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Huang Z, Cui W, Ratnayake I, Tawil R, Pfeifer GP. SMCHD1 maintains heterochromatin and genome compartments in human myoblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602392. [PMID: 39026812 PMCID: PMC11257445 DOI: 10.1101/2024.07.07.602392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Mammalian genomes are subdivided into euchromatic A compartments that contain mostly active chromatin, and inactive, heterochromatic B compartments. However, it is unknown how A and B genome compartments are established and maintained. Here we studied SMCHD1, an SMC-like protein in human male myoblasts. SMCHD1 colocalizes with Lamin B1 and the heterochromatin mark H3K9me3. Loss of SMCHD1 leads to extensive heterochromatin depletion at the nuclear lamina and acquisition of active chromatin states along all chromosomes. In absence of SMCHD1, long range intra-chromosomal and inter-chromosomal contacts between B compartments are lost while many new TADs and loops are formed. Inactivation of SMCHD1 promotes numerous B to A compartment transitions accompanied by activation of silenced genes. SMCHD1 functions as an anchor for heterochromatin domains ensuring that these domains are inaccessible to epigenome modification enzymes that typically operate in active chromatin. Therefore, A compartments are formed by default when not prevented by SMCHD1.
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2
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Gao C, Gao X, Gao F, Du X, Wu S. A CRISPR/Cas9 screen in embryonic stem cells reveals that Mdm2 regulates totipotency exit. Commun Biol 2024; 7:809. [PMID: 38961268 PMCID: PMC11222520 DOI: 10.1038/s42003-024-06507-9] [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: 11/10/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
During early embryonic development, the transition from totipotency to pluripotency is a fundamental and critical process for proper development. However, the regulatory mechanisms governing this transition remain elusive. Here, we conducted a comprehensive genome-wide CRISPR/Cas9 screen to investigate the 2-cell-like cells (2CLCs) phenotype in mouse embryonic stem cells (mESCs). This effort led to the identification of ten regulators that play a pivotal role in determining cell fate during this transition. Notably, our study revealed Mdm2 as a significant negative regulator of 2CLCs, as perturbation of Mdm2 resulted in a higher proportion of 2CLCs. Mdm2 appears to influence cell fate through its impact on cell cycle progression and H3K27me3 epigenetic modifications. In summary, the results of our CRISPR/Cas9 screen have uncovered several genes with distinct functions in regulating totipotency and pluripotency at various levels, offering a valuable resource for potential targets in future molecular studies.
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Affiliation(s)
- Chen Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xin Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Fei Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Xuguang Du
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
| | - Sen Wu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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3
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Freund MM, Harrison MM, Torres-Zelada EF. Exploring the reciprocity between pioneer factors and development. Development 2024; 151:dev201921. [PMID: 38958075 PMCID: PMC11266817 DOI: 10.1242/dev.201921] [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] [Indexed: 07/04/2024]
Abstract
Development is regulated by coordinated changes in gene expression. Control of these changes in expression is largely governed by the binding of transcription factors to specific regulatory elements. However, the packaging of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because of these properties, pioneer factors act at the top of gene-regulatory networks and drive developmental transitions. Despite the ability to bind target motifs in closed chromatin, pioneer factors have cell type-specific chromatin occupancy and activity. Thus, developmental context clearly shapes pioneer-factor function. Here, we discuss this reciprocal interplay between pioneer factors and development: how pioneer factors control changes in cell fate and how cellular environment influences pioneer-factor binding and activity.
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Affiliation(s)
- Meghan M. Freund
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Eliana F. Torres-Zelada
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
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4
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Su Z, Dong Y, Sun J, Wu Y, Wei Q, Liang Y, Lin Z, Li Y, Shen L, Xi C, Wu L, Xu Y, Liu Y, Yin J, Wang H, Shi K, Le R, Gao S, Xu X. RNA m 6A modification regulates cell fate transition between pluripotent stem cells and 2-cell-like cells. Cell Prolif 2024:e13696. [PMID: 38952035 DOI: 10.1111/cpr.13696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 07/03/2024] Open
Abstract
N6-methyladenosine (m6A) exerts essential roles in early embryos, especially in the maternal-to-zygotic transition stage. However, the landscape and roles of RNA m6A modification during the transition between pluripotent stem cells and 2-cell-like (2C-like) cells remain elusive. Here, we utilised ultralow-input RNA m6A immunoprecipitation to depict the dynamic picture of transcriptome-wide m6A modifications during 2C-like transitions. We found that RNA m6A modification was preferentially enriched in zygotic genome activation (ZGA) transcripts and MERVL with high expression levels in 2C-like cells. During the exit of the 2C-like state, m6A facilitated the silencing of ZGA genes and MERVL. Notably, inhibition of m6A methyltransferase METTL3 and m6A reader protein IGF2BP2 is capable of significantly delaying 2C-like state exit and expanding 2C-like cells population. Together, our study reveals the critical roles of RNA m6A modification in the transition between 2C-like and pluripotent states, facilitating the study of totipotency and cell fate decision in the future.
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Affiliation(s)
- Zhongqu Su
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yu Dong
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiatong Sun
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - You Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qingqing Wei
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yuwei Liang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhiyi Lin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujun Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lu Shen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenxiang Xi
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Li Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yiliang Xu
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yingdong Liu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiqing Yin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kerong Shi
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaocui Xu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
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Talley MJ, Longworth MS. Retrotransposons in embryogenesis and neurodevelopment. Biochem Soc Trans 2024; 52:1159-1171. [PMID: 38716891 DOI: 10.1042/bst20230757] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/27/2024]
Abstract
Retrotransposable elements (RTEs) are genetic elements that can replicate and insert new copies into different genomic locations. RTEs have long been identified as 'parasitic genes', as their mobilization can cause mutations, DNA damage, and inflammation. Interestingly, high levels of retrotransposon activation are observed in early embryogenesis and neurodevelopment, suggesting that RTEs may possess functional roles during these stages of development. Recent studies demonstrate that RTEs can function as transcriptional regulatory elements through mechanisms such as chromatin organization and noncoding RNAs. It is clear, however, that RTE expression and activity must be restrained at some level during development, since overactivation of RTEs during neurodevelopment is associated with several developmental disorders. Further investigation is needed to understand the importance of RTE expression and activity during neurodevelopment and the balance between RTE-regulated development and RTE-mediated pathogenesis.
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Affiliation(s)
- Mary Jo Talley
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, U.S.A
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, U.S.A
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44195, U.S.A
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Guo Y, Kitano T, Inoue K, Murano K, Hirose M, Li TD, Sakashita A, Ishizu H, Ogonuki N, Matoba S, Sato M, Ogura A, Siomi H. Obox4 promotes zygotic genome activation upon loss of Dux. eLife 2024; 13:e95856. [PMID: 38856708 PMCID: PMC11196112 DOI: 10.7554/elife.95856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024] Open
Abstract
Once fertilized, mouse zygotes rapidly proceed to zygotic genome activation (ZGA), during which long terminal repeats (LTRs) of murine endogenous retroviruses with leucine tRNA primer (MERVL) are activated by a conserved homeodomain-containing transcription factor, DUX. However, Dux-knockout embryos produce fertile mice, suggesting that ZGA is redundantly driven by an unknown factor(s). Here, we present multiple lines of evidence that the multicopy homeobox gene, Obox4, encodes a transcription factor that is highly expressed in mouse two-cell embryos and redundantly drives ZGA. Genome-wide profiling revealed that OBOX4 specifically binds and activates MERVL LTRs as well as a subset of murine endogenous retroviruses with lysine tRNA primer (MERVK) LTRs. Depletion of Obox4 is tolerated by embryogenesis, whereas concomitant Obox4/Dux depletion markedly compromises embryonic development. Our study identified OBOX4 as a transcription factor that provides genetic redundancy to preimplantation development.
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Grants
- Grant-in-Aid for Scientific Research in Innovative Areas,19H05753 Ministry of Education, Culture, Sports, Science and Technology
- Project to Elucidate and Control Mechanisms of Aging and Longevity Japan Agency for Medical Research and Development
- Grant-in-Aid for Scientific Research in Innovative Areas,19H05758 Ministry of Education, Culture, Sports, Science and Technology
- Grant-in-Aid for Scientific Research KAKENHI,20K21507 Japan Society for the Promotion of Science
- Grant-in-Aid for Scientific Research KAKENHI,22H02534 Japan Society for the Promotion of Science
- Student Grant-in-Aid Program Keio University
- Doctoral Program Student Support Fellowship Japan Science and Technology Agency
- Grant-in-Aid for Scientific Research in Innovative Areas 19H05753 Ministry of Education, Culture, Sports, Science and Technology
- Grant-in-Aid for Scientific Research in Innovative Areas 19H05758 Ministry of Education, Culture, Sports, Science and Technology
- Grant-in-Aid for Scientific Research KAKENHI 20K21507 Japan Society for the Promotion of Science
- Grant-in-Aid for Scientific Research KAKENHI 22H02534 Japan Society for the Promotion of Science
- Mochida Memorial Foundation for Medical and Pharmaceutical Research
- Sumitomo Foundation
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Affiliation(s)
- Youjia Guo
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Tomohiro Kitano
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Kimiko Inoue
- Bioresource Engineering Division, Bioresource Center, RIKENTsukubaJapan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Michiko Hirose
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio UniversityTokyoJapan
| | - Ten D Li
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
| | - Hirotsugu Ishizu
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Narumi Ogonuki
- Bioresource Engineering Division, Bioresource Center, RIKENTsukubaJapan
| | - Shogo Matoba
- Bioresource Engineering Division, Bioresource Center, RIKENTsukubaJapan
| | - Masayuki Sato
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Atsuo Ogura
- Bioresource Engineering Division, Bioresource Center, RIKENTsukubaJapan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukubaJapan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of MedicineTokyoJapan
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio UniversityTokyoJapan
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7
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Funaya S, Takahashi Y, Suzuki MG, Suzuki Y, Aoki F. H3.1/3.2 regulate the initial progression of the gene expression program. Nucleic Acids Res 2024; 52:6158-6170. [PMID: 38567720 PMCID: PMC11194095 DOI: 10.1093/nar/gkae214] [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: 11/24/2023] [Revised: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 06/25/2024] Open
Abstract
In mice, transcription from the zygotic genome is initiated at the mid-one-cell stage, and occurs promiscuously in many areas of the genome, including intergenic regions. Regulated transcription from selected genes is established during the two-cell stage. This dramatic change in the gene expression pattern marks the initiation of the gene expression program and is essential for early development. We investigated the involvement of the histone variants H3.1/3.2 in the regulation of changes in gene expression pattern during the two-cell stage. Immunocytochemistry analysis showed low nuclear deposition of H3.1/3.2 in the one-cell stage, followed by a rapid increase in the late two-cell stage. Where chromatin structure is normally closed between the one- and two-cell stages, it remained open until the late two-cell stage when H3.1/3.2 were knocked down by small interfering RNA. Hi-C analysis showed that the formation of the topologically associating domain was disrupted in H3.1/3.2 knockdown (KD) embryos. Promiscuous transcription was also maintained in the late two-cell stage in H3.1/3.2 KD embryos. These results demonstrate that H3.1/3.2 are involved in the initial process of the gene expression program after fertilization, through the formation of a closed chromatin structure to execute regulated gene expression during the two-cell stage.
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Affiliation(s)
- Satoshi Funaya
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Yusuke Takahashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Fugaku Aoki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
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8
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Fu B, Ma H, Liu D. Pioneer Transcription Factors: The First Domino in Zygotic Genome Activation. Biomolecules 2024; 14:720. [PMID: 38927123 PMCID: PMC11202083 DOI: 10.3390/biom14060720] [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] [Revised: 05/31/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Zygotic genome activation (ZGA) is a pivotal event in mammalian embryogenesis, marking the transition from maternal to zygotic control of development. During the ZGA process that is characterized by the intricate cascade of gene expression, who tipped the first domino in a meticulously arranged sequence is a subject of paramount interest. Recently, Dux, Obox and Nr5a2 were identified as pioneer transcription factors that reside at the top of transcriptional hierarchy. Through co-option of retrotransposon elements as hubs for transcriptional activation, these pioneer transcription factors rewire the gene regulatory network, thus initiating ZGA. In this review, we provide a snapshot of the mechanisms underlying the functions of these pioneer transcription factors. We propose that ZGA is the starting point where the embryo's own genome begins to influence development trajectory, therefore in-depth dissecting the functions of pioneer transcription factors during ZGA will form a cornerstone of our understanding for early embryonic development, which will pave the way for advancing our grasp of mammalian developmental biology and optimizing in vitro production (IVP) techniques.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Hong Ma
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Di Liu
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
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9
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Du Z, Lin M, Li Q, Guo D, Xue Y, Liu W, Shi H, Chen T, Dan J. The totipotent 2C-like state safeguards genomic stability of mouse embryonic stem cells. J Cell Physiol 2024. [PMID: 38860420 DOI: 10.1002/jcp.31337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Mouse embryonic stem cells (mESCs) sporadically transition to a transient totipotent state that resembles blastomeres of the two-cell (2C) embryo stage, which has been proposed to contribute to exceptional genomic stability, one of the key features of mESCs. However, the biological significance of the rare population of 2C-like cells (2CLCs) in ESC cultures remains to be tested. Here we generated an inducible reporter cell system for specific elimination of 2CLCs from the ESC cultures to disrupt the equilibrium between ESCs and 2CLCs. We show that removing 2CLCs from the ESC cultures leads to dramatic accumulation of DNA damage, genomic mutations, and rearrangements, indicating impaired genomic instability. Furthermore, 2CLCs removal results in increased apoptosis and reduced proliferation of mESCs in both serum/LIF and 2i/LIF culture conditions. Unexpectedly, p53 deficiency results in defective response to DNA damage, leading to early accumulation of DNA damage, micronuclei, indicative of genomic instability, cell apoptosis, and reduced self-renewal capacity of ESCs when devoid of 2CLCs in cultures. Together, our data reveal that transition to the privileged 2C-like state is a major component of the intrinsic mechanisms that maintain the exceptional genomic stability of mESCs for long-term self-renewal.
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Affiliation(s)
- Zeling Du
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Meiqi Lin
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Qiaohua Li
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Dan Guo
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Yanna Xue
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Wei Liu
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jiameng Dan
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
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10
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Hu X, Huang X, Yang Y, Sun Y, Zhao Y, Zhang Z, Qiu D, Wu Y, Wu G, Lei L. Dux activates metabolism-lactylation-MET network during early iPSC reprogramming with Brg1 as the histone lactylation reader. Nucleic Acids Res 2024; 52:5529-5548. [PMID: 38512058 PMCID: PMC11162783 DOI: 10.1093/nar/gkae183] [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: 06/25/2023] [Revised: 02/24/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
The process of induced pluripotent stem cells (iPSCs) reprogramming involves several crucial events, including the mesenchymal-epithelial transition (MET), activation of pluripotent genes, metabolic reprogramming, and epigenetic rewiring. Although these events intricately interact and influence each other, the specific element that regulates the reprogramming network remains unclear. Dux, a factor known to promote totipotency during the transition from embryonic stem cells (ESC) to 2C-like ESC (2CLC), has not been extensively studied in the context of iPSC reprogramming. In this study, we demonstrate that the modification of H3K18la induced by Dux overexpression controls the metabolism-H3K18la-MET network, enhancing the efficiency of iPSC reprogramming through a metabolic switch and the recruitment of p300 via its C-terminal domain. Furthermore, our proteomic analysis of H3K18la immunoprecipitation experiment uncovers the specific recruitment of Brg1 during reprogramming, with both H3K18la and Brg1 being enriched on the promoters of genes associated with pluripotency and epithelial junction. In summary, our study has demonstrated the significant role of Dux-induced H3K18la in the early reprogramming process, highlighting its function as a potent trigger. Additionally, our research has revealed, for the first time, the binding of Brg1 to H3K18la, indicating its role as a reader of histone lactylation.
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Affiliation(s)
- Xinglin Hu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Xingwei Huang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 Guangdong Province, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Yue Yang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yuchen Sun
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yanhua Zhao
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Zhijing Zhang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Dan Qiu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yanshuang Wu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Guangming Wu
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 Guangdong Province, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Lei Lei
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
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11
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Pineda JMB, Bradley RK. DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers. eLife 2024; 12:RP89017. [PMID: 38829686 PMCID: PMC11147511 DOI: 10.7554/elife.89017] [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] [Indexed: 06/05/2024] Open
Abstract
Cancer immune evasion contributes to checkpoint immunotherapy failure in many patients with metastatic cancers. The embryonic transcription factor DUX4 was recently characterized as a suppressor of interferon-γ signaling and antigen presentation that is aberrantly expressed in a small subset of primary tumors. Here, we report that DUX4 expression is a common feature of metastatic tumors, with ~10-50% of advanced bladder, breast, kidney, prostate, and skin cancers expressing DUX4. DUX4 expression is significantly associated with immune cell exclusion and decreased objective response to PD-L1 blockade in a large cohort of urothelial carcinoma patients. DUX4 expression is a significant predictor of survival even after accounting for tumor mutational burden and other molecular and clinical features in this cohort, with DUX4 expression associated with a median reduction in survival of over 1 year. Our data motivate future attempts to develop DUX4 as a biomarker and therapeutic target for checkpoint immunotherapy resistance.
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Affiliation(s)
- Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Medical Scientist Training Program, University of WashingtonSeattleUnited States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
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12
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Vendrell X, de Castro P, Escrich L, Grau N, Gonzalez-Martin R, Quiñonero A, Escribá MJ, Domínguez F. Longitudinal profiling of human androgenotes through single-cell analysis unveils paternal gene expression dynamics in early embryo development. Hum Reprod 2024; 39:1186-1196. [PMID: 38622061 PMCID: PMC11145015 DOI: 10.1093/humrep/deae072] [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: 11/06/2023] [Revised: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
STUDY QUESTION How do transcriptomics vary in haploid human androgenote embryos at single cell level in the first four cell cycles of embryo development? SUMMARY ANSWER Gene expression peaks at the fourth cell cycle, however some androcytes exhibit unique transcriptional behaviors. WHAT IS KNOWN ALREADY The developmental potential of an embryo is determined by the competence of the oocyte and the sperm. However, studies of the contribution of the paternal genome using pure haploid androgenotes are very scarce. STUDY DESIGN, SIZE, DURATION This study was performed analyzing the single-cell transcriptomic sequencing of 38 androcytes obtained from 10 androgenote bioconstructs previously produced in vitro (de Castro et al., 2023). These results were analyzed through different bioinformatics software such as g: Profiler, GSEA, Cytoscape, and Reactome. PARTICIPANTS/MATERIALS, SETTING, METHODS Single cell sequencing was used to obtain the transcriptomic profiles of the different androcytes. The results obtained were compared between the different cycles studied using the DESeq2 program and functional enrichment pathways using g: Profiler, Cytoscape, and Reactome. MAIN RESULTS AND THE ROLE OF CHANCE A wave of paternally driven transcriptomic activation was found during the third-cell cycle, with 1128 upregulated and 225 downregulated genes and the fourth-cell cycle, with 1373 upregulated and 286 downregulated genes, compared to first-cell cycle androcytes. Differentially expressed routes related to cell differentiation, DNA-binding transcription, RNA biosynthesis and RNA polymerase II transcription regulatory complex, and cell death were found in the third and fourth with respect to the first-cell cycle. Conversely, in the fourth cell cycle, 153 downregulated and 332 upregulated genes were found compared with third cell cycle, associated with differentially expressed processes related to E-box binding and zinc finger protein 652 (ZNF652) transcription factor. Further, significant overexpression of LEUTX, PRAMEF1, DUXA, RFPL4A, TRIM43, and ZNF675 found in androgenotes, compared to biparental embryos, highlights the paternal contributions to zygote genome activation. LARGE SCALE DATA All raw sequencing data are available through the Gene Expression Omnibus (GEO) under accessions number: GSE216501. LIMITATIONS, REASONS FOR CAUTION Extrapolation of biological events from uniparental constructs to biparental embryos should be done with caution. Maternal and paternal genomes do not act independently of each other in a natural condition. The absence of one genome may affect gene transcription of the other. In this sense, the haploid condition of the bioconstructs could mask the transcriptomic patterns of the single cells. WIDER IMPLICATIONS OF THE FINDINGS The results obtained demonstrated the level of involvement of the human paternal haploid genome in the early stages of embryo development as well as its evolution at the transcriptomic level, laying the groundwork for the use of these bioconstructs as reliable models to dispel doubts about the genetic role played by the paternal genome in the early cycles of embryo development. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by Instituto de Salud Carlos III (ISCIII) through the project 'PI22/00924', co-funded by European Regional Development Fund (ERDF); 'A way to make Europe'. F.D. was supported by the Spanish Ministry of Economy and Competitiveness through the Miguel Servet program (CPII018/00002). M.J.E. was supported by Instituto de Salud Carlos III (PI19/00577 [M.J.E.]) and FI20/00086. P.dC. was supported by a predoctoral grant for training in research into health (PFIS PI19/00577) from the Instituto de Salud Carlos III. All authors declare having no conflict of interest with regard to this trial.
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Affiliation(s)
- X Vendrell
- Reproductive Genetics Department, Sistemas Genómicos-Synlab, Valencia, Spain
| | - P de Castro
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - L Escrich
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - N Grau
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - R Gonzalez-Martin
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - A Quiñonero
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - M J Escribá
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - F Domínguez
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
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13
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Liu B, He Y, Wu X, Lin Z, Ma J, Qiu Y, Xiang Y, Kong F, Lai F, Pal M, Wang P, Ming J, Zhang B, Wang Q, Wu J, Xia W, Shen W, Na J, Torres-Padilla ME, Li J, Xie W. Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators. Nat Cell Biol 2024; 26:962-974. [PMID: 38839978 DOI: 10.1038/s41556-024-01422-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/11/2024] [Indexed: 06/07/2024]
Abstract
Dynamic epigenomic reprogramming occurs during mammalian oocyte maturation and early development. However, the underlying transcription circuitry remains poorly characterized. By mapping cis-regulatory elements using H3K27ac, we identified putative enhancers in mouse oocytes and early embryos distinct from those in adult tissues, enabling global transitions of regulatory landscapes around fertilization and implantation. Gene deserts harbour prevalent putative enhancers in fully grown oocytes linked to oocyte-specific genes and repeat activation. Embryo-specific enhancers are primed before zygotic genome activation and are restricted by oocyte-inherited H3K27me3. Putative enhancers in oocytes often manifest H3K4me3, bidirectional transcription, Pol II binding and can drive transcription in STARR-seq and a reporter assay. Finally, motif analysis of these elements identified crucial regulators of oogenesis, TCF3 and TCF12, the deficiency of which impairs activation of key oocyte genes and folliculogenesis. These data reveal distinctive regulatory landscapes and their interacting transcription factors that underpin the development of mammalian oocytes and early embryos.
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Affiliation(s)
- Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuanlin He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Innovation Center of Suzhou Nanjing Medical University, Suzhou, China
| | - Xiaotong Wu
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jing Ma
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuexin Qiu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Yunlong Xiang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Mrinmoy Pal
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany
| | - Peizhe Wang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Jia Ming
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Bingjie Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jingyi Wu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Weikun Xia
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Weimin Shen
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China
| | - Jie Na
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | | | - Jing Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China.
- Innovation Center of Suzhou Nanjing Medical University, Suzhou, China.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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14
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Huang B, Peng X, Zhai X, Hu J, Chen J, Yang S, Huang Q, Deng E, Li H, Barakat TS, Chen J, Pei D, Fan X, Chambers I, Zhang M. Inhibition of HDAC activity directly reprograms murine embryonic stem cells to trophoblast stem cells. Dev Cell 2024:S1534-5807(24)00326-5. [PMID: 38823394 DOI: 10.1016/j.devcel.2024.05.009] [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: 07/11/2023] [Revised: 01/23/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Embryonic stem cells (ESCs) can differentiate into all cell types of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which is not fully understood. Here, we show that treating mouse ESCs with sodium butyrate (NaB) increases the population of 2C-like cells and enables direct reprogramming of ESCs into trophoblast stem cells (TSCs) without a transition through a 2C-like state. Mechanistically, NaB inhibits histone deacetylase activities in the LSD1-HDAC1/2 corepressor complex. This increases acetylation levels in the regulatory regions of both 2C- and TSC-specific genes, promoting their expression. In addition, NaB-treated cells acquire the capacity to generate blastocyst-like structures that can develop beyond the implantation stage in vitro and form deciduae in vivo. These results identify how epigenetics restrict the totipotent and trophectoderm fate in mouse ESCs.
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Affiliation(s)
- Boyan Huang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Xing Peng
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Xuzhao Zhai
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China; Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jie Hu
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Junyu Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China; School of Life Science, South China Normal University, Guangzhou 510005, China
| | - Suming Yang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Qingpei Huang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Enze Deng
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Huanhuan Li
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510525, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510525, China
| | - Xiaoying Fan
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China.
| | - Ian Chambers
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, Scotland.
| | - Man Zhang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China.
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15
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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.
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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.
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16
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Gong X, He W, Jin W, Ma H, Wang G, Li J, Xiao Y, Zhao Y, Chen Q, Guo H, Yang J, Qi Y, Dong W, Fu M, Li X, Liu J, Liu X, Yin A, Zhang Y, Wei Y. Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia. Genome Biol 2024; 25:117. [PMID: 38715110 PMCID: PMC11075363 DOI: 10.1186/s13059-024-03265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. RESULTS By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia is attributed to immature trophoblast and maldeveloped endothelial cells. Delayed epigenetic reprogramming during early extraembryonic tissue development leads to generation of excessive immature trophoblast cells. We find reduction of de novo DNA methylation in these trophoblast cells results in selective overexpression of maternally imprinted genes, including the endoretrovirus-derived gene PEG10 (paternally expressed gene 10). PEG10 forms virus-like particles, which are transferred from the trophoblast to the closely proximate endothelial cells. In normal pregnancy, only a low amount of PEG10 is transferred to maternal cells; however, in preeclampsia, excessive PEG10 disrupts maternal vascular development by inhibiting TGF-beta signaling. CONCLUSIONS Our study reveals the intricate epigenetic mechanisms that regulate trans-generational genetic conflict and ultimately ensure proper maternal-fetal interface formation.
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Affiliation(s)
- Xiaoli Gong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wei He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wan Jin
- Euler Technology, Beijing, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Ma
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiaxin Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | | | | | - Jiexia Yang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Dong
- Maternity Ward, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Meng Fu
- Department of Obstetrics and Gynecology, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiaojuan Li
- Euler Technology, Beijing, China
- Present Address: International Max Planck Research School for Genome Science, and University of Göttingen, Göttingen Center for Molecular Biosciences, Göttingen, Germany
| | | | - Xinghui Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China.
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China.
| | - Yi Zhang
- Euler Technology, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
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17
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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.
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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.
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18
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Nunes AM, Ramirez MM, Garcia-Collazo E, Jones TI, Jones PL. Muscle eosinophilia is a hallmark of chronic disease in facioscapulohumeral muscular dystrophy. Hum Mol Genet 2024; 33:872-883. [PMID: 38340007 PMCID: PMC11070135 DOI: 10.1093/hmg/ddae019] [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: 10/09/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a progressive myopathy caused by the aberrant increased expression of the DUX4 retrogene in skeletal muscle cells. The DUX4 gene encodes a transcription factor that functions in zygotic genome activation and then is silenced in most adult somatic tissues. DUX4 expression in FSHD disrupts normal muscle cell function; however, the downstream pathogenic mechanisms are still unclear. Histologically, FSHD affected muscles show a characteristic dystrophic phenotype that is often accompanied by a pronounced immune cell infiltration, but the role of the immune system in FSHD is not understood. Previously, we used ACTA1;FLExDUX4 FSHD-like mouse models varying in severity as discovery tools to identify increased Interleukin 6 and microRNA-206 levels as serum biomarkers for FSHD disease severity. In this study, we use the ACTA1;FLExDUX4 chronic FSHD-like mouse model to provide insight into the immune response to DUX4 expression in skeletal muscles. We demonstrate that these FSHD-like muscles are enriched with the chemoattractant eotaxin and the cytotoxic eosinophil peroxidase, and exhibit muscle eosinophilia. We further identified muscle fibers with positive staining for eosinophil peroxidase in human FSHD muscle. Our data supports that skeletal muscle eosinophilia is a hallmark of FSHD pathology.
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Affiliation(s)
- Andreia M Nunes
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 N. Virginia St., Reno, NV 89557, United States
| | - Monique M Ramirez
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 N. Virginia St., Reno, NV 89557, United States
| | - Enrique Garcia-Collazo
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 N. Virginia St., Reno, NV 89557, United States
| | - Takako Iida Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 N. Virginia St., Reno, NV 89557, United States
| | - Peter L Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 N. Virginia St., Reno, NV 89557, United States
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19
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Kagan F, Hejnol A. Comparative Analysis of Maternal Gene Expression Patterns Unravels Evolutionary Signatures Across Reproductive Modes. Mol Biol Evol 2024; 41:msae081. [PMID: 38679468 DOI: 10.1093/molbev/msae081] [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: 11/27/2023] [Revised: 03/09/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024] Open
Abstract
Maternal genes have a pivotal role in regulating metazoan early development. As such their functions have been extensively studied since the dawn of developmental biology. The temporal and spatial dynamics of their transcripts have been thoroughly described in model organisms and their functions have been undergoing heavy investigations. Yet, less is known about the evolutionary changes shaping their presence within diverse oocytes. Due to their unique maternal inheritance pattern, a high degree is predicted to be present when it comes to their expression. Insofar only limited and conflicting results have emerged around it. Here, we set out to elucidate which evolutionary changes could be detected in the maternal gene expression patterns using phylogenetic comparative methods on RNAseq data from 43 species. Using normalized gene expression values and fold change information throughout early development we set out to find the best-fitting evolutionary model. Through modeling, we find evidence supporting both the high degree of divergence and constraint on gene expression values, together with their temporal dynamics. Furthermore, we find that maternal gene expression alone can be used to explain the reproductive modes of different species. Together, these results suggest a highly dynamic evolutionary landscape of maternal gene expression. We also propose a possible functional dichotomy of maternal genes which is influenced by the reproductive strategy undertaken by examined species.
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Affiliation(s)
- Ferenc Kagan
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Andreas Hejnol
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Faculty of Biological Sciences, Friedrich Schiller University, Institute for Zoology and Evolutionary Research, Jena, Germany
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20
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Chen K, Liu W, Zhu J, Kou X, Zhao Y, Wang H, Jiang C, Gao S, Kang L. Pivotal role for long noncoding RNAs in zygotic genome activation in mice. SCIENCE CHINA. LIFE SCIENCES 2024; 67:958-969. [PMID: 38305985 DOI: 10.1007/s11427-023-2502-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/22/2023] [Indexed: 02/03/2024]
Abstract
Vertebrate life begins with fertilization, and then the zygote genome is activated after transient silencing, a process termed zygotic genome activation (ZGA). Despite its fundamental role in totipotency and the initiation of life, the precise mechanism underlying ZGA initiation remains unclear. The existence of minor ZGA implies the possible critical role of noncoding RNAs in the initiation of ZGA. Here, we delineate the expression profile of long noncoding RNAs (lncRNAs) in early mouse embryonic development and elucidate their critical role in minor ZGA. Compared with protein-coding genes (PCGs), lncRNAs exhibit a stronger correlation with minor ZGA. Distinct H3K9me3 profiles can be observed between lncRNA genes and PCGs, and the enrichment of H3K9me3 before ZGA might explain the suspended expression of major ZGA-related PCGs despite possessing PolII pre-configuration. Furthermore, we identified the presence of PolII-enriched MuERV-L around the transcriptional start site of minor ZGA-related lncRNAs, and these repeats are responsible for the activation of minor ZGA-related lncRNAs and subsequent embryo development. Our study suggests that MuERV-L mediates minor ZGA lncRNA activation as a critical driver between epigenetic reprogramming triggered by fertilization and the embryo developmental program, thus providing clues for understanding the regulatory mechanism of totipotency and establishing bona fide totipotent stem cells.
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Affiliation(s)
- Kang Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenju Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiang Zhu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Xiaochen Kou
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Yanhong Zhao
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Hong Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Lan Kang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
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21
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Fu B, Ma H, Liu D. Essential roles of the nucleolus during early embryonic development: a regulatory hub for chromatin organization. Open Biol 2024; 14:230358. [PMID: 38689555 PMCID: PMC11065130 DOI: 10.1098/rsob.230358] [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: 10/02/2023] [Revised: 12/26/2023] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
The nucleolus is the most prominent liquid droplet-like membrane-less organelle in mammalian cells. Unlike the nucleolus in terminally differentiated somatic cells, those in totipotent cells, such as murine zygotes or two-cell embryos, have a unique nucleolar structure known as nucleolus precursor bodies (NPBs). Previously, it was widely accepted that NPBs in zygotes are simply passive repositories of materials that will be gradually used to construct a fully functional nucleolus after zygotic genome activation (ZGA). However, recent research studies have challenged this simplistic view and demonstrated that functions of the NPBs go beyond ribosome biogenesis. In this review, we provide a snapshot of the functions of NPBs in zygotes and early two-cell embryos in mice. We propose that these membrane-less organelles function as a regulatory hub for chromatin organization. On the one hand, NPBs provide the structural platform for centric and pericentric chromatin remodelling. On the other hand, the dynamic changes in nucleolar structure control the release of the pioneer factors (i.e. double homeobox (Dux)). It appears that during transition from totipotency to pluripotency, decline of totipotency and initiation of fully functional nucleolus formation are not independent events but are interconnected. Consequently, it is reasonable to hypothesize that dissecting more unknown functions of NPBs may shed more light on the enigmas of early embryonic development and may ultimately provide novel approaches to improve reprogramming efficiency.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| | - Hong Ma
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| | - Di Liu
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
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22
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Han Q, Ma R, Liu N. Epigenetic reprogramming in the transition from pluripotency to totipotency. J Cell Physiol 2024; 239:e31222. [PMID: 38375873 DOI: 10.1002/jcp.31222] [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: 10/17/2023] [Revised: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
Mammalian development commences with the zygote, which can differentiate into both embryonic and extraembryonic tissues, a capability known as totipotency. Only the zygote and embryos around zygotic genome activation (ZGA) (two-cell embryo stage in mice and eight-cell embryo in humans) are totipotent cells. Epigenetic modifications undergo extremely extensive changes during the acquisition of totipotency and subsequent development of differentiation. However, the underlying molecular mechanisms remain elusive. Recently, the discovery of mouse two-cell embryo-like cells, human eight-cell embryo-like cells, extended pluripotent stem cells and totipotent-like stem cells with extra-embryonic developmental potential has greatly expanded our understanding of totipotency. Experiments with these in vitro models have led to insights into epigenetic changes in the reprogramming of pluri-to-totipotency, which have informed the exploration of preimplantation development. In this review, we highlight the recent findings in understanding the mechanisms of epigenetic remodeling during totipotency capture, including RNA splicing, DNA methylation, chromatin configuration, histone modifications, and nuclear organization.
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Affiliation(s)
- Qingsheng Han
- School of Medicine, Nankai University, Tianjin, China
| | - Ru Ma
- School of Medicine, Nankai University, Tianjin, China
| | - Na Liu
- School of Medicine, Nankai University, Tianjin, China
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23
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Yu H, Zhao J, Shen Y, Qiao L, Liu Y, Xie G, Chang S, Ge T, Li N, Chen M, Li H, Zhang J, Wang X. The dynamic landscape of enhancer-derived RNA during mouse early embryo development. Cell Rep 2024; 43:114077. [PMID: 38592974 DOI: 10.1016/j.celrep.2024.114077] [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: 10/03/2023] [Revised: 01/10/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024] Open
Abstract
Enhancer-derived RNAs (eRNAs) play critical roles in diverse biological processes by facilitating their target gene expression. However, the abundance and function of eRNAs in early embryos are not clear. Here, we present a comprehensive eRNA atlas by systematically integrating publicly available datasets of mouse early embryos. We characterize the transcriptional and regulatory network of eRNAs and show that different embryo developmental stages have distinct eRNA expression and regulatory profiles. Paternal eRNAs are activated asymmetrically during zygotic genome activation (ZGA). Moreover, we identify an eRNA, MZGAe1, which plays an important function in regulating mouse ZGA and early embryo development. MZGAe1 knockdown leads to a developmental block from 2-cell embryo to blastocyst. We create an online data portal, M2ED2, to query and visualize eRNA expression and regulation. Our study thus provides a systematic landscape of eRNA and reveals the important role of eRNAs in regulating mouse early embryo development.
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Affiliation(s)
- Hua Yu
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China; School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; Institute of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Jing Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Yuxuan Shen
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lu Qiao
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Yuheng Liu
- HPC Center, Westlake University, Hangzhou 310024, China
| | - Guanglei Xie
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Shuhui Chang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Tingying Ge
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Nan Li
- HPC Center, Westlake University, Hangzhou 310024, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55904, USA
| | - Jin Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Xi Wang
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China.
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24
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Hou W, Chen L, Ji J, Xiao S, Linghu H, Zhang L, Ping Y, Wang C, Kong Q, Cai W, Yang X. Maternal factor Trim75 contributes to zygotic genome activation program in mouse early embryos. Mol Biol Rep 2024; 51:560. [PMID: 38643284 DOI: 10.1007/s11033-024-09349-0] [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: 06/28/2023] [Accepted: 02/12/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Zygotic genome activation (ZGA) is an important event in the early embryo development, and human embryo developmental arrest has been highly correlated with ZGA failure in clinical studies. Although a few studies have linked maternal factors to mammalian ZGA, more studies are needed to fully elucidate the maternal factors that are involved in ZGA. METHODS AND RESULTS In this study, we utilized published single-cell RNA sequencing data from a Dux-mediated mouse embryonic stem cell to induce a 2-cell-like transition state and selected potential drivers for the transition according to an RNA velocity analysis. CONCLUSIONS An overlap of potential candidate markers of 2-cell-like-cells identified in this research with markers generated by various data sets suggests that Trim75 is a potential driver of minor ZGA and may recruit EP300 and establish H3K27ac in the gene body of minor ZGA genes, thereby contributing to mammalian preimplantation embryo development.
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Affiliation(s)
- Weibo Hou
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lijun Chen
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jingzhang Ji
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Songling Xiao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hongye Linghu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lixin Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yue Ping
- College of Life Science, Northeast Forestry University, No. 26, hexing Road, Harbin, China
| | - Chunsheng Wang
- College of Life Science, Northeast Forestry University, No. 26, hexing Road, Harbin, China
| | - Qingran Kong
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Wenpin Cai
- Department of Laboratory Medicine, Wenzhou Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou, Zhejiang, People's Republic of China.
| | - Xu Yang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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25
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Lin Y, Yu L, Xu Q, Qiu P, Zhang Y, Dong X, Yan G, Sun H, Cao G. GATAD2B is required for pre-implantation embryonic development by regulating zygotic genome activation. Cell Prolif 2024:e13647. [PMID: 38605678 DOI: 10.1111/cpr.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
Major zygotic genome activation (ZGA) occurs at the late 2-cell stage and involves the activation of thousands of genes, supporting early embryonic development. The reasons underlying the regulation of ZGA are not clear. Acetylation modifications of histone tails promote transcriptional activation, and the maternal deletion of H4K16ac leads to failure in ZGA. GATAD2B is one of the core subunits of the nucleosome remodelling and histone deacetylation (NuRD) complex. Our research has shown that GATAD2B exhibits specific nucleus localization and high protein expression from the late 2-cell stage to the 8-cell stage. This intriguing phenomenon prompted us to investigate the relationship between GATAD2B and the ZGA. We discovered a distinctive pattern of GATAD2B, starting from the late 2-cell stage with nuclear localization. GATAD2B depletion resulted in defective embryonic development, including increased DNA damage at morula, decreased blastocyst formation rate, and abnormal differentiation of ICM/TE lineages. Consistent with the delay during the cleavage stage, the transcriptome analysis of the 2-cell embryo revealed inhibition of the cell cycle G2/M phase transition pathway. Furthermore, the GATAD2B proteomic data provided clear evidence of a certain association between GATAD2B and molecules involved in the cell cycle pathway. As hypothesized, GATAD2B-deficient 2-cell embryos exhibited abnormalities in ZGA during the maternal-to-embryonic transition, with lower expression of the major ZGA marker MERVL. Overall, our results demonstrate that GATAD2B is essential for early embryonic development, in part through facilitating ZGA.
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Affiliation(s)
- Yuling Lin
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Lina Yu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Qian Xu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Panpan Qiu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Yang Zhang
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Xiaohan Dong
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Guijun Yan
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Haixiang Sun
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Guangyi Cao
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China
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26
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Wong CJ, Friedman SD, Snider L, Bennett SR, Jones TI, Jones PL, Shaw DWW, Blemker SS, Riem L, DuCharme O, Lemmers RJFL, van der Maarel SM, Wang LH, Tawil R, Statland JM, Tapscott SJ. Regional and bilateral MRI and gene signatures in facioscapulohumeral dystrophy: implications for clinical trial design and mechanisms of disease progression. Hum Mol Genet 2024; 33:698-708. [PMID: 38268317 PMCID: PMC11000661 DOI: 10.1093/hmg/ddae007] [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: 09/24/2023] [Revised: 11/11/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
Identifying the aberrant expression of DUX4 in skeletal muscle as the cause of facioscapulohumeral dystrophy (FSHD) has led to rational therapeutic development and clinical trials. Several studies support the use of MRI characteristics and the expression of DUX4-regulated genes in muscle biopsies as biomarkers of FSHD disease activity and progression. We performed lower-extremity MRI and muscle biopsies in the mid-portion of the tibialis anterior (TA) muscles bilaterally in FSHD subjects and validated our prior reports of the strong association between MRI characteristics and expression of genes regulated by DUX4 and other gene categories associated with FSHD disease activity. We further show that measurements of normalized fat content in the entire TA muscle strongly predict molecular signatures in the mid-portion of the TA, indicating that regional biopsies can accurately measure progression in the whole muscle and providing a strong basis for inclusion of MRI and molecular biomarkers in clinical trial design. An unanticipated finding was the strong correlations of molecular signatures in the bilateral comparisons, including markers of B-cells and other immune cell populations, suggesting that a systemic immune cell infiltration of skeletal muscle might have a role in disease progression.
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Affiliation(s)
- Chao-Jen Wong
- Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, United States
| | - Seth D Friedman
- Department of Radiology, Seattle Children’s Hospital, 4540 Sandpoint Way, Seattle, WA 98105, United States
| | - Lauren Snider
- Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, United States
| | - Sean R Bennett
- Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, United States
| | - Takako I Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, NV 89557, United States
| | - Peter L Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, NV 89557, United States
| | - Dennis W W Shaw
- Department of Radiology, Seattle Children’s Hospital, 4540 Sandpoint Way, Seattle, WA 98105, United States
| | - Silvia S Blemker
- Springbok Analytics, 100 W South St, Charlottesville, VA 22902, United States
| | - Lara Riem
- Springbok Analytics, 100 W South St, Charlottesville, VA 22902, United States
| | - Olivia DuCharme
- Springbok Analytics, 100 W South St, Charlottesville, VA 22902, United States
| | - Richard J F L Lemmers
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Leo H Wang
- Department of Neurology, University of Washington, 1959 NE Pacific St, Seattle, WA 98105, United States
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, 601 Elm St, Rochester, NY 14642, United States
| | - Jeffrey M Statland
- Department of Neurology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KA 66160, United States
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, United States
- Department of Neurology, University of Washington, 1959 NE Pacific St, Seattle, WA 98105, United States
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27
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Oomen ME, Torres-Padilla ME. Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo. EMBO Rep 2024; 25:1721-1733. [PMID: 38528171 PMCID: PMC11015026 DOI: 10.1038/s44319-024-00118-5] [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: 12/07/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Remnants of transposable elements (TEs) are widely expressed throughout mammalian embryo development. Originally infesting our genomes as selfish elements and acting as a source of genome instability, several of these elements have been co-opted as part of a complex system of genome regulation. Many TEs have lost transposition ability and their transcriptional potential has been tampered as a result of interactions with the host throughout evolutionary time. It has been proposed that TEs have been ultimately repurposed to function as gene regulatory hubs scattered throughout our genomes. In the early embryo in particular, TEs find a perfect environment of naïve chromatin to escape transcriptional repression by the host. As a consequence, it is thought that hosts found ways to co-opt TE sequences to regulate large-scale changes in chromatin and transcription state of their genomes. In this review, we discuss several examples of TEs expressed during embryo development, their potential for co-option in genome regulation and the evolutionary pressures on TEs and on our genomes.
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Affiliation(s)
- Marlies E Oomen
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany.
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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28
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Hu K, Li W, Ma S, Fang D, Xu J. The identification and classification of candidate genes during the zygotic genome activation in the mammals. ZYGOTE 2024; 32:119-129. [PMID: 38248909 DOI: 10.1017/s0967199423000631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Zygotic genome activation (ZGA) is a critical event in early embryonic development, and thousands of genes are involved in this delicate and sophisticated biological process. To date, however, only a handful of these genes have revealed their core functions in this special process, and therefore the roles of other genes still remain unclear. In the present study, we used previously published transcriptome profiling to identify potential key genes (candidate genes) in minor ZGA and major ZGA in both human and mouse specimens, and further identified the conserved genes across species. Our results showed that 887 and 760 genes, respectively, were thought to be specific to human and mouse in major ZGA, and the other 135 genes were considered to be orthologous genes. Moreover, the conserved genes were most enriched in rRNA processing in the nucleus and cytosol, ribonucleoprotein complex biogenesis, ribonucleoprotein complex assembly and ribosome large subunit biogenesis. The findings of this first comprehensive identification and characterization of candidate genes in minor and major ZGA provide relevant insights for future studies on ZGA.
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Affiliation(s)
- Kaiyue Hu
- Luoyang maternal and Child Health Hospital, 206, Tongqu Road, Luoyang, Henan, 47100China
| | - Wenbo Li
- The First Affiliated Hospital of Zhengzhou University, 40, Daxue Road, Zhengzhou, Henan, 450052China
| | - Shuxia Ma
- Luoyang maternal and Child Health Hospital, 206, Tongqu Road, Luoyang, Henan, 47100China
| | - Dong Fang
- Luoyang maternal and Child Health Hospital, 206, Tongqu Road, Luoyang, Henan, 47100China
| | - Jiawei Xu
- The First Affiliated Hospital of Zhengzhou University, 40, Daxue Road, Zhengzhou, Henan, 450052China
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29
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Vega-Sendino M, Lüttmann FF, Olbrich T, Chen Y, Kuenne C, Stein P, Tillo D, Carey GI, Zhong J, Savy V, Radonova L, Lu T, Saykali B, Kim KP, Domingo CN, Schüler L, Günther S, Bentsen M, Bosnakovski D, Schöler H, Kyba M, Maity TK, Jenkins LM, Looso M, Williams CJ, Kim J, Ruiz S. The homeobox transcription factor DUXBL controls exit from totipotency. Nat Genet 2024; 56:697-709. [PMID: 38509386 PMCID: PMC11149696 DOI: 10.1038/s41588-024-01692-z] [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: 11/18/2022] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
In mice, exit from the totipotent two-cell (2C) stage embryo requires silencing of the 2C-associated transcriptional program. However, the molecular mechanisms involved in this process remain poorly understood. Here we demonstrate that the 2C-specific transcription factor double homeobox protein (DUX) mediates an essential negative feedback loop by inducing the expression of DUXBL to promote this silencing. We show that DUXBL gains accessibility to DUX-bound regions specifically upon DUX expression. Furthermore, we determine that DUXBL interacts with TRIM24 and TRIM33, members of the TRIM superfamily involved in gene silencing, and colocalizes with them in nuclear foci upon DUX expression. Importantly, DUXBL overexpression impairs 2C-associated transcription, whereas Duxbl inactivation in mouse embryonic stem cells increases DUX-dependent induction of the 2C-transcriptional program. Consequently, DUXBL deficiency in embryos results in sustained expression of 2C-associated transcripts leading to early developmental arrest. Our study identifies DUXBL as an essential regulator of totipotency exit enabling the first divergence of cell fates.
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Affiliation(s)
| | - Felipe F Lüttmann
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
| | - Teresa Olbrich
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Yanpu Chen
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Carsten Kuenne
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Paula Stein
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | | | - Grace I Carey
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Jiasheng Zhong
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Virginia Savy
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Lenka Radonova
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Tianlin Lu
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Frankfurt, Germany
| | - Bechara Saykali
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA
| | - Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | | | - Leah Schüler
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Darko Bosnakovski
- Lillehei Heart Institute, Department of Pediatrics, University of Minnesota, Minneapolis, USA
| | - Hans Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Michael Kyba
- Lillehei Heart Institute, Department of Pediatrics, University of Minnesota, Minneapolis, USA
| | - Tapan K Maity
- Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, MD, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, MD, USA
| | - Mario Looso
- Cardio-Pulmonary Institute, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany
| | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Johnny Kim
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute, Frankfurt, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein/Main, Germany.
- German Center for Lung Research (DZL), Partner Site Rhein/Main, Germany.
- Institute of Lung Health (ILH), Justus-Liebig-University Giessen, Giessen, Germany.
- The Center for Cardiovascular Regeneration and Immunology at TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany.
| | - Sergio Ruiz
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD, USA.
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30
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Barra J, Taverna F, Bong F, Ahmed I, Karakach TK. Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression. Brief Bioinform 2024; 25:bbae233. [PMID: 38770716 PMCID: PMC11106635 DOI: 10.1093/bib/bbae233] [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: 12/21/2023] [Revised: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 05/22/2024] Open
Abstract
Temporal RNA-sequencing (RNA-seq) studies of bulk samples provide an opportunity for improved understanding of gene regulation during dynamic phenomena such as development, tumor progression or response to an incremental dose of a pharmacotherapeutic. Moreover, single-cell RNA-seq (scRNA-seq) data implicitly exhibit temporal characteristics because gene expression values recapitulate dynamic processes such as cellular transitions. Unfortunately, temporal RNA-seq data continue to be analyzed by methods that ignore this ordinal structure and yield results that are often difficult to interpret. Here, we present Error Modelled Gene Expression Analysis (EMOGEA), a framework for analyzing RNA-seq data that incorporates measurement uncertainty, while introducing a special formulation for those acquired to monitor dynamic phenomena. This method is specifically suited for RNA-seq studies in which low-count transcripts with small-fold changes lead to significant biological effects. Such transcripts include genes involved in signaling and non-coding RNAs that inherently exhibit low levels of expression. Using simulation studies, we show that this framework down-weights samples that exhibit extreme responses such as batch effects allowing them to be modeled with the rest of the samples and maintain the degrees of freedom originally envisioned for a study. Using temporal experimental data, we demonstrate the framework by extracting a cascade of gene expression waves from a well-designed RNA-seq study of zebrafish embryogenesis and an scRNA-seq study of mouse pre-implantation and provide unique biological insights into the regulation of genes in each wave. For non-ordinal measurements, we show that EMOGEA has a much higher rate of true positive calls and a vanishingly small rate of false negative discoveries compared to common approaches. Finally, we provide two packages in Python and R that are self-contained and easy to use, including test data.
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Affiliation(s)
- Jasmine Barra
- Laboratory of Integrative Multi-Omics Research, Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Beatrice Hunter Cancer Research Institute, 5743 University Avenue, Suite 98, Halifax, NS, B3H 0A2, Canada
- Department of Microbiology & Immunology, Dalhousie University, 5850 College Street, Halifax, NS, B3H 4R2, Canada
| | - Federico Taverna
- Laboratory of Integrative Multi-Omics Research, Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Beatrice Hunter Cancer Research Institute, 5743 University Avenue, Suite 98, Halifax, NS, B3H 0A2, Canada
| | - Fabian Bong
- Laboratory of Integrative Multi-Omics Research, Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Beatrice Hunter Cancer Research Institute, 5743 University Avenue, Suite 98, Halifax, NS, B3H 0A2, Canada
| | - Ibrahim Ahmed
- Laboratory of Integrative Multi-Omics Research, Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Beatrice Hunter Cancer Research Institute, 5743 University Avenue, Suite 98, Halifax, NS, B3H 0A2, Canada
| | - Tobias K Karakach
- Laboratory of Integrative Multi-Omics Research, Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS, B3H 4R2, Canada
- Beatrice Hunter Cancer Research Institute, 5743 University Avenue, Suite 98, Halifax, NS, B3H 0A2, Canada
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31
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Ye Y, Homer HA. A surge in cytoplasmic viscosity triggers nuclear remodeling required for Dux silencing and pre-implantation embryo development. Cell Rep 2024; 43:113917. [PMID: 38446665 DOI: 10.1016/j.celrep.2024.113917] [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: 08/23/2023] [Revised: 12/17/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Embryonic genome activation (EGA) marks the transition from dependence on maternal transcripts to an embryonic transcriptional program. The precise temporal regulation of gene expression, specifically the silencing of the Dux/murine endogenous retrovirus type L (MERVL) program during late 2-cell interphase, is crucial for developmental progression in mouse embryos. How this finely tuned regulation is achieved within this specific window is poorly understood. Here, using particle-tracking microrheology throughout the mouse oocyte-to-embryo transition, we identify a surge in cytoplasmic viscosity specific to late 2-cell interphase brought about by high microtubule and endomembrane density. Importantly, preventing the rise in 2-cell viscosity severely impairs nuclear reorganization, resulting in a persistently open chromatin configuration and failure to silence Dux/MERVL. This, in turn, derails embryo development beyond the 2- and 4-cell stages. Our findings reveal a mechanical role of the cytoplasm in regulating Dux/MERVL repression via nuclear remodeling during a temporally confined period in late 2-cell interphase.
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Affiliation(s)
- Yunan Ye
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia
| | - Hayden Anthony Homer
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia.
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32
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Giaccari C, Cecere F, Argenziano L, Pagano A, Galvao A, Acampora D, Rossi G, Hay Mele B, Acurzio B, Coonrod S, Cubellis MV, Cerrato F, Andrews S, Cecconi S, Kelsey G, Riccio A. A maternal-effect Padi6 variant causes nuclear and cytoplasmic abnormalities in oocytes, as well as failure of epigenetic reprogramming and zygotic genome activation in embryos. Genes Dev 2024; 38:131-150. [PMID: 38453481 PMCID: PMC10982689 DOI: 10.1101/gad.351238.123] [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: 10/09/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024]
Abstract
Maternal inactivation of genes encoding components of the subcortical maternal complex (SCMC) and its associated member, PADI6, generally results in early embryo lethality. In humans, SCMC gene variants were found in the healthy mothers of children affected by multilocus imprinting disturbances (MLID). However, how the SCMC controls the DNA methylation required to regulate imprinting remains poorly defined. We generated a mouse line carrying a Padi6 missense variant that was identified in a family with Beckwith-Wiedemann syndrome and MLID. If homozygous in female mice, this variant resulted in interruption of embryo development at the two-cell stage. Single-cell multiomic analyses demonstrated defective maturation of Padi6 mutant oocytes and incomplete DNA demethylation, down-regulation of zygotic genome activation (ZGA) genes, up-regulation of maternal decay genes, and developmental delay in two-cell embryos developing from Padi6 mutant oocytes but little effect on genomic imprinting. Western blotting and immunofluorescence analyses showed reduced levels of UHRF1 in oocytes and abnormal localization of DNMT1 and UHRF1 in both oocytes and zygotes. Treatment with 5-azacytidine reverted DNA hypermethylation but did not rescue the developmental arrest of mutant embryos. Taken together, this study demonstrates that PADI6 controls both nuclear and cytoplasmic oocyte processes that are necessary for preimplantation epigenetic reprogramming and ZGA.
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Affiliation(s)
- Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Lucia Argenziano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Angela Pagano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Antonio Galvao
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn 10-748, Poland
| | - Dario Acampora
- Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso," Consiglio Nazionale delle Ricerche (CNR), Naples 80131, Italy
| | - Gianna Rossi
- Department of Life, Health, and Environmental Sciences, Università dell'Aquila, L'Aquila 67100, Italy
| | - Bruno Hay Mele
- Department of Biology, University of Naples "Federico II," Napoli 80126, Italy
| | - Basilia Acurzio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Scott Coonrod
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | | | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Simon Andrews
- Bioinformatics Unit, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Sandra Cecconi
- Department of Life, Health, and Environmental Sciences, Università dell'Aquila, L'Aquila 67100, Italy
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge CB2 0QQ, United Kingdom
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy;
- Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso," Consiglio Nazionale delle Ricerche (CNR), Naples 80131, Italy
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33
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Nguyen TH, Limpens M, Bouhmidi S, Paprzycki L, Legrand A, Declèves AE, Heher P, Belayew A, Banerji CRS, Zammit PS, Tassin A. The DUX4-HIF1α Axis in Murine and Human Muscle Cells: A Link More Complex Than Expected. Int J Mol Sci 2024; 25:3327. [PMID: 38542301 PMCID: PMC10969790 DOI: 10.3390/ijms25063327] [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: 12/29/2023] [Revised: 02/20/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
FacioScapuloHumeral muscular Dystrophy (FSHD) is one of the most prevalent inherited muscle disorders and is linked to the inappropriate expression of the DUX4 transcription factor in skeletal muscles. The deregulated molecular network causing FSHD muscle dysfunction and pathology is not well understood. It has been shown that the hypoxia response factor HIF1α is critically disturbed in FSHD and has a major role in DUX4-induced cell death. In this study, we further explored the relationship between DUX4 and HIF1α. We found that the DUX4 and HIF1α link differed according to the stage of myogenic differentiation and was conserved between human and mouse muscle. Furthermore, we found that HIF1α knockdown in a mouse model of DUX4 local expression exacerbated DUX4-mediated muscle fibrosis. Our data indicate that the suggested role of HIF1α in DUX4 toxicity is complex and that targeting HIF1α might be challenging in the context of FSHD therapeutic approaches.
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Affiliation(s)
- Thuy-Hang Nguyen
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium
| | - Maelle Limpens
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium
| | - Sihame Bouhmidi
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium
| | - Lise Paprzycki
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium
| | - Alexandre Legrand
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium
| | - Anne-Emilie Declèves
- Department of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium
| | - Philipp Heher
- Randall Centre for Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Alexandra Belayew
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium
| | - Christopher R. S. Banerji
- Randall Centre for Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London SE1 1UL, UK
- The Alan Turing Institute, The British Library, London NW1 2DB, UK
| | - Peter S. Zammit
- Randall Centre for Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Alexandra Tassin
- Laboratory of Respiratory Physiology, Pathophysiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 7000 Mons, Belgium
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34
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Du P, Wu J. Hallmarks of totipotent and pluripotent stem cell states. Cell Stem Cell 2024; 31:312-333. [PMID: 38382531 PMCID: PMC10939785 DOI: 10.1016/j.stem.2024.01.009] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for the development of all mammals. Studying these in vivo has been challenging due to limited access and ethical constraints, particularly in humans. Recent progress has led to diverse culture adaptations of epiblast cells in vitro in the form of totipotent and pluripotent stem cells, which not only deepen our understanding of embryonic development but also serve as invaluable resources for animal reproduction and regenerative medicine. This review delves into the hallmarks of totipotent and pluripotent stem cells, shedding light on their key molecular and functional features.
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Affiliation(s)
- Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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35
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Vega-Sendino M, Ruiz S. Transition from totipotency to pluripotency in mice: insights into molecular mechanisms. Biochem Soc Trans 2024; 52:231-239. [PMID: 38288760 DOI: 10.1042/bst20230442] [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: 11/02/2023] [Revised: 12/26/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
Totipotency is the ability of a single cell to develop into a full organism and, in mammals, is strictly associated with the early stages of development following fertilization. This unlimited developmental potential becomes quickly restricted as embryonic cells transition into a pluripotent state. The loss of totipotency seems a consequence of the zygotic genome activation (ZGA), a process that determines the switch from maternal to embryonic transcription, which in mice takes place following the first cleavage. ZGA confers to the totipotent cell a transient transcriptional profile characterized by the expression of stage-specific genes and a set of transposable elements that prepares the embryo for subsequent development. The timely silencing of this transcriptional program during the exit from totipotency is required to ensure proper development. Importantly, the molecular mechanisms regulating the transition from totipotency to pluripotency have remained elusive due to the scarcity of embryonic material. However, the development of new in vitro totipotent-like models together with advances in low-input genome-wide technologies, are providing a better mechanistic understanding of how this important transition is achieved. This review summarizes the current knowledge on the molecular determinants that regulate the exit from totipotency.
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Affiliation(s)
- Maria Vega-Sendino
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD 20814, U.S.A
| | - Sergio Ruiz
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD 20814, U.S.A
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Wu B, Wang Y, Wei X, Zhang J, Wu J, Cao G, Zhang Y, Liu J, Li X, Bao S. NELFA and BCL2 induce the 2C-like state in mouse embryonic stem cells in a chemically defined medium. Cell Prolif 2024; 57:e13534. [PMID: 37592709 PMCID: PMC10849787 DOI: 10.1111/cpr.13534] [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: 05/11/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
A minority of mouse embryonic stem cells (ESCs) display totipotent features resembling 2-cell stage embryos and are known as 2-cell-like (2C-like) cells. However, how ESCs transit into this 2C-like state remains largely unknown. Here, we report that the overexpression of negative elongation factor A (Nelfa), a maternally provided factor, enhances the conversion of ESCs into 2C-like cells in chemically defined conditions, while the deletion of endogenous Nelfa does not block this transition. We also demonstrate that Nelfa overexpression significantly enhances somatic cell reprogramming efficiency. Interestingly, we found that the co-overexpression of Nelfa and Bcl2 robustly activates the 2C-like state in ESCs and endows the cells with dual cell fate potential. We further demonstrate that Bcl2 overexpression upregulates endogenous Nelfa expression and can induce the 2C-like state in ESCs even in the absence of Nelfa. Our findings highlight the importance of BCL2 in the regulation of the 2C-like state and provide insights into the mechanism underlying the roles of Nelfa and Bcl2 in the establishment and regulation of the totipotent state in mouse ESCs.
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Affiliation(s)
- Baojiang Wu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Yanqiu Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Xinhua Wei
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Jiahui Wu
- School of Veterinary MedicineInner Mongolia Agricultural UniversityHohhotChina
| | - Guifang Cao
- School of Veterinary MedicineInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic AnimalHohhotChina
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Xihe Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic AnimalHohhotChina
| | - Siqin Bao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
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Akiyama T, Ishiguro KI, Chikazawa N, Ko SBH, Yukawa M, Ko MSH. ZSCAN4-binding motif-TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes. DNA Res 2024; 31:dsad029. [PMID: 38153767 PMCID: PMC10785592 DOI: 10.1093/dnares/dsad029] [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: 09/25/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 12/29/2023] Open
Abstract
The Zinc finger and SCAN domain containing 4 (ZSCAN4) protein, expressed transiently in pluripotent stem cells, gametes, and early embryos, extends telomeres, enhances genome stability, and improves karyotypes in mouse embryonic stem (mES) cells. To gain insights into the mechanism of ZSCAN4 function, we identified genome-wide binding sites of endogenous ZSCAN4 protein using ChIP-seq technology in mouse and human ES cells, where the expression of endogenous ZSCAN4 was induced by treating cells with retinoic acids or by overexpressing DUX4. We revealed that both mouse and human ZSCAN4 bind to the TGCACAC motif located in CA/TG microsatellite repeats, which are known to form unstable left-handed duplexes called Z-DNA that can induce double-strand DNA breaks and mutations. These ZSCAN4 binding sites are mostly located in intergenic and intronic regions of the genomes. By generating ZSCAN4 knockout in human ES cells, we showed that ZSCAN4 does not seem to be involved in transcriptional regulation. We also found that ectopic expression of mouse ZSCAN4 enhances the suppression of chromatin at ZSCAN4-binding sites. These results together suggest that some of the ZSCAN4 functions are mediated by binding to the error-prone regions in mouse and human genomes.
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Affiliation(s)
- Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Molecular Biology, Yokohama City University, School of Medicine, Kanagawa 236-0027, Japan
| | - Kei-ichiro Ishiguro
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto 860-0811, Japan
| | - Nana Chikazawa
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shigeru B H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masashi Yukawa
- Integrated Medical and Agricultural School of Public Health, Ehime University, Ehime 791-0295, Japan
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3026, USA
| | - Minoru S H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA
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38
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Yakhou L, Azogui A, Therizols P, Defossez PA. [Using 2C-like cells to understand embryonic totipotency]. Med Sci (Paris) 2024; 40:147-153. [PMID: 38411422 DOI: 10.1051/medsci/2023217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Totipotency is the ability of a cell to generate a whole organism, a property that characterizes the first embryonic cells, such as the zygote and the blastomeres. This review provides a retrospective on the progress made in the last decade in the study of totipotency, especially with the discovery of mouse ES cells expressing markers of the 2-cell stage (2C-like cells). This model has greatly contributed to a better understanding of the molecular mechanisms involved in totipotency (pioneer factors, epigenetic regulation, splicing, nuclear maturation). 2C-like cells have also paved the way for the development of new cellular models of human totipotency.
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Affiliation(s)
- Lounis Yakhou
- Équipe dynamiquede la méthylation de l'ADN des génomes eucaryotes, Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris-Cité, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Anaelle Azogui
- Équipe dynamiquede la méthylation de l'ADN des génomes eucaryotes, Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris-Cité, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Pierre Therizols
- Équipe dynamiquede la méthylation de l'ADN des génomes eucaryotes, Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris-Cité, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Pierre-Antoine Defossez
- Équipe dynamiquede la méthylation de l'ADN des génomes eucaryotes, Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris-Cité, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
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39
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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40
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Lemmers RJLF, Butterfield R, van der Vliet PJ, de Bleecker JL, van der Pol L, Dunn DM, Erasmus CE, D'Hooghe M, Verhoeven K, Balog J, Bigot A, van Engelen B, Statland J, Bugiardini E, van der Stoep N, Evangelista T, Marini-Bettolo C, van den Bergh P, Tawil R, Voermans NC, Vissing J, Weiss RB, van der Maarel SM. Autosomal dominant in cis D4Z4 repeat array duplication alleles in facioscapulohumeral dystrophy. Brain 2024; 147:414-426. [PMID: 37703328 PMCID: PMC10834250 DOI: 10.1093/brain/awad312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/26/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) has a unique genetic aetiology resulting in partial chromatin relaxation of the D4Z4 macrosatellite repeat array on 4qter. This D4Z4 chromatin relaxation facilitates inappropriate expression of the transcription factor DUX4 in skeletal muscle. DUX4 is encoded by a retrogene that is embedded within the distal region of the D4Z4 repeat array. In the European population, the D4Z4 repeat array is usually organized in a single array that ranges between 8 and 100 units. D4Z4 chromatin relaxation and DUX4 derepression in FSHD is most often caused by repeat array contraction to 1-10 units (FSHD1) or by a digenic mechanism requiring pathogenic variants in a D4Z4 chromatin repressor like SMCHD1, combined with a repeat array between 8 and 20 units (FSHD2). With a prevalence of 1.5% in the European population, in cis duplications of the D4Z4 repeat array, where two adjacent D4Z4 arrays are interrupted by a spacer sequence, are relatively common but their relationship to FSHD is not well understood. In cis duplication alleles were shown to be pathogenic in FSHD2 patients; however, there is inconsistent evidence for the necessity of an SMCHD1 mutation for disease development. To explore the pathogenic nature of these alleles we compared in cis duplication alleles in FSHD patients with or without pathogenic SMCHD1 variant. For both groups we showed duplication-allele-specific DUX4 expression. We studied these alleles in detail using pulsed-field gel electrophoresis-based Southern blotting and molecular combing, emphasizing the challenges in the characterization of these rearrangements. Nanopore sequencing was instrumental to study the composition and methylation of the duplicated D4Z4 repeat arrays and to identify the breakpoints and the spacer sequence between the arrays. By comparing the composition of the D4Z4 repeat array of in cis duplication alleles in both groups, we found that specific combinations of proximal and distal repeat array sizes determine their pathogenicity. Supported by our algorithm to predict pathogenicity, diagnostic laboratories should now be furnished to accurately interpret these in cis D4Z4 repeat array duplications, alleles that can easily be missed in routine settings.
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Affiliation(s)
- Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | | | - Patrick J van der Vliet
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | | | - Ludo van der Pol
- University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Corrie E Erasmus
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Marc D'Hooghe
- Department of Neurology, Algemeen Ziekenhuis Sint-Jan, 8000, Brugge, Belgium
| | - Kristof Verhoeven
- Department of Neurology, Algemeen Ziekenhuis Sint-Jan, 8000, Brugge, Belgium
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Anne Bigot
- Sorbonne Université, Inserm UMRS974, Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France
| | - Baziel van Engelen
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | | | - Enrico Bugiardini
- National Hospital For Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Teresinha Evangelista
- Unité de Morphologie Neuromusculaire, Institut de Myologie, AP-HP, F-75013, Paris, France
| | - Chiara Marini-Bettolo
- The John Walton Muscular Dystrophy Research Centre, Faculty of Medical Sciences, Newcastle upon Tyne, NE1 3BZ, UK
| | | | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, NY 14642, Rochester, USA
| | - Nicol C Voermans
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - John Vissing
- Department of Neurology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
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41
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de la Rosa S, del Mar Rigual M, Vargiu P, Ortega S, Djouder N. Endogenous retroviruses shape pluripotency specification in mouse embryos. SCIENCE ADVANCES 2024; 10:eadk9394. [PMID: 38266080 PMCID: PMC10807815 DOI: 10.1126/sciadv.adk9394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The smooth and precise transition from totipotency to pluripotency is a key process in embryonic development, generating pluripotent stem cells capable of forming all cell types. While endogenous retroviruses (ERVs) are essential for early development, their precise roles in this transition remains mysterious. Using cutting-edge genetic and biochemical techniques in mice, we identify MERVL-gag, a retroviral protein, as a crucial modulator of pluripotent factors OCT4 and SOX2 during lineage specification. MERVL-gag tightly operates with URI, a prefoldin protein that concurs with pluripotency bias in mouse blastomeres, and which is indeed required for totipotency-to-pluripotency transition. Accordingly, URI loss promotes a stable totipotent-like state and embryo arrest at 2C stage. Mechanistically, URI binds and shields OCT4 and SOX2 from proteasome degradation, while MERVL-gag displaces URI from pluripotent factor interaction, causing their degradation. Our findings reveal the symbiotic coevolution of ERVs with their host cells to ensure the smooth and timely progression of early embryo development.
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Affiliation(s)
- Sergio de la Rosa
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - María del Mar Rigual
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Pierfrancesco Vargiu
- Mouse Genome Editing Core Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sagrario Ortega
- Mouse Genome Editing Core Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
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42
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Lu X. Regulation of endogenous retroviruses in murine embryonic stem cells and early embryos. J Mol Cell Biol 2024; 15:mjad052. [PMID: 37604781 PMCID: PMC10794949 DOI: 10.1093/jmcb/mjad052] [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: 06/08/2022] [Revised: 11/24/2022] [Accepted: 08/19/2023] [Indexed: 08/23/2023] Open
Abstract
Endogenous retroviruses (ERVs) are important components of transposable elements that constitute ∼40% of the mouse genome. ERVs exhibit dynamic expression patterns during early embryonic development and are engaged in numerous biological processes. Therefore, ERV expression must be closely monitored in cells. Most studies have focused on the regulation of ERV expression in mouse embryonic stem cells (ESCs) and during early embryonic development. This review touches on the classification, expression, and functions of ERVs in mouse ESCs and early embryos and mainly discusses ERV modulation strategies from the perspectives of transcription, epigenetic modification, nucleosome/chromatin assembly, and post-transcriptional control.
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Affiliation(s)
- Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China
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43
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Guo Y, Li TD, Modzelewski AJ, Siomi H. Retrotransposon renaissance in early embryos. Trends Genet 2024; 40:39-51. [PMID: 37949723 DOI: 10.1016/j.tig.2023.10.010] [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: 07/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Despite being the predominant genetic elements in mammalian genomes, retrotransposons were often dismissed as genomic parasites with ambiguous biological significance. However, recent studies reveal their functional involvement in early embryogenesis, encompassing crucial processes such as zygotic genome activation (ZGA) and cell fate decision. This review underscores the paradigm shift in our understanding of retrotransposon roles during early preimplantation development, as well as their rich functional reservoir that is exploited by the host to provide cis-regulatory elements, noncoding RNAs, and functional proteins. The rapid advancement in long-read sequencing, low input multiomics profiling, advanced in vitro systems, and precise gene editing techniques encourages further dissection of retrotransposon functions that were once obscured by the intricacies of their genomic footprints.
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Affiliation(s)
- Youjia Guo
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Ten D Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA
| | - Andrew J Modzelewski
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA.
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo 160-8582, Japan.
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44
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Pineda JMB, Bradley RK. DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548412. [PMID: 37502871 PMCID: PMC10369889 DOI: 10.1101/2023.07.10.548412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cancer immune evasion contributes to checkpoint immunotherapy failure in many patients with metastatic cancers. The embryonic transcription factor DUX4 was recently characterized as a suppressor of interferon-γ signaling and antigen presentation that is aberrantly expressed in a small subset of primary tumors. Here, we report that DUX4 expression is a common feature of metastatic tumors, with ~10-50% of advanced bladder, breast, kidney, prostate, and skin cancers expressing DUX4. DUX4 expression is significantly associated with immune cell exclusion and decreased objective response to PD-L1 blockade in a large cohort of urothelial carcinoma patients. DUX4 expression is a significant predictor of survival even after accounting for tumor mutational burden and other molecular and clinical features in this cohort, with DUX4 expression associated with a median reduction in survival of over one year. Our data motivate future attempts to develop DUX4 as a biomarker and therapeutic target for checkpoint immunotherapy resistance.
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Affiliation(s)
- Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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45
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Full F, Walter S, Neugebauer E, Tan J, Drayman N, Franke V, Tay S, Landthaler M, Akalin A, Ensser A, Wyler E. Herpesviruses mimic zygotic genome activation to promote viral replication. RESEARCH SQUARE 2023:rs.3.rs-3125635. [PMID: 38168299 PMCID: PMC10760233 DOI: 10.21203/rs.3.rs-3125635/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: 01/05/2024]
Abstract
DUX4 is a germline transcription factor and a master regulator of zygotic genome activation. During early embryogenesis, DUX4 is crucial for maternal to zygotic transition at the 2-8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In adult somatic cells, DUX4 expression is silenced and its activation in adult muscle cells causes the genetic disorder Facioscapulohumeral Muscular Dystrophy (FSHD). Here we show that herpesviruses from alpha-, beta- and gamma-herpesvirus subfamilies as well as papillomaviruses actively induce DUX4 expression to promote viral transcription and replication. We demonstrate that HSV-1 immediate early proteins directly induce expression of DUX4 and its target genes including endogenous retroelements, which mimics zygotic genome activation. We further show that DUX4 directly binds to the viral genome and promotes viral transcription. DUX4 is functionally required for herpesvirus infection, since genetic depletion of DUX4 by CRISPR/Cas9 abrogates viral replication. Our results show that herpesviruses induce DUX4 expression and its downstream germline-specific genes and retroelements, thus mimicking an early embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression.
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Affiliation(s)
- Florian Full
- University Medical Center, and Faculty of Medicine, Albert-Ludwig-University Freiburg
| | - Stephanie Walter
- Institute for Clinical and Molecular Virology, University Hospital Erlangen
| | - Eva Neugebauer
- Institute of Virology, University Medical Center, and Faculty of Medicine, Albert-Ludwig-University Freiburg
| | - Jiang Tan
- Institute of Virology, University Medical Center, and Faculty of Medicine, Albert-Ludwig-University Freiburg
| | - Nir Drayman
- The Department of Molecular Biology and Biochemistry, the Center for Virus Research and the Center for Complex Biological Systems, The University of California, Irvine
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Kretschmer M, Fischer V, Gapp K. When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development. Biomolecules 2023; 13:1750. [PMID: 38136621 PMCID: PMC10742275 DOI: 10.3390/biom13121750] [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: 11/04/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Multiple lines of evidence suggest that paternal psychological stress contributes to an increased prevalence of neuropsychiatric and metabolic diseases in the progeny. While altered paternal care certainly plays a role in such transmitted disease risk, molecular factors in the germline might additionally be at play in humans. This is supported by findings on changes to the molecular make up of germ cells and suggests an epigenetic component in transmission. Several rodent studies demonstrate the correlation between paternal stress induced changes in epigenetic modifications and offspring phenotypic alterations, yet some intriguing cases also start to show mechanistic links in between sperm and the early embryo. In this review, we summarise efforts to understand the mechanism of intergenerational transmission from sperm to the early embryo. In particular, we highlight how stress alters epigenetic modifications in sperm and discuss the potential for these modifications to propagate modified molecular trajectories in the early embryo to give rise to aberrant phenotypes in adult offspring.
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Affiliation(s)
- Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
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Perera CD, Idrees M, Khan AM, Haider Z, Ullah S, Kang JS, Lee SH, Kang SM, Kong IK. PDGFRβ Activation Induced the Bovine Embryonic Genome Activation via Enhanced NFYA Nuclear Localization. Int J Mol Sci 2023; 24:17047. [PMID: 38069370 PMCID: PMC10707662 DOI: 10.3390/ijms242317047] [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: 10/30/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Embryonic genome activation (EGA) is a critical step during embryonic development. Several transcription factors have been identified that play major roles in initiating EGA; however, this gradual and complex mechanism still needs to be explored. In this study, we investigated the role of nuclear transcription factor Y subunit A (NFYA) in bovine EGA and bovine embryonic development and its relationship with the platelet-derived growth factor receptor-β (PDGFRβ) by using a potent selective activator (PDGF-BB) and inhibitor (CP-673451) of PDGF receptors. Activation and inhibition of PDGFRβ using PDGF-BB and CP-673451 revealed that NFYA expression is significantly (p < 0.05) affected by the PDGFRβ. In addition, PDGFRβ mRNA expression was significantly increased (p < 0.05) in the activator group and significantly decreased (p < 0.05) in the inhibitor group when compared with PDGFRα. Downregulation of NFYA following PDGFRβ inhibition was associated with the expression of critical EGA-related genes, bovine embryo development rate, and implantation potential. Moreover, ROS and mitochondrial apoptosis levels and expression of pluripotency-related markers necessary for inner cell mass development were also significantly (p < 0.05) affected by the downregulation of NFYA while interrupting trophoblast cell (CDX2) differentiation. In conclusion, the PDGFRβ-NFYA axis is critical for bovine embryonic genome activation and embryonic development.
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Affiliation(s)
- Chalani Dilshani Perera
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Muhammad Idrees
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Abdul Majid Khan
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Zaheer Haider
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Safeer Ullah
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Ji-Su Kang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Seo-Hyun Lee
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Seon-Min Kang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Il-Keun Kong
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
- The King Kong Corp. Ltd., Gyeongsang National University, Jinju 52828, Republic of Korea
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48
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Mwalilino L, Yamane M, Ishiguro KI, Usuki S, Endoh M, Niwa H. The role of Zfp352 in the regulation of transient expression of 2-cell specific genes in mouse embryonic stem cells. Genes Cells 2023; 28:831-844. [PMID: 37778747 DOI: 10.1111/gtc.13070] [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: 08/07/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Mouse ES cell populations contain a minor sub-population that expresses genes specifically expressed in 2-cell stage embryos. This sub-population consists of 2-cell-gene labeled cells (2CLCs) generated by the transient activation of the 2-cell specific genes initiated by the master regulator, Dux. However, the mechanism regulating the transient expression remains largely unclear. Here we reported a novel function of Zfp352, one of the 2-cell specific genes, in regulating the 2CLC sub-population. Zfp352 encodes zinc-finger transcription factor belonging to the Klf family. Dux transiently activates Zfp352 after the activation of Zscan4c in a subset of the 2CLC subpopulation. Interestingly, in the reporter assay, the transcriptional activation of Zscan4c by Dux is strongly repressed by the co-expression of Zfp352. However, the knockout of Zfp352 resulted in the repression of a subset of the 2-cell-specific genes. These data suggest the dual roles of Zfp352 in regulating the transient activation of the 2-cell-specific genes.
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Affiliation(s)
- Lusubilo Mwalilino
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Mariko Yamane
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Department of Functional Genome Informatics, Division of Medical Genomics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Kei-Ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, Japan
| | - Mitsuhiro Endoh
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
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Jiang Z. Molecular and cellular programs underlying the development of bovine pre-implantation embryos. Reprod Fertil Dev 2023; 36:34-42. [PMID: 38064195 PMCID: PMC10962643 DOI: 10.1071/rd23146] [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] [Indexed: 12/18/2023] Open
Abstract
Early embryonic mortality is a major cause of infertility in cattle, yet the underlying molecular causes remain a mystery. Over the past half century, assisted reproductive technologies such as in vitro fertilisation and somatic cell nuclear transfer have been used to improve cattle reproductive efficiency; however, reduced embryo developmental potential is seen compared to their in vivo counterparts. Recent years have seen exciting progress across bovine embryo research, including genomic profiling of embryogenesis, new methods for improving embryo competence, and experimenting on building bovine embryos from stem cell cultures. These advances are beginning to define bovine embryo molecular and cellular programs and could potentially lead to improved embryo health. Here, I highlight the current status of molecular determinants and cellular programs of bovine embryo development and new opportunities to improve the bovine embryo health.
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Affiliation(s)
- Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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50
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Cohen J, Huang S, Koczwara KE, Woods KT, Ho V, Woodman KG, Arbiser JL, Daman K, Lek M, Emerson CP, DeSimone AM. Flavones provide resistance to DUX4-induced toxicity via an mTor-independent mechanism. Cell Death Dis 2023; 14:749. [PMID: 37973788 PMCID: PMC10654915 DOI: 10.1038/s41419-023-06257-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 10/10/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is among the most common of the muscular dystrophies, affecting nearly 1 in 8000 individuals, and is a cause of profound disability. Genetically, FSHD is linked to the contraction and/or epigenetic de-repression of the D4Z4 repeat array on chromosome 4, thereby allowing expression of the DUX4 gene in skeletal muscle. If the DUX4 transcript incorporates a stabilizing polyadenylation site the myotoxic DUX4 protein will be synthesized, resulting in muscle wasting. The mechanism of toxicity remains unclear, as many DUX4-induced cytopathologies have been described, however cell death does primarily occur through caspase 3/7-dependent apoptosis. To date, most FSHD therapeutic development has focused on molecular methods targeting DUX4 expression or the DUX4 transcript, while therapies targeting processes downstream of DUX4 activity have received less attention. Several studies have demonstrated that inhibition of multiple signal transduction pathways can ameliorate DUX4-induced toxicity, and thus compounds targeting these pathways have the potential to be developed into FSHD therapeutics. To this end, we have screened a group of small molecules curated based on their reported activity in relevant pathways and/or structural relationships with known toxicity-modulating molecules. We have identified a panel of five compounds that function downstream of DUX4 activity to inhibit DUX4-induced toxicity. Unexpectedly, this effect was mediated through an mTor-independent mechanism that preserved expression of ULK1 and correlated with an increase in a marker of active cellular autophagy. This identifies these flavones as compounds of interest for therapeutic development, and potentially identifies the autophagy pathway as a target for therapeutics.
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Affiliation(s)
- Justin Cohen
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Shushu Huang
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | - Kristen T Woods
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Disease Research University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Vincent Ho
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Keryn G Woodman
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | - Katelyn Daman
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Disease Research University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Disease Research University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alec M DeSimone
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Modalis Therapeutics, Waltham, MA, USA.
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