how and when neural crest cells and pluripotency evolved in vertebrates and the evolutionary relationship between these populations.
Collapse
Affiliation(s)
| | | | - Carole LaBonne
- Dept. of Molecular Biosciences; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, United States.
| |
Collapse
|
45
|
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.
Collapse
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)
| |
Collapse
|
46
|
Mazid MA, Ward C, Luo Z, Liu C, Li Y, Lai Y, Wu L, Li J, Jia W, Jiang Y, Liu H, Fu L, Yang Y, Ibañez DP, Lai J, Wei X, An J, Guo P, Yuan Y, Deng Q, Wang Y, Liu Y, Gao F, Wang J, Zaman S, Qin B, Wu G, Maxwell PH, Xu X, Liu L, Li W, Esteban MA. Rolling back human pluripotent stem cells to an eight-cell embryo-like stage. Nature 2022; 605:315-324. [PMID: 35314832 DOI: 10.1038/s41586-022-04625-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/10/2022] [Indexed: 11/08/2022]
Abstract
After fertilization, the quiescent zygote experiences a burst of genome activation that initiates a short-lived totipotent state. Understanding the process of totipotency in human cells would have broad applications. However, in contrast to in mice1,2, demonstration of the time of zygotic genome activation or the eight-cell (8C) stage in in vitro cultured human cells has not yet been reported, and the study of embryos is limited by ethical and practical considerations. Here we describe a transgene-free, rapid and controllable method for producing 8C-like cells (8CLCs) from human pluripotent stem cells. Single-cell analysis identified key molecular events and gene networks associated with this conversion. Loss-of-function experiments identified fundamental roles for DPPA3, a master regulator of DNA methylation in oocytes3, and TPRX1, a eutherian totipotent cell homeobox (ETCHbox) family transcription factor that is absent in mice4. DPPA3 induces DNA demethylation throughout the 8CLC conversion process, whereas TPRX1 is a key executor of 8CLC gene networks. We further demonstrate that 8CLCs can produce embryonic and extraembryonic lineages in vitro or in vivo in the form of blastoids5 and complex teratomas. Our approach provides a resource to uncover the molecular process of early human embryogenesis.
Collapse
Affiliation(s)
- Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- BGI-Shenzhen, Shenzhen, China
| | - Liang Wu
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Jinxiu Li
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Wenqi Jia
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Jiang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Lixin Fu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yueli Yang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - David P Ibañez
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjian Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyu Wei
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Juan An
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Pengcheng Guo
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yue Yuan
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Qiuting Deng
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Shahriar Zaman
- Department of Genetic Engineering and Biotechnology, Faculty of Life and Earth Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Baoming Qin
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- BGI-Shenzhen, Shenzhen, China.
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
47
|
Kenny C, Dilshat R, Seberg HE, Van Otterloo E, Bonde G, Helverson A, Franke CM, Steingrímsson E, Cornell RA. TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes. PLoS Genet 2022; 18:e1010207. [PMID: 35580127 PMCID: PMC9159589 DOI: 10.1371/journal.pgen.1010207] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/01/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that TFAP2 facilitates MITF's ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa-expressing cells that also express tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the former necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.
Collapse
Affiliation(s)
- Colin Kenny
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hannah E. Seberg
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Eric Van Otterloo
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Gregory Bonde
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Christopher M. Franke
- Department of Surgery, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Robert A. Cornell
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| |
Collapse
|
48
|
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]
|
49
|
Darwish NHE, Glinsky GV, Sudha T, Mousa SA. Targeting Thyrointegrin αvβ3 Using Fluorobenzyl Polyethylene Glycol Conjugated Tetraiodothyroacetic Acid (NP751) in Acute Myeloid Leukemia. Front Oncol 2022; 11:793810. [PMID: 35155195 PMCID: PMC8828484 DOI: 10.3389/fonc.2021.793810] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/14/2021] [Indexed: 12/28/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is associated with poor long-term survival, even with newer therapeutic agents. Here, we show the results of our preclinical study, in which we evaluated the efficacy of a new thyrointegrin αvβ3 antagonist, named fluorobenzyl polyethylene glycol conjugated tetraiodothyroacetic acid (fb-PMT). Methods and Results fb-PMT (NP751) is a potent αvβ3 antagonist of molecular weight of 2,478.9 Da. it represents a conjugate of tetraiodothyroacetic acid (tetrac) and monodisperse polyethylene glycol (PEG36), with a 4-fluorobenzyl group capping the other end of the PEG. fb-PMT effectively suppresses the malignant growth of human acute myeloid leukemia (AML) after successful engraftment in transgenic NSG-S xenograft mouse models of either established human AML cell line or primary AML cells. Daily treatment with fb-PMT (1–10 mg/kg body weight) subcutaneously (s.c.) for 3–4 weeks was associated with marked regression of leukemogenesis and extended survival in both models. The efficiency of the fb-PMT therapy was verified using in vivo imaging system (IVIS) imaging, flow cytometry, and histopathological examination to monitor the engraftment of leukemic cells in the bone marrow and other organs. fb-PMT therapy for 3–4 weeks at 3 and 10 mg/kg daily doses exhibited significant reduction (p < 0.0001) of leukemic cell burden of 74% and >95%, respectively. All fb-PMT-treated mice in the 10 mg/kg treatment arm successfully maintained remission after discontinuing the daily treatment. Comprehensive fb-PMT safety assessments demonstrated excellent safety and tolerability at multiple folds above the anticipated human therapeutic doses. Lastly, our genome-wide microarray screens demonstrated that fb-PMT works through the molecular interference mechanism with multiple signaling pathways contributing to growth and survival of leukemic cells. Conclusion Our preclinical findings of the potent anticancer activities of fb-PMT and its favorable safety profiles warrant its clinical investigation for the effective and safe management of AML.
Collapse
Affiliation(s)
- Noureldien H E Darwish
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States.,Hematology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California San Diego, San Diego, CA, United States
| | - Thangirala Sudha
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States
| | - Shaker A Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States
| |
Collapse
|
50
|
Xiang X, Tao Y, DiRusso J, Hsu FM, Zhang J, Xue Z, Pontis J, Trono D, Liu W, Clark AT. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nat Commun 2022; 13:463. [PMID: 35075135 PMCID: PMC8786967 DOI: 10.1038/s41467-022-28105-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/16/2021] [Indexed: 12/26/2022] Open
Abstract
Germ cells are essential to pass DNA from one generation to the next. In human reproduction, germ cell development begins with the specification of primordial germ cells (PGCs) and a failure to specify PGCs leads to human infertility. Recent studies have revealed that the transcription factor network required for PGC specification has diverged in mammals, and this has a significant impact on our understanding of human reproduction. Here, we reveal that the Hominidae-specific Transposable Elements (TEs) LTR5Hs, may serve as TEENhancers (TE Embedded eNhancers) to facilitate PGC specification. LTR5Hs TEENhancers become transcriptionally active during PGC specification both in vivo and in vitro with epigenetic reprogramming leading to increased chromatin accessibility, localized DNA demethylation, enrichment of H3K27ac, and occupation of key hPGC transcription factors. Inactivation of LTR5Hs TEENhancers with KRAB mediated CRISPRi has a significant impact on germ cell specification. In summary, our data reveals the essential role of Hominidae-specific LTR5Hs TEENhancers in human germ cell development. The transcription factor network required for primordial germ cell (PGC) specification is known to diverge in mammals. Here the authors show that hominidae-specific transposable element (TE) LTR5Hs becomes transcriptionally active during PGC specification, and LTR5Hs inactivation abrogates human PGC specification
Collapse
Affiliation(s)
- Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Yu Tao
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonathan DiRusso
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei-Man Hsu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jinchun Zhang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Ziwei Xue
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China. .,Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China. .,Alibaba-Zhejiang University Joint Research Center of Future DigitalHealthcare, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, 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. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| |
Collapse
|