1
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Kafida M, Karela M, Giakountis A. RNA-Independent Regulatory Functions of lncRNA in Complex Disease. Cancers (Basel) 2024; 16:2728. [PMID: 39123456 PMCID: PMC11311644 DOI: 10.3390/cancers16152728] [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: 07/06/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
During the metagenomics era, high-throughput sequencing efforts both in mice and humans indicate that non-coding RNAs (ncRNAs) constitute a significant fraction of the transcribed genome. During the past decades, the regulatory role of these non-coding transcripts along with their interactions with other molecules have been extensively characterized. However, the study of long non-coding RNAs (lncRNAs), an ncRNA regulatory class with transcript lengths that exceed 200 nucleotides, revealed that certain non-coding transcripts are transcriptional "by-products", while their loci exert their downstream regulatory functions through RNA-independent mechanisms. Such mechanisms include, but are not limited to, chromatin interactions and complex promoter-enhancer competition schemes that involve the underlying ncRNA locus with or without its nascent transcription, mediating significant or even exclusive roles in the regulation of downstream target genes in mammals. Interestingly, such RNA-independent mechanisms often drive pathological manifestations, including oncogenesis. In this review, we summarize selective examples of lncRNAs that regulate target genes independently of their produced transcripts.
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Affiliation(s)
| | | | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Mezourlo, 41500 Larissa, Greece
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2
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Kushida Y, Oguma Y, Abe K, Deguchi T, Barbera FG, Nishimura N, Fujioka K, Iwatani S, Dezawa M. Human post-implantation blastocyst-like characteristics of Muse cells isolated from human umbilical cord. Cell Mol Life Sci 2024; 81:297. [PMID: 38992309 DOI: 10.1007/s00018-024-05339-4] [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: 01/31/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Muse cells, identified as cells positive for the pluripotent surface marker SSEA-3, are pluripotent-like endogenous stem cells located in the bone marrow (BM), peripheral blood, and organ connective tissues. The detailed characteristics of SSEA-3(+) cells in extraembryonic tissue, however, are unknown. Here, we demonstrated that similar to human-adult tissue-Muse cells collected from the BM, adipose tissue, and dermis as SSEA-3(+), human-umbilical cord (UC)-SSEA-3(+) cells express pluripotency markers, differentiate into triploblastic-lineage cells at a single cell level, migrate to damaged tissue, and exhibit low telomerase activity and non-tumorigenicity. Notably, ~ 20% of human-UC-SSEA-3(+) cells were negative for X-inactive specific transcript (XIST), a naïve pluripotent stem cell characteristic, whereas all human adult tissue-Muse cells are XIST-positive. Single-cell RNA sequencing revealed that the gene expression profile of human-UC-SSEA-3(+) cells was more similar to that of human post-implantation blastocysts than human-adult tissue-Muse cells. The DNA methylation level showed the same trend, and notably, the methylation levels in genes particularly related to differentiation were lower in human-UC-SSEA-3(+) cells than in human-adult tissue-Muse cells. Furthermore, human-UC-SSEA-3(+) cells newly express markers specific to extraembryonic-, germline-, and hematopoietic-lineages after differentiation induction in vitro whereas human-adult tissue-Muse cells respond only partially to the induction. Among various stem/progenitor cells in living bodies, those that exhibit properties similar to post-implantation blastocysts in a naïve state have not yet been found in humans. Easily accessible human-UC-SSEA-3(+) cells may be a valuable tool for studying early-stage human development and human reproductive medicine.
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Affiliation(s)
- Yoshihiro Kushida
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan.
| | - Yo Oguma
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Kana Abe
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Taichi Deguchi
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Federico Girolamo Barbera
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Noriyuki Nishimura
- Department of Public Health, Kobe University Graduate School of Health Science, Kobe, Japan
| | - Kazumichi Fujioka
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Sota Iwatani
- Department of Neonatology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Mari Dezawa
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan.
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3
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Hazra R, Debnath R, Tuppad A. Glioblastoma stem cell long non-coding RNAs: therapeutic perspectives and opportunities. Front Genet 2024; 15:1416772. [PMID: 39015773 PMCID: PMC11249581 DOI: 10.3389/fgene.2024.1416772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/27/2024] [Indexed: 07/18/2024] Open
Abstract
Glioblastoma poses a formidable challenge among primary brain tumors: its tumorigenic stem cells, capable of self-renewal, proliferation, and differentiation, contribute substantially to tumor initiation and therapy resistance. These glioblastoma stem cells (GSCs), resembling conventional stem and progenitor cells, adopt pathways critical for tissue development and repair, promoting uninterrupted tumor expansion. Long non-coding RNAs (lncRNAs), a substantial component of the human transcriptome, have garnered considerable interest for their pivotal roles in normal physiological processes and cancer pathogenesis. They display cell- or tissue-specific expression patterns, and extensive investigations have highlighted their impact on regulating GSC properties and cellular differentiation, thus offering promising avenues for therapeutic interventions. Consequently, lncRNAs, with their ability to exert regulatory control over tumor initiation and progression, have emerged as promising targets for innovative glioblastoma therapies. This review explores notable examples of GSC-associated lncRNAs and elucidates their functional roles in driving glioblastoma progression. Additionally, we delved deeper into utilizing a 3D in vitro model for investigating GSC biology and elucidated four primary methodologies for targeting lncRNAs as potential therapeutics in managing glioblastoma.
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Affiliation(s)
- Rasmani Hazra
- University of New Haven, Biology and Environmental Science Department, West Haven, CT, United States
| | - Rinku Debnath
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Arati Tuppad
- University of New Haven, Biology and Environmental Science Department, West Haven, CT, United States
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4
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Naciri I, Andrade-Ludena MD, Yang Y, Kong M, Sun S. An emerging link between lncRNAs and cancer sex dimorphism. Hum Genet 2024; 143:831-842. [PMID: 38095719 PMCID: PMC11176266 DOI: 10.1007/s00439-023-02620-7] [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: 05/25/2023] [Accepted: 11/05/2023] [Indexed: 06/15/2024]
Abstract
The prevalence and progression of cancer differ in males and females, and thus, sexual dimorphism in tumor development directly impacts clinical research and medicine. Long non-coding RNAs (lncRNAs) are increasingly recognized as important players in gene expression and various cellular processes, including cancer development and progression. In recent years, lncRNAs have been implicated in the differences observed in cancer incidence, progression, and treatment responses between men and women. Here, we present a brief overview of the current knowledge regarding the role of lncRNAs in cancer sex dimorphism, focusing on how they affect epigenetic processes in male and female mammalian cells. We discuss the potential mechanisms by which lncRNAs may contribute to sex differences in cancer, including transcriptional control of sex chromosomes, hormonal signaling pathways, and immune responses. We also propose strategies for studying lncRNA functions in cancer sex dimorphism. Furthermore, we emphasize the importance of considering sex as a biological variable in cancer research and the need to investigate the role lncRNAs play in mediating these sex differences. In summary, we highlight the emerging link between lncRNAs and cancer sex dimorphism and their potential as therapeutic targets.
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Affiliation(s)
- Ikrame Naciri
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Maria D Andrade-Ludena
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Ying Yang
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Mei Kong
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA.
| | - Sha Sun
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA.
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5
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Chung TH, Zhuravskaya A, Makeyev EV. Regulation potential of transcribed simple repeated sequences in developing neurons. Hum Genet 2024; 143:875-895. [PMID: 38153590 PMCID: PMC11294396 DOI: 10.1007/s00439-023-02626-1] [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: 07/19/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Simple repeated sequences (SRSs), defined as tandem iterations of microsatellite- to satellite-sized DNA units, occupy a substantial part of the human genome. Some of these elements are known to be transcribed in the context of repeat expansion disorders. Mounting evidence suggests that the transcription of SRSs may also contribute to normal cellular functions. Here, we used genome-wide bioinformatics approaches to systematically examine SRS transcriptional activity in cells undergoing neuronal differentiation. We identified thousands of long noncoding RNAs containing >200-nucleotide-long SRSs (SRS-lncRNAs), with hundreds of these transcripts significantly upregulated in the neural lineage. We show that SRS-lncRNAs often originate from telomere-proximal regions and that they have a strong potential to form multivalent contacts with a wide range of RNA-binding proteins. Our analyses also uncovered a cluster of neurally upregulated SRS-lncRNAs encoded in a centromere-proximal part of chromosome 9, which underwent an evolutionarily recent segmental duplication. Using a newly established in vitro system for rapid neuronal differentiation of induced pluripotent stem cells, we demonstrate that at least some of the bioinformatically predicted SRS-lncRNAs, including those encoded in the segmentally duplicated part of chromosome 9, indeed increase their expression in developing neurons to readily detectable levels. These and other lines of evidence suggest that many SRSs may be expressed in a cell type and developmental stage-specific manner, providing a valuable resource for further studies focused on the functional consequences of SRS-lncRNAs in the normal development of the human brain, as well as in the context of neurodevelopmental disorders.
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Affiliation(s)
- Tek Hong Chung
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK.
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6
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Lehmann U. Epigenetic Therapies in Triple-Negative Breast Cancer: Concepts, Visions, and Challenges. Cancers (Basel) 2024; 16:2164. [PMID: 38927870 PMCID: PMC11202282 DOI: 10.3390/cancers16122164] [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: 03/27/2024] [Revised: 05/17/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Breast cancer, the most frequent malignancy in women worldwide, is a molecularly and clinically very heterogeneous disease. Triple-negative breast cancer is defined by the absence of hormone receptor and growth factor receptor ERBB2/HER2 expression. It is characterized by a more aggressive course of disease and a shortage of effective therapeutic approaches. Hallmarks of cancer cells are not only genetic alterations, but also epigenetic aberrations. The most studied and best understood alterations are methylation of the DNA base cytosine and the covalent modification of histone proteins. The reversibility of these covalent modifications make them attractive targets for therapeutic intervention, as documented in numerous ongoing clinical trials. Epidrugs, targeting DNA methylation and histone modifications, might offer attractive new options in treating triple-negative breast cancer. Currently, the most promising options are combination therapies in which the epidrug increases the efficiency of immuncheckpoint inhibitors. This review focusses exclusively on DNA methylation and histone modifications. In reviewing the knowledge about epigenetic therapies in breast cancer, and especially triple-negative breast cancer, the focus is on explaining concepts and raising awareness of what is not yet known and what has to be clarified in the future.
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Affiliation(s)
- Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
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7
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McClain AK, Monteleone PP, Zoldan J. Sex in cardiovascular disease: Why this biological variable should be considered in in vitro models. SCIENCE ADVANCES 2024; 10:eadn3510. [PMID: 38728407 PMCID: PMC11086622 DOI: 10.1126/sciadv.adn3510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/09/2024] [Indexed: 05/12/2024]
Abstract
Cardiovascular disease (CVD), the world's leading cause of death, exhibits notable epidemiological, clinical, and pathophysiological differences between sexes. Many such differences can be linked back to cardiovascular sexual dimorphism, yet sex-specific in vitro models are still not the norm. A lack of sex reporting and apparent male bias raises the question of whether in vitro CVD models faithfully recapitulate the biology of intended treatment recipients. To ensure equitable treatment for the overlooked female patient population, sex as a biological variable (SABV) inclusion must become commonplace in CVD preclinical research. Here, we discuss the role of sex in CVD and underlying cardiovascular (patho)physiology. We review shortcomings in current SABV practices, describe the relevance of sex, and highlight emerging strategies for SABV inclusion in three major in vitro model types: primary cell, stem cell, and three-dimensional models. Last, we identify key barriers to inclusive design and suggest techniques for overcoming them.
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Affiliation(s)
- Anna K. McClain
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78751, USA
| | - Peter P. Monteleone
- Ascension Texas Cardiovascular, Austin, TX 78705, USA
- Dell School of Medicine, The University of Texas at Austin, Austin, TX 78712, USA
| | - Janet Zoldan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78751, USA
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8
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Cao H, Fang C, Liu LL, Farnir F, Liu WJ. Identification of Susceptibility Genes Underlying Bovine Respiratory Disease in Xinjiang Brown Cattle Based on DNA Methylation. Int J Mol Sci 2024; 25:4928. [PMID: 38732144 PMCID: PMC11084705 DOI: 10.3390/ijms25094928] [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: 03/16/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
DNA methylation is a form of epigenetic regulation, having pivotal parts in controlling cellular expansion and expression levels within genes. Although blood DNA methylation has been studied in humans and other species, its prominence in cattle is largely unknown. This study aimed to methodically probe the genomic methylation map of Xinjiang brown (XJB) cattle suffering from bovine respiratory disease (BRD), consequently widening cattle blood methylome ranges. Genome-wide DNA methylation profiling of the XJB blood was investigated through whole-genome bisulfite sequencing (WGBS). Many differentially methylated regions (DMRs) obtained by comparing the cases and controls groups were found within the CG, CHG, and CHH (where H is A, T, or C) sequences (16,765, 7502, and 2656, respectively), encompassing 4334 differentially methylated genes (DMGs). Furthermore, GO/KEGG analyses showed that some DMGs were involved within immune response pathways. Combining WGBS-Seq data and existing RNA-Seq data, we identified 71 significantly differentially methylated (DMGs) and expressed (DEGs) genes (p < 0.05). Next, complementary analyses identified nine DMGs (LTA, STAT3, IKBKG, IRAK1, NOD2, TLR2, TNFRSF1A, and IKBKB) that might be involved in the immune response of XJB cattle infected with respiratory diseases. Although further investigations are needed to confirm their exact implication in the involved immune processes, these genes could potentially be used for a marker-assisted selection of animals resistant to BRD. This study also provides new knowledge regarding epigenetic control for the bovine respiratory immune process.
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Affiliation(s)
- Hang Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (H.C.); (L.-L.L.)
| | - Chao Fang
- Faculte de Medecine Veterinaire, Universite de Liege, Quartier Vallee 2, Avenue de Cureghem 6 (B43), 4000 Liege, Belgium;
| | - Ling-Ling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (H.C.); (L.-L.L.)
| | - Frederic Farnir
- Faculte de Medecine Veterinaire, Universite de Liege, Quartier Vallee 2, Avenue de Cureghem 6 (B43), 4000 Liege, Belgium;
| | - Wu-Jun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (H.C.); (L.-L.L.)
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9
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Song QH, Zhao KX, Huang S, Chen T, He L. Escape from X-chromosome inactivation and sex differences in Alzheimer's disease. Rev Neurosci 2024; 35:341-354. [PMID: 38157427 DOI: 10.1515/revneuro-2023-0108] [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: 09/06/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
Sex differences exist in the onset and progression of Alzheimer's disease. Globally, women have a higher prevalence, while men with Alzheimer's disease experience earlier mortality and more pronounced cognitive decline than women. The cause of sex differences in Alzheimer's disease remains unclear. Accumulating evidence suggests the potential role of X-linked genetic factors in the sex difference of Alzheimer's disease (AD). During embryogenesis, a remarkable process known as X-chromosome inactivation (XCI) occurs in females, leading to one of the X chromosomes undergoing transcriptional inactivation, which balances the effects of two X chromosomes in females. Nevertheless, certain genes exceptionally escape from XCI, which provides a basis for dual expression dosage of specific genes in females. Based on recent research findings, we explore key escape genes and their potential therapeutic use associated with Alzheimer's disease. Also, we discuss their possible role in driving the sex differences in Alzheimer's disease. This will provide new perspectives for precision medicine and gender-specific treatment of AD.
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Affiliation(s)
- Qing-Hua Song
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Ke-Xuan Zhao
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Shuai Huang
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Tong Chen
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Ling He
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
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10
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Nogueira D, Fatemi HM, Lawrenz B, Elkhatib I, Abdala A, Bayram A, Melado L. Primary sex ratio in euploid embryos of consanguine couples after IVF/ICSI. J Assist Reprod Genet 2024; 41:957-965. [PMID: 38315419 PMCID: PMC11052735 DOI: 10.1007/s10815-024-03044-6] [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: 06/24/2023] [Accepted: 01/24/2024] [Indexed: 02/07/2024] Open
Abstract
PURPOSE To assess the primary sex ratio (males-to-females at time of conception) in blastocysts from consanguine couples undergoing IVF/ICSI treatments and its correlation with chromosomal constitution. METHOD A total of 5135 blastocysts were analyzed by preimplantation-genetic testing for aneuploidy (PGT-A) with next-generation sequencing (NGS) from November 2016 to December 2020. From those, a total of 1138 blastocysts were from consanguine couples (CS) and 3997 from non-consanguine couples (NCS). Only blastocysts presenting normal sex chromosome constitution with or without autosomal aneuploidies were included. Primary sex ratio (PSR) of biopsied blastocysts was compared between CS and NCS couples. RESULTS Expanded blastocysts derived from CS had 47.7% XY versus 52.3% XX constitutions, presenting a PSR of 0.91. In NCS, 48.9% of expanded blastocysts were XY and 51.2% XX, with a less pronounced PSR of 0.95. When stratifying embryos by ploidy, euploid embryos from CS had the lowest PSR (0.87) with 46.6% XY versus 53.4% XX blastocysts (OR 0.89, 95% CI 0.70-1.14; NS), but it did not achieve statistical significance. The lower PSR seemed rather related to euploid embryos from first-degree cousins (PSR = 0.80 versus 0.98 in second-degree cousins, NS). Euploid embryos from NCS presented a PSR of 0.96, with 49.1% XY versus 50.9% XX blastocysts (OR 0.98, 95% CI 0.79-1.22; NS). Significant differences in prevalence of euploidy of specific chromosomes were encountered between CS and NCS. CONCLUSIONS The primary sex ratio was generally similar in expanded blastocysts from consanguine and non-consanguine couples, with a slight decrease in primary sex ratio of euploid blastocysts from consanguine couples.
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Affiliation(s)
- Daniela Nogueira
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates.
- INOVIE Fertilité, Toulouse, France.
| | | | | | | | - Andrea Abdala
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
| | - Aşina Bayram
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
| | - Laura Melado
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
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11
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Aksit MA, Yu B, Roelen BAJ, Migeon BR. Silencing XIST on the future active X: Searching human and bovine preimplantation embryos for the repressor. Eur J Hum Genet 2024; 32:399-406. [PMID: 35585273 PMCID: PMC10999447 DOI: 10.1038/s41431-022-01115-9] [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: 12/12/2021] [Revised: 03/28/2022] [Accepted: 04/26/2022] [Indexed: 11/09/2022] Open
Abstract
X inactivation is the means of equalizing the dosage of X chromosomal genes in male and female eutherian mammals, so that only one X is active in each cell. The XIST locus (in cis) on each additional X chromosome initiates the transcriptional silence of that chromosome, making it an inactive X. How the active X in both males and females is protected from inactivation by its own XIST locus is not well understood in any mammal. Previous studies of autosomal duplications suggest that gene(s) on the short arm of human chromosome 19 repress XIST on the active X. Here, we examine the time of transcription of some candidate genes in preimplantation embryos using single-cell RNA sequencing data from human embryos and qRT-PCR from bovine embryos. The candidate genes assayed are those transcribed from 19p13.3-13.2, which are widely expressed and can remodel chromatin. Our results confirm that XIST is expressed at low levels from the future active X in embryos of both sexes; they also show that the XIST locus is repressed in both sexes when pluripotency factors are being upregulated, during the 4-8 cell and morula stages in human and bovine embryos - well before the early blastocyst (E5) when XIST on the inactive X in females starts to be upregulated. Our data suggest a role for DNMT1, UHRF1, SAFB and SAFB2 in XIST repression; they also exclude XACT and other 19p candidate genes and provide the transcriptional timing for some genes not previously assayed in human or bovine preimplantation embryos.
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Affiliation(s)
- Melis A Aksit
- McKusick Nathans Department of Genetic Medicine and Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Bo Yu
- Farm Animal Health, Department of Population Health Sciences, and Utrecht University, 3584CM, Utrecht, The Netherlands
| | - Bernard A J Roelen
- Embryology, Anatomy and Physiology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CM, Utrecht, The Netherlands
| | - Barbara R Migeon
- McKusick Nathans Department of Genetic Medicine and Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
- The Department of Pediatrics, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
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12
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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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13
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Rohm D, Black JB, McCutcheon SR, Barrera A, Morone DJ, Nuttle X, de Esch CE, Tai DJ, Talkowski ME, Iglesias N, Gersbach CA. Activation of the imprinted Prader-Willi Syndrome locus by CRISPR-based epigenome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583177. [PMID: 38496583 PMCID: PMC10942373 DOI: 10.1101/2024.03.03.583177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Epigenome editing with DNA-targeting technologies such as CRISPR-dCas9 can be used to dissect gene regulatory mechanisms and potentially treat associated disorders. For example, Prader-Willi Syndrome (PWS) is caused by loss of paternally expressed imprinted genes on chromosome 15q11.2-q13.3, although the maternal allele is intact but epigenetically silenced. Using CRISPR repression and activation screens in human induced pluripotent stem cells (iPSCs), we identified genomic elements that control expression of the PWS gene SNRPN from the paternal and maternal chromosomes. We showed that either targeted transcriptional activation or DNA demethylation can activate the silenced maternal SNRPN and downstream PWS transcripts. However, these two approaches function at unique regions, preferentially activating different transcript variants and involving distinct epigenetic reprogramming mechanisms. Remarkably, transient expression of the targeted demethylase leads to stable, long-term maternal SNRPN expression in PWS iPSCs. This work uncovers targeted epigenetic manipulations to reprogram a disease-associated imprinted locus and suggests possible therapeutic interventions.
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Affiliation(s)
- Dahlia Rohm
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Joshua B. Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Sean R. McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Daniel J. Morone
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Xander Nuttle
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Celine E. de Esch
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Derek J.C. Tai
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael E. Talkowski
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nahid Iglesias
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Charles A. Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
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14
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Zhang Y, Shu Z, Li Y, Piao Y, Sun F, Han T, Wang T, Mao H. X-linked chronic granulomatous disease secondary to skewed X-chromosome inactivation in female patients. Clin Exp Immunol 2024; 215:261-267. [PMID: 38066563 PMCID: PMC10876111 DOI: 10.1093/cei/uxad129] [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: 06/21/2023] [Revised: 10/19/2023] [Accepted: 12/06/2023] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Chronic granulomatous disease (CGD) is a heterogeneous primary immunodeficiency. X-linked (XL) CGD caused by gene defects of CYBB is the most prevalent type of CGD. OBJECTIVE We aim to understand the clinical and molecule features of XL-CGD secondary to skewed X-chromosome inactivation (XCI) in female. METHODS We retrospectively reviewed the medical records of a female patient diagnosed with XL-CGD. Flow cytometry was used to detect the respiratory burst function. After restriction enzyme digestion of DNA, XCI was calculated by detecting fluorescent PCR products with capillary electrophoresis. The previously published female XL-CGD cases secondary to skewed XCI was summarized. RESULTS Clinical data were available for 15 female subjects. The median age of diagnosis was 16 years. Consistent with XL-CGD in males, infection was the most frequent manifestation in the female patients. Catalase-positive pathogens including Serratia marcescens and Staphylococcus aureus infections were the most common pathogens. Autoimmune/autoinflammation manifestations were observed in five patients. Dihydrorhodamine (DHR) assay showed that median %DHR+ values were 6.5% and the values varying with age were observed in 2 patients. All patients had a skewing XCI and there was no consistency between the daughter and carrier mother. Anti-infective treatment was effective in majority and there was no mortality reported in XL-CGD female patients to date. CONCLUSION XL-CGD should not be neglected in female patients manifested as CGD phenotype and it is necessary to make periodic clinical evaluation of CGD female carriers as the neutrophil oxidative function may decline with aging and increase the risk for infection.
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Affiliation(s)
- Yue Zhang
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
| | - Zhou Shu
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
| | - Yan Li
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
| | - Yurong Piao
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
| | - Fei Sun
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
| | - Tongxin Han
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
| | - Tianyou Wang
- Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Capital Medical University, Beijing, People's Republic of China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, People's Republic of China
| | - Huawei Mao
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing, People's Republic of China
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15
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Lopes AG, Loganathan SK, Caliaperumal J. Rett Syndrome and the Role of MECP2: Signaling to Clinical Trials. Brain Sci 2024; 14:120. [PMID: 38391695 PMCID: PMC10886956 DOI: 10.3390/brainsci14020120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/24/2024] Open
Abstract
Rett syndrome (RTT) is a neurological disorder that mostly affects females, with a frequency of 1 in 10,000 to 20,000 live birth cases. Symptoms include stereotyped hand movements; impaired learning, language, and communication skills; sudden loss of speech; reduced lifespan; retarded growth; disturbance of sleep and breathing; seizures; autism; and gait apraxia. Pneumonia is the most common cause of death for patients with Rett syndrome, with a survival rate of 77.8% at 25 years of age. Survival into the fifth decade is typical in Rett syndrome, and the leading cause of death is cardiorespiratory compromise. Rett syndrome progression has multiple stages; however, most phenotypes are associated with the nervous system and brain. In total, 95% of Rett syndrome cases are due to mutations in the MECP2 gene, an X-linked gene that encodes for the methyl CpG binding protein, a regulator of gene expression. In this review, we summarize the recent developments in the field of Rett syndrome and therapeutics targeting MECP2.
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Affiliation(s)
- Adele Gaspar Lopes
- Department of Pharmacology, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 2M1, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Sampath Kumar Loganathan
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Biochemistry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H4A 3J1, Canada
- Department of Otolaryngology, Head & Neck Surgery, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H4A 3J1, Canada
- Departments of Experimental Surgery and Experimental Medicine, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H4A 3J1, Canada
| | - Jayalakshmi Caliaperumal
- Ingram School of Nursing, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2M7, Canada
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16
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Huang L, Lai Y, Sun L, Li S, Ding X. HIGH MYOPIA IS COMMON IN PATIENTS WITH X-LINKED RETINOPATHIES: Myopic Maculopathy Analysis. Retina 2024; 44:117-126. [PMID: 38117582 DOI: 10.1097/iae.0000000000003934] [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] [Indexed: 12/22/2023]
Abstract
PURPOSE High myopia can occur as a single or syndromic condition. The aim of this study was to evaluate the refractive error and myopic maculopathy in patients with X-linked retinopathies. METHODS Whole exome sequencing, Sanger sequencing, and comprehensive ocular examinations were performed in patients with X-linked retinopathies. RESULTS A total of 17 patients were recruited, including six with CACNA1F, seven with RPGR, three with NYX, and one with OPN1MW mutations. The diagnoses were congenital stationary night blindness (6), cone-rod dystrophy (4), retinitis pigmentosa (4), achromatopsia (1), Leber congenital amaurosis (1), and myopia (1). Myopia was present in 88.2% patients, and 64.7% patients had high myopia. Gene analysis showed that high myopia was present in 80% patients with CACNA1F, 100% patients with NYX, and 57.1% patients with RPGR mutations. In the ATN classification, 64.7% of the patients were A1T0N0 and 35.3% were A0T0N0. The refractive errors progressed over time, even in patients with congenital stationary night blindness. Two females with heterozygous de novo RPGR mutations presented with retinitis pigmentosa or cone rod dystrophy combined with high myopia. CONCLUSION High myopia is common in patients with X-linked retinopathies, and myopic maculopathy was only mild atrophy without traction and neovascularization.
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Affiliation(s)
- Li Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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17
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Rodríguez Doyágüez P, Furlano M, Ars Criach E, Arce Y, Guirado L, Torra Balcells R. Correlation of X chromosome inactivation with clinical presentation of Fabry disease in a case report. Nefrologia 2023; 43 Suppl 2:91-95. [PMID: 38278716 DOI: 10.1016/j.nefroe.2024.01.018] [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: 11/13/2022] [Accepted: 12/09/2022] [Indexed: 01/28/2024] Open
Abstract
Fabry disease or also called Anderson-Fabry disease (FD) is a rare disease caused by pathogenic variants in the GLA gene, located on the X chromosome. This gene is involved in the metabolism of glycosphingolipids and its pathogenic variants cause a deficit or absence of α-galactosidase A causing the deposition of globotriaosylceramide throughout the body. Females have a variable phenotypic expression and a better prognosis than males. This is due to the X chromosome inactivation phenomenon. We present a clinical case of Fabry disease in a female with predominantly renal involvement and demonstrate how the X chromosome inactivation phenomenon is tissue dependent, showing preferential inactivation of the mutated allele at the renal level.
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Affiliation(s)
- Pablo Rodríguez Doyágüez
- Sección de Nefrología, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Madrid, Spain
| | - Mónica Furlano
- Enfermedades Renales Hereditarias, Servicio de Nefrologia, Fundació Puigvert, Institut d'Investigació Biomèdica Sant Pau (IIB-SANT PAU), Universidad Autónoma Barcelona, Barcelona, Spain
| | - Elisabet Ars Criach
- Laboratorio de Biología Molecular, Fundació Puigvert, Institut d'Investigació Biomèdica Sant Pau (IIB-SANT PAU), Barcelona, Spain
| | - Yolanda Arce
- Sección de Anatomía Patológica, Fundació Puigvert, Barcelona, Spain
| | - Lluís Guirado
- Servicio de Nefrología, Fundació Puigvert, Institut d'Investigació Biomèdica Sant Pau (IIB-SANT PAU), Universidad Autónoma Barcelona, Universitat Central de Catalunya (UVIC), Barcelona, Spain
| | - Roser Torra Balcells
- Enfermedades Renales Hereditarias, Servicio de Nefrologia, Fundació Puigvert, Institut d'Investigació Biomèdica Sant Pau (IIB-SANT PAU), Universidad Autónoma Barcelona, Barcelona, Spain.
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18
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Peeters SB, Posynick BJ, Brown CJ. Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation. EPIGENOMES 2023; 7:29. [PMID: 38131901 PMCID: PMC10742877 DOI: 10.3390/epigenomes7040029] [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: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be expressed from the otherwise inactive X chromosome-in some cases constitutively, while other genes are variable between individuals, tissues or cells. In this review we discuss the advantages and disadvantages of the approaches that have been used to identify escapees. The identity of escapees provides important clues to mechanisms underlying escape from XCI, an arena of study now moving from correlation to functional studies. As most escapees show greater expression in females, the not-so-inactive X chromosome is a substantial contributor to sex differences in humans, and we highlight some examples of such impact.
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Affiliation(s)
| | | | - Carolyn J. Brown
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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19
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Keniry A, Blewitt ME. Chromatin-mediated silencing on the inactive X chromosome. Development 2023; 150:dev201742. [PMID: 37991053 DOI: 10.1242/dev.201742] [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: 11/23/2023]
Abstract
In mammals, the second X chromosome in females is silenced to enable dosage compensation between XX females and XY males. This essential process involves the formation of a dense chromatin state on the inactive X (Xi) chromosome. There is a wealth of information about the hallmarks of Xi chromatin and the contribution each makes to silencing, leaving the tantalising possibility of learning from this knowledge to potentially remove silencing to treat X-linked diseases in females. Here, we discuss the role of each chromatin feature in the establishment and maintenance of the silent state, which is of crucial relevance for such a goal.
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Affiliation(s)
- Andrew Keniry
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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20
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Khan SA, Theunissen TW. Modeling X-chromosome inactivation and reactivation during human development. Curr Opin Genet Dev 2023; 82:102096. [PMID: 37597506 PMCID: PMC10588740 DOI: 10.1016/j.gde.2023.102096] [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: 02/28/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 08/21/2023]
Abstract
Stem-cell-based embryo models generate much excitement as they offer a window into an early phase of human development that has remained largely inaccessible to scientific investigation. An important epigenetic phenomenon during early embryogenesis is the epigenetic silencing of one of the two X chromosomes in female embryos, which ensures an equal output of X-linked gene expression between the sexes. X-chromosome inactivation (XCI) is thought to be established within the first three weeks of human development, although the inactive X-chromosome is reactivated in primordial germ cells (PGCs) that migrate to the embryonic gonads. Here, we summarize our current understanding of X-chromosome dynamics during human development and comment on the potential of recently established stem-cell-based models to reveal the underlying mechanisms.
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Affiliation(s)
- Shafqat A Khan
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA. https://twitter.com/@sakhan2019
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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21
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Agostinho de Sousa J, Wong CW, Dunkel I, Owens T, Voigt P, Hodgson A, Baker D, Schulz EG, Reik W, Smith A, Rostovskaya M, von Meyenn F. Epigenetic dynamics during capacitation of naïve human pluripotent stem cells. SCIENCE ADVANCES 2023; 9:eadg1936. [PMID: 37774033 PMCID: PMC10541016 DOI: 10.1126/sciadv.adg1936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are of fundamental relevance in regenerative medicine. Naïve hPSCs hold promise to overcome some of the limitations of conventional (primed) hPSCs, including recurrent epigenetic anomalies. Naïve-to-primed transition (capacitation) follows transcriptional dynamics of human embryonic epiblast and is necessary for somatic differentiation from naïve hPSCs. We found that capacitated hPSCs are transcriptionally closer to postimplantation epiblast than conventional hPSCs. This prompted us to comprehensively study epigenetic and related transcriptional changes during capacitation. Our results show that CpG islands, gene regulatory elements, and retrotransposons are hotspots of epigenetic dynamics during capacitation and indicate possible distinct roles of specific epigenetic modifications in gene expression control between naïve and primed hPSCs. Unexpectedly, PRC2 activity appeared to be dispensable for the capacitation. We find that capacitated hPSCs acquire an epigenetic state similar to conventional hPSCs. Significantly, however, the X chromosome erosion frequently observed in conventional female hPSCs is reversed by resetting and subsequent capacitation.
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Affiliation(s)
- João Agostinho de Sousa
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Chee-Wai Wong
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Ilona Dunkel
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thomas Owens
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Philipp Voigt
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Hodgson
- School of Biosciences, The Julia Garnham Centre, University of Sheffield, S10 2TN Sheffield, UK
| | - Duncan Baker
- Sheffield Diagnostic Genetics Services, Sheffield Children’s NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Edda G. Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1QR, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Altos Labs Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Austin Smith
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Living Systems Institute, University of Exeter, EX4 4QD Exeter, UK
| | - Maria Rostovskaya
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
- Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, SE1 9RT London, UK
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22
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Limouse C, Smith OK, Jukam D, Fryer KA, Greenleaf WJ, Straight AF. Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions. Nat Commun 2023; 14:6073. [PMID: 37770513 PMCID: PMC10539311 DOI: 10.1038/s41467-023-41848-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA-chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.
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Affiliation(s)
- Charles Limouse
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Owen K Smith
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - David Jukam
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Kelsey A Fryer
- Department of Biochemistry, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | | | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, California, USA.
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23
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Johansson J, Lidéus S, Höijer I, Ameur A, Gudmundsson S, Annerén G, Bondeson ML, Wilbe M. A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing. Sci Rep 2023; 13:12856. [PMID: 37553382 PMCID: PMC10409790 DOI: 10.1038/s41598-023-34413-3] [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: 04/12/2022] [Accepted: 04/29/2023] [Indexed: 08/10/2023] Open
Abstract
X-chromosome inactivation (XCI) analyses often assist in diagnostics of X-linked traits, however accurate assessment remains challenging with current methods. We developed a novel strategy using amplification-free Cas9 enrichment and Oxford nanopore technologies sequencing called XCI-ONT, to investigate and rigorously quantify XCI in human androgen receptor gene (AR) and human X-linked retinitis pigmentosa 2 gene (RP2). XCI-ONT measures methylation over 116 CpGs in AR and 58 CpGs in RP2, and separate parental X-chromosomes without PCR bias. We show the usefulness of the XCI-ONT strategy over the PCR-based golden standard XCI technique that only investigates one or two CpGs per gene. The results highlight the limitations of using the golden standard technique when the XCI pattern is partially skewed and the advantages of XCI-ONT to rigorously quantify XCI. This study provides a universal XCI-method on DNA, which is highly valuable in clinical and research framework of X-linked traits.
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Affiliation(s)
- Josefin Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Sarah Lidéus
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Ida Höijer
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Sanna Gudmundsson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Marie-Louise Bondeson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden
| | - Maria Wilbe
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 815, SE-751 08, Uppsala, Sweden.
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24
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Tenorio M, Serwatowska J, Fernandez-Valverde SL, Oktaba K, Cortez D. Genome-wide analysis of RNA-chromatin interactions in lizards as a mean for functional lncRNA identification. BMC Genomics 2023; 24:444. [PMID: 37550606 PMCID: PMC10405410 DOI: 10.1186/s12864-023-09545-5] [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: 03/30/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are defined as transcribed molecules longer than 200 nucleotides with little to no protein-coding potential. LncRNAs can regulate gene expression of nearby genes (cis-acting) or genes located on other chromosomes (trans-acting). Several methodologies have been developed to capture lncRNAs associated with chromatin at a genome-wide level. Analysis of RNA-DNA contacts can be combined with epigenetic and RNA-seq data to define potential lncRNAs involved in the regulation of gene expression. RESULTS We performed Chromatin Associated RNA sequencing (ChAR-seq) in Anolis carolinensis to obtain the genome-wide map of the associations that RNA molecules have with chromatin. We analyzed the frequency of DNA contacts for different classes of RNAs and were able to define cis- and trans-acting lncRNAs. We integrated the ChAR-seq map of RNA-DNA contacts with epigenetic data for the acetylation of lysine 16 on histone H4 (H4K16ac), a mark connected to actively transcribed chromatin in lizards. We successfully identified three trans-acting lncRNAs significantly associated with the H4K16ac signal, which are likely involved in the regulation of gene expression in A. carolinensis. CONCLUSIONS We show that the ChAR-seq method is a powerful tool to explore the RNA-DNA map of interactions. Moreover, in combination with epigenetic data, ChAR-seq can be applied in non-model species to establish potential roles for predicted lncRNAs that lack functional annotations.
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Affiliation(s)
- Mariela Tenorio
- Center for Genome Sciences, National Autonomous University of Mexico (UNAM), Cuernavaca, Mexico
| | | | - Selene L Fernandez-Valverde
- Center for Research and Advanced Studies (Cinvestav), Irapuato, Mexico
- School of Biotechnology and Biomolecular Sciences and the RNA Institute, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Katarzyna Oktaba
- Center for Research and Advanced Studies (Cinvestav), Irapuato, Mexico
| | - Diego Cortez
- Center for Genome Sciences, National Autonomous University of Mexico (UNAM), Cuernavaca, Mexico.
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Krueger K, Lamenza F, Gu H, El-Hodiri H, Wester J, Oberdick J, Fischer AJ, Oghumu S. Sex differences in susceptibility to substance use disorder: Role for X chromosome inactivation and escape? Mol Cell Neurosci 2023; 125:103859. [PMID: 37207894 PMCID: PMC10286730 DOI: 10.1016/j.mcn.2023.103859] [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: 12/26/2022] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
There is a sex-based disparity associated with substance use disorders (SUDs) as demonstrated by clinical and preclinical studies. Females are known to escalate from initial drug use to compulsive drug-taking behavior (telescoping) more rapidly, and experience greater negative withdrawal effects than males. Although these biological differences have largely been attributed to sex hormones, there is evidence for non-hormonal factors, such as the influence of the sex chromosome, which underlie sex disparities in addiction behavior. However, genetic and epigenetic mechanisms underlying sex chromosome influences on substance abuse behavior are not completely understood. In this review, we discuss the role that escape from X-chromosome inactivation (XCI) in females plays in sex-associated differences in addiction behavior. Females have two X chromosomes (XX), and during XCI, one X chromosome is randomly chosen to be transcriptionally silenced. However, some X-linked genes escape XCI and display biallelic gene expression. We generated a mouse model using an X-linked gene specific bicistronic dual reporter mouse as a tool to visualize allelic usage and measure XCI escape in a cell specific manner. Our results revealed a previously undiscovered X-linked gene XCI escaper (CXCR3), which is variable and cell type dependent. This illustrates the highly complex and context dependent nature of XCI escape which is largely understudied in the context of SUD. Novel approaches such as single cell RNA sequencing will provide a global molecular landscape and impact of XCI escape in addiction and facilitate our understanding of the contribution of XCI escape to sex disparities in SUD.
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Affiliation(s)
- Kate Krueger
- Department of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Felipe Lamenza
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Howard Gu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Heithem El-Hodiri
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Jason Wester
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - John Oberdick
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Andy J Fischer
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Steve Oghumu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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26
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Mattimoe T, Payer B. The compleX balancing act of controlling X-chromosome dosage and how it impacts mammalian germline development. Biochem J 2023; 480:521-537. [PMID: 37096944 DOI: 10.1042/bcj20220450] [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: 08/24/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 04/26/2023]
Abstract
In female mammals, the two X chromosomes are subject to epigenetic gene regulation in order to balance X-linked gene dosage with autosomes and in relation to males, which have one X and one Y chromosome. This is achieved by an intricate interplay of several processes; X-chromosome inactivation and reactivation elicit global epigenetic regulation of expression from one X chromosome in a stage-specific manner, whilst the process of X-chromosome upregulation responds to this by fine-tuning transcription levels of the second X. The germline is unique in its function of transmitting both the genetic and epigenetic information from one generation to the next, and remodelling of the X chromosome is one of the key steps in setting the stage for successful development. Here, we provide an overview of the complex dynamics of X-chromosome dosage control during embryonic and germ cell development, and aim to decipher its potential role for normal germline competency.
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Affiliation(s)
- Tom Mattimoe
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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27
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Towers EB, Williams IL, Qillawala EI, Rissman EF, Lynch WJ. Sex/Gender Differences in the Time-Course for the Development of Substance Use Disorder: A Focus on the Telescoping Effect. Pharmacol Rev 2023; 75:217-249. [PMID: 36781217 PMCID: PMC9969523 DOI: 10.1124/pharmrev.121.000361] [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: 04/06/2021] [Revised: 10/05/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022] Open
Abstract
Sex/gender effects have been demonstrated for multiple aspects of addiction, with one of the most commonly cited examples being the "telescoping effect" where women meet criteria and/or seek treatment of substance use disorder (SUD) after fewer years of drug use as compared with men. This phenomenon has been reported for multiple drug classes including opioids, psychostimulants, alcohol, and cannabis, as well as nonpharmacological addictions, such as gambling. However, there are some inconsistent reports that show either no difference between men and women or opposite effects and a faster course to addiction in men than women. Thus, the goals of this review are to evaluate evidence for and against the telescoping effect in women and to determine the conditions/populations for which the telescoping effect is most relevant. We also discuss evidence from preclinical studies, which strongly support the validity of the telescoping effect and show that female animals develop addiction-like features (e.g., compulsive drug use, an enhanced motivation for the drug, and enhanced drug-craving/vulnerability to relapse) more readily than male animals. We also discuss biologic factors that may contribute to the telescoping effect, such as ovarian hormones, and its neurobiological basis focusing on the mesolimbic dopamine reward pathway and the corticomesolimbic glutamatergic pathway considering the critical roles these pathways play in the rewarding/reinforcing effects of addictive drugs and SUD. We conclude with future research directions, including intervention strategies to prevent the development of SUD in women. SIGNIFICANCE STATEMENT: One of the most widely cited gender/sex differences in substance use disorder (SUD) is the "telescoping effect," which reflects an accelerated course in women versus men for the development and/or seeking treatment for SUD. This review evaluates evidence for and against a telescoping effect drawing upon data from both clinical and preclinical studies. We also discuss the contribution of biological factors and underlying neurobiological mechanisms and highlight potential targets to prevent the development of SUD in women.
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Affiliation(s)
- Eleanor Blair Towers
- Psychiatry and Neurobehavioral Sciences (E.B.T., I.L.W., E.I.Q., W.J.L.) and Medical Scientist Training Program (E.B.T.), University of Virginia, Charlottesville, Virginia, and Center for Human Health and the Environment and Program in Genetics, North Carolina State University, Raleigh, North Carolina (E.F.R.)
| | - Ivy L Williams
- Psychiatry and Neurobehavioral Sciences (E.B.T., I.L.W., E.I.Q., W.J.L.) and Medical Scientist Training Program (E.B.T.), University of Virginia, Charlottesville, Virginia, and Center for Human Health and the Environment and Program in Genetics, North Carolina State University, Raleigh, North Carolina (E.F.R.)
| | - Emaan I Qillawala
- Psychiatry and Neurobehavioral Sciences (E.B.T., I.L.W., E.I.Q., W.J.L.) and Medical Scientist Training Program (E.B.T.), University of Virginia, Charlottesville, Virginia, and Center for Human Health and the Environment and Program in Genetics, North Carolina State University, Raleigh, North Carolina (E.F.R.)
| | - Emilie F Rissman
- Psychiatry and Neurobehavioral Sciences (E.B.T., I.L.W., E.I.Q., W.J.L.) and Medical Scientist Training Program (E.B.T.), University of Virginia, Charlottesville, Virginia, and Center for Human Health and the Environment and Program in Genetics, North Carolina State University, Raleigh, North Carolina (E.F.R.)
| | - Wendy J Lynch
- Psychiatry and Neurobehavioral Sciences (E.B.T., I.L.W., E.I.Q., W.J.L.) and Medical Scientist Training Program (E.B.T.), University of Virginia, Charlottesville, Virginia, and Center for Human Health and the Environment and Program in Genetics, North Carolina State University, Raleigh, North Carolina (E.F.R.)
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28
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Farzaneh M, Nasrolahi A, Ghaedrahmati F, Masoodi T, Najafi S, Sheykhi-Sabzehpoush M, Dari MAG, Radoszkiewicz K, Uddin S, Azizidoost S, Khoshnam SE. Potential roles of lncRNA-XIST/miRNAs/mRNAs in human cancer cells. Clin Transl Oncol 2023:10.1007/s12094-023-03110-y. [PMID: 36853400 DOI: 10.1007/s12094-023-03110-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/31/2023] [Indexed: 03/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs that contain more than 200 nucleotides but do not code for proteins. In tumorigenesis, lncRNAs can have both oncogenic and tumor-suppressive properties. X inactive-specific transcript (XIST) is a known lncRNA that has been implicated in X chromosome silencing in female cells. Dysregulation of XIST is associated with an increased risk of various cancers. Therefore, XIST can be a beneficial prognostic biomarker for human malignancies. In this review, we attempt to summarize the emerging roles of XIST in human cancers.
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Affiliation(s)
- Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tariq Masoodi
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, 26999, Doha, Qatar
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mahrokh Abouali Gale Dari
- Department of Obstetrics and Gynecology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Klaudia Radoszkiewicz
- Translational Platform for Regenerative Medicine, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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29
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Amate-García G, Ballesta-Martínez MJ, Serrano-Lorenzo P, Garrido-Moraga R, González-Quintana A, Blázquez A, Rubio JC, García-Consuegra I, Arenas J, Ugalde C, Morán M, Guillén-Navarro E, Martín MA. A Novel Mutation Associated with Neonatal Lethal Cardiomyopathy Leads to an Alternative Transcript Expression in the X-Linked Complex I NDUFB11 Gene. Int J Mol Sci 2023; 24:ijms24021743. [PMID: 36675256 PMCID: PMC9865986 DOI: 10.3390/ijms24021743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
We report a neonatal patient with hypertrophic cardiomyopathy (HCM), lactic acidosis and isolated complex I deficiency. Using a customized next-generation sequencing panel, we identified a novel hemizygous variant c.338G>A in the X-linked NDUFB11 gene that encodes the NADH: ubiquinone oxidoreductase subunit B11 of the mitochondrial respiratory chain (MRC) complex I (CI). Molecular and functional assays performed in the proband’s target tissues—skeletal and heart muscle—showed biochemical disturbances of the MRC, suggesting a pathogenic role for this variant. In silico analyses initially predicted an amino acid missense change p.(Arg113Lys) in the NDUFB11 CI subunit. However, we showed that the molecular effect of the c.338G>A variant, which is located at the last nucleotide of exon 2 of the NDUFB11 gene in the canonical ‘short’ transcript (sized 462 bp), instead causes a splicing defect triggering the up-regulation of the expression of an alternative ‘long’ transcript (sized 492 bp) that can also be detected in the control individuals. Our results support the hypothesis that the canonical ‘short’ transcript is required for the proper NDUFB11 protein synthesis, which is essential for optimal CI assembly and activity, whereas the longer alternative transcript seems to represent a non-functional, unprocessed splicing intermediate. Our results highlight the importance of characterizing the molecular effect of new variants in the affected patient’s tissues to demonstrate their pathogenicity and association with the clinical phenotypes.
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Affiliation(s)
- Guillermo Amate-García
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - María Juliana Ballesta-Martínez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120 Murcia, Spain
| | - Pablo Serrano-Lorenzo
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Rocío Garrido-Moraga
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Adrián González-Quintana
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Alberto Blázquez
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Juan C. Rubio
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Inés García-Consuegra
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Joaquín Arenas
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Cristina Ugalde
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - María Morán
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Encarnación Guillén-Navarro
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120 Murcia, Spain
- Facultad de Medicina, Universidad de Murcia, 30120 Murcia, Spain
| | - Miguel A. Martín
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Servicio de Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Correspondence:
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30
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Matsumoto S, Okamura E, Muto M, Ema M. Similarities and differences in placental development between humans and cynomolgus monkeys. Reprod Med Biol 2023; 22:e12522. [PMID: 37377753 PMCID: PMC10292683 DOI: 10.1002/rmb2.12522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Background The placenta is an extraembryonic organ, which is essential to maintain a normal pregnancy. However, placental development in humans is poorly understood because of technical and ethical reasons. Methods We analyzed the anatomical localization of each trophoblastic subtype in the cynomolgus monkey placenta by immunohistochemistry in the early second trimester. Histological differences among the mouse, cynomolgus monkey, and human placenta were compared. The PubMed database was used to search for studies on placentation in rodents and primates. Main findings The anatomical structures and subtypes of the placenta in cynomolgus monkeys are highly similar to those in humans, with the exception of fewer interstitial extravillous trophoblasts in cynomolgus monkeys. Conclusion The cynomolgus monkey appears to be a good animal model to investigate human placentation.
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Affiliation(s)
- Shoma Matsumoto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Eiichi Okamura
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Masanaga Muto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
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31
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Xing X, Karlow JA, Li D, Jang HS, Lee HJ, Wang T. Capture Methylation-Sensitive Restriction Enzyme Sequencing (Capture MRE-Seq) for Methylation Analysis of Highly Degraded DNA Samples. Methods Mol Biol 2023; 2621:73-89. [PMID: 37041441 DOI: 10.1007/978-1-0716-2950-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Understanding the impact of DNA methylation within different disease contexts often requires accurate assessment of these modifications in a genome-wide fashion. Frequently, patient-derived tissues stored in long-term hospital tissue banks have been preserved using formalin-fixation paraffin-embedding (FFPE). While these samples can comprise valuable resources for studying disease, the fixation process ultimately compromises the DNA's integrity and leads to degradation. Degraded DNA can complicate CpG methylome profiling using traditional techniques, particularly when performing methylation-sensitive restriction enzyme sequencing (MRE-seq), yielding high backgrounds and resulting in lowered library complexity. Here, we describe Capture MRE-seq, a new MRE-seq protocol tailored to preserving unmethylated CpG information when using samples with highly degraded DNA. The results using Capture MRE-seq correlate well (0.92) with traditional MRE-seq calls when profiling non-degraded samples, and can recover unmethylated regions in highly degraded samples when traditional MRE-seq fails, which we validate using bisulfite sequencing-based data (WGBS) as well as methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq).
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Affiliation(s)
- Xiaoyun Xing
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer A Karlow
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Daofeng Li
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hyo Sik Jang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Hyung Joo Lee
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Pin Pharmaceuticals, South San Francisco, CA, USA
| | - Ting Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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32
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Juchniewicz P, Kloska A, Portalska K, Jakóbkiewicz-Banecka J, Węgrzyn G, Liss J, Głodek P, Tukaj S, Piotrowska E. X-chromosome inactivation patterns depend on age and tissue but not conception method in humans. Chromosome Res 2023; 31:4. [PMID: 36695960 PMCID: PMC9877087 DOI: 10.1007/s10577-023-09717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/27/2022] [Accepted: 12/06/2022] [Indexed: 01/26/2023]
Abstract
Female somatic X-chromosome inactivation (XCI) balances the X-linked transcriptional dosages between the sexes, randomly silencing the maternal or paternal X chromosome in each cell of 46,XX females. Skewed XCI toward one parental X has been observed in association with ageing and in some female carriers of X-linked diseases. To address the problem of non-random XCI, we quantified the XCI skew in different biological samples of naturally conceived females of different age groups and girls conceived after in vitro fertilization (IVF). Generally, XCI skew differed between saliva, blood, and buccal swabs, while saliva and blood had the most similar XCI patterns in individual females. XCI skew increased with age in saliva, but not in other tissues. We showed no significant differences in the XCI patterns in tissues of naturally conceived and IVF females. The gene expression profile of the placenta and umbilical cord blood was determined depending on the XCI pattern. The increased XCI skewing in the placental tissue was associated with the differential expression of several genes out of 40 considered herein. Notably, skewed XCI patterns (> 80:20) were identified with significantly increased expression levels of four genes: CD44, KDM6A, PHLDA2, and ZRSR2. The differences in gene expression patterns between samples with random and non-random XCI may shed new light on factors contributing to the XCI pattern outcome and indicate new paths in future research on the phenomenon of XCI skewing.
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Affiliation(s)
- Patrycja Juchniewicz
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Anna Kloska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Karolina Portalska
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Joanna Jakóbkiewicz-Banecka
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Joanna Liss
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland ,Research and Development Center, INVICTA, Sopot, Poland
| | - Piotr Głodek
- Research and Development Center, INVICTA, Sopot, Poland
| | - Stefan Tukaj
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Ewa Piotrowska
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
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33
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Huang Y, Ma L, Zhang Z, Nie S, Zhou Y, Zhang J, Wang C, Fang X, Quan Y, He T, Liu A, Peng D. Nance-Horan syndrome pedigree due to a novel microdeletion and skewed X chromosome inactivation. Mol Genet Genomic Med 2022; 11:e2100. [PMID: 36370055 PMCID: PMC9938751 DOI: 10.1002/mgg3.2100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/16/2022] [Accepted: 11/03/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Nance-Horan syndrome (NHS) is a rare and often overlooked X-linked dominant disorder characterized by dense congenital cataracts, dental abnormalities, and mental retardation. The majority of NHS variations include frameshift mutations, nonsense mutations, microdeletions, and insertions. METHODS Copy number variation sequencing was performed to determine the microdeletion. The expression of NHS was detected by RT-PCR. Four family members were tested for X chromosome inactivation. RESULTS In this study, all members were examined for systemic examinations and genetic testing of four members and two affected subjects are observed. We identified a heterozygous microdeletion of -0.52 Mb at Xp22.13 in a female proband presenting NHS phenotypically. The microdeletion contains the REPS2 and NHS genes and was inherited from a phenotypically normal mother. Of interest, the expression NHS of proband was reduced and the skewed X chromosome inactivation rate reached more than 85% compared with her mother and the control. It was concluded that the haploinsufficiency of the NHS gene may account for the majority of clinical symptoms in the affected subjects. The variability among female carriers presumably results from nonrandom X chromosome inactivation. CONCLUSION Our findings broaden the spectrum of NHS mutations and provide molecular insight into NHS clinical prenatal genetic diagnosis.
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Affiliation(s)
- Yazhou Huang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Linya Ma
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Zhaoxia Zhang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Shujuan Nie
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Yuan Zhou
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Jibo Zhang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Chao Wang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Xingxin Fang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Yingting Quan
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Ting He
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Anhui Liu
- Affiliated Hospital of Changde CityUniversity of South ChinaHengyangChina
| | - Dan Peng
- Department of Medical GeneticsChangde First People's HospitalChangdeChina,Affiliated Hospital of Changde CityUniversity of South ChinaHengyangChina
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Zhang C, Gao R, Zhou R, Chen H, Liu C, Zhu T, Chen C. The emerging power and promise of non-coding RNAs in chronic pain. Front Mol Neurosci 2022; 15:1037929. [PMID: 36407760 PMCID: PMC9668864 DOI: 10.3389/fnmol.2022.1037929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/07/2022] [Indexed: 08/26/2023] Open
Abstract
Chronic pain (CP) is an unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage lasting longer than 3 months. CP is the main reason why people seek medical care and exerts an enormous economic burden. Genome-wide expression analysis has revealed that diverse essential genetic elements are altered in CP patients. Although many possible mechanisms of CP have been revealed, we are still unable to meet all the analgesic needs of patients. In recent years, non-coding RNAs (ncRNAs) have been shown to play essential roles in peripheral neuropathy and axon regeneration, which is associated with CP occurrence and development. Multiple key ncRNAs have been identified in animal models of CP, such as microRNA-30c-5p, ciRS-7, and lncRNA MRAK009713. This review highlights different kinds of ncRNAs in the regulation of CP, which provides a more comprehensive understanding of the pathogenesis of the disease. It mainly focuses on the contributions of miRNAs, circRNAs, and lncRNAs to CP, specifically peripheral neuropathic pain (NP), diabetic NP, central NP associated with spinal cord injury, complex regional pain syndrome, inflammatory pain, and cancer-induced pain. In addition, we summarize some potential ncRNAs as novel biomarkers for CP and its complications. With an in-depth understanding of the mechanism of CP, ncRNAs may provide novel insight into CP and could become new therapeutic targets in the future.
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Affiliation(s)
- Changteng Zhang
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Rui Gao
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Ruihao Zhou
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Hai Chen
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Changliang Liu
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Zhu
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Chan Chen
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and The Research Units of West China (2018RU012), Chinese Academy of Medical Sciences, Chengdu, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
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35
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Evidence of Sex Differences in Cellular Senescence. Neurobiol Aging 2022; 120:88-104. [DOI: 10.1016/j.neurobiolaging.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/20/2022]
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36
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Li Y, Sun Q. Epigenetic manipulation to improve mouse SCNT embryonic development. Front Genet 2022; 13:932867. [PMID: 36110221 PMCID: PMC9468881 DOI: 10.3389/fgene.2022.932867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
Cloned mammals can be achieved through somatic cell nuclear transfer (SCNT), which involves reprogramming of differentiated somatic cells into a totipotent state. However, low cloning efficiency hampers its application severely. Cloned embryos have the same DNA as donor somatic cells. Therefore, incomplete epigenetic reprogramming accounts for low development of cloned embryos. In this review, we describe recent epigenetic barriers in SCNT embryos and strategies to correct these epigenetic defects and avoid the occurrence of abnormalities in cloned animals.
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Affiliation(s)
- Yamei Li
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qiang Sun
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
- *Correspondence: Qiang Sun,
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37
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Mizuta K, Katou Y, Nakakita B, Kishine A, Nosaka Y, Saito S, Iwatani C, Tsuchiya H, Kawamoto I, Nakaya M, Tsukiyama T, Nagano M, Kojima Y, Nakamura T, Yabuta Y, Horie A, Mandai M, Ohta H, Saitou M. Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys. EMBO J 2022; 41:e110815. [PMID: 35912849 PMCID: PMC9475534 DOI: 10.15252/embj.2022110815] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/14/2022] Open
Abstract
In vitro oogenesis is key to elucidating the mechanism of human female germ-cell development and its anomalies. Accordingly, pluripotent stem cells have been induced into primordial germ cell-like cells and into oogonia with epigenetic reprogramming, yet further reconstitutions remain a challenge. Here, we demonstrate ex vivo reconstitution of fetal oocyte development in both humans and cynomolgus monkeys (Macaca fascicularis). With an optimized culture of fetal ovary reaggregates over three months, human and monkey oogonia enter and complete the first meiotic prophase to differentiate into diplotene oocytes that form primordial follicles, the source for oogenesis in adults. The cytological and transcriptomic progressions of fetal oocyte development in vitro closely recapitulate those in vivo. A comparison of single-cell transcriptomes among humans, monkeys, and mice unravels primate-specific and conserved programs driving fetal oocyte development, the former including a distinct transcriptomic transformation upon oogonia-to-oocyte transition and the latter including two active X chromosomes with little X-chromosome upregulation. Our study provides a critical step forward for realizing human in vitro oogenesis and uncovers salient characteristics of fetal oocyte development in primates.
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Affiliation(s)
- Ken Mizuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Katou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Baku Nakakita
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aoi Kishine
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshiaki Nosaka
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Saki Saito
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chizuru Iwatani
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Ikuo Kawamoto
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Masataka Nakaya
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Tomoyuki Tsukiyama
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Masahiro Nagano
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoji Kojima
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihito Horie
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Ohta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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38
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D'Ignazio L, Jacomini RS, Qamar B, Benjamin KJM, Arora R, Sawada T, Evans TA, Diffenderfer KE, Pankonin AR, Hendriks WT, Hyde TM, Kleinman JE, Weinberger DR, Bragg DC, Paquola ACM, Erwin JA. Variation in TAF1 expression in female carrier induced pluripotent stem cells and human brain ontogeny has implications for adult neostriatum vulnerability in X-linked Dystonia Parkinsonism. eNeuro 2022; 9:ENEURO.0129-22.2022. [PMID: 35868859 PMCID: PMC9428949 DOI: 10.1523/eneuro.0129-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/14/2022] [Accepted: 07/03/2022] [Indexed: 11/21/2022] Open
Abstract
X-linked Dystonia-Parkinsonism (XDP) is an inherited, X-linked, adult-onset movement disorder characterized by degeneration in the neostriatum. No therapeutics alter disease progression. The mechanisms underlying regional differences in degeneration and adult onset are unknown. Developing therapeutics requires a deeper understanding of how XDP-relevant features vary in health and disease. XDP is possibly due, in part, to a partial loss of TAF1 function. A disease-specific SINE-VNTR-Alu (SVA) retrotransposon insertion occurs within intron 32 of TAF1, a subunit of TFIID involved in transcription initiation. While all XDP males are usually clinically affected, females are heterozygous carriers generally not manifesting the full syndrome. As a resource for disease modeling, we characterized eight iPSC lines from three XDP female carrier individuals for X chromosome inactivation status and identified clonal lines that express either the wild-type X or XDP haplotype. Furthermore, we characterized XDP-relevant transcript expression in neurotypical humans, and found that SVA-F expression decreases after 30 years of age in the brain and that TAF1 is decreased in most female samples. Uniquely in the caudate nucleus, TAF1 expression is not sexually dimorphic and decreased after adolescence. These findings indicate that regional-, age- and sex-specific mechanisms regulate TAF1, highlighting the importance of disease-relevant models and postmortem tissue. We propose that the decreased TAF1 expression in the adult caudate may synergize with the XDP-specific partial loss of TAF1 function in patients, thereby passing a minimum threshold of TAF1 function, and triggering degeneration in the neostriatum.Significance StatementXDP is an inherited, X-linked, adult-onset movement disorder characterized by degeneration in the neostriatum. No therapeutics alter disease progression. Developing therapeutics requires a deeper understanding of how XDP-relevant features vary in health and disease. XDP is possibly due to a partial loss of TAF1 function. While all XDP males are usually affected, females are heterozygous carriers generally not manifesting the full syndrome. As a resource for disease modeling, we characterized eight stem cell lines from XDP female carrier individuals. Furthermore, we found that, uniquely in the caudate nucleus, TAF1 expression decreases after adolescence in healthy humans. We hypothesize that the decrease of TAF1 after adolescence in human caudate, in general, may underlie the vulnerability of the adult neostriatum in XDP.
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Affiliation(s)
- Laura D'Ignazio
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ricardo S Jacomini
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Bareera Qamar
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ria Arora
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Biology, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tomoyo Sawada
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Taylor A Evans
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Aimee R Pankonin
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - William T Hendriks
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University Baltimore, MD 21205, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Apua C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jennifer A Erwin
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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39
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Cloutier M, Kumar S, Buttigieg E, Keller L, Lee B, Williams A, Mojica-Perez S, Erliandri I, Rocha AMD, Cadigan K, Smith GD, Kalantry S. Preventing erosion of X-chromosome inactivation in human embryonic stem cells. Nat Commun 2022; 13:2516. [PMID: 35523820 PMCID: PMC9076865 DOI: 10.1038/s41467-022-30259-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
X-chromosome inactivation is a paradigm of epigenetic transcriptional regulation. Female human embryonic stem cells (hESCs) often undergo erosion of X-inactivation upon prolonged culture. Here, we investigate the sources of X-inactivation instability by deriving new primed pluripotent hESC lines. We find that culture media composition dramatically influenced the expression of XIST lncRNA, a key regulator of X-inactivation. hESCs cultured in a defined xenofree medium stably maintained XIST RNA expression and coating, whereas hESCs cultured in the widely used mTeSR1 medium lost XIST RNA expression. We pinpointed lithium chloride in mTeSR1 as a cause of XIST RNA loss. The addition of lithium chloride or inhibitors of GSK-3 proteins that are targeted by lithium to the defined hESC culture medium impeded XIST RNA expression. GSK-3 inhibition in differentiating female mouse embryonic stem cells and epiblast stem cells also resulted in a loss of XIST RNA expression. Together, these data may reconcile observed variations in X-inactivation in hESCs and inform the faithful culture of pluripotent stem cells.
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Affiliation(s)
- Marissa Cloutier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Surinder Kumar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emily Buttigieg
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Laura Keller
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brandon Lee
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Aaron Williams
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sandra Mojica-Perez
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Indri Erliandri
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Andre Monteiro Da Rocha
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine & Cardiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Cadigan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Gary D Smith
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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40
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Ross JP, van Dijk S, Phang M, Skilton MR, Molloy PL, Oytam Y. Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data. Clin Epigenetics 2022; 14:58. [PMID: 35488315 PMCID: PMC9055778 DOI: 10.1186/s13148-022-01277-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/10/2022] [Indexed: 11/20/2022] Open
Abstract
Background Genomic technologies can be subject to significant batch-effects which are known to reduce experimental power and to potentially create false positive results. The Illumina Infinium Methylation BeadChip is a popular technology choice for epigenome-wide association studies (EWAS), but presently, little is known about the nature of batch-effects on these designs. Given the subtlety of biological phenotypes in many EWAS, control for batch-effects should be a consideration.
Results Using the batch-effect removal approaches in the ComBat and Harman software, we examined two in-house datasets and compared results with three large publicly available datasets, (1214 HumanMethylation450 and 1094 MethylationEPIC BeadChips in total), and find that despite various forms of preprocessing, some batch-effects persist. This residual batch-effect is associated with the day of processing, the individual glass slide and the position of the array on the slide. Consistently across all datasets, 4649 probes required high amounts of correction. To understand the impact of this set to EWAS studies, we explored the literature and found three instances where persistently batch-effect prone probes have been reported in abstracts as key sites of differential methylation. As well as batch-effect susceptible probes, we also discover a set of probes which are erroneously corrected. We provide batch-effect workflows for Infinium Methylation data and provide reference matrices of batch-effect prone and erroneously corrected features across the five datasets spanning regionally diverse populations and three commonly collected biosamples (blood, buccal and saliva). Conclusions Batch-effects are ever present, even in high-quality data, and a strategy to deal with them should be part of experimental design, particularly for EWAS. Batch-effect removal tools are useful to reduce technical variance in Infinium Methylation data, but they need to be applied with care and make use of post hoc diagnostic measures. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01277-9.
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Affiliation(s)
- Jason P Ross
- Human Health Program, Health and Biosecurity, CSIRO, Sydney, Australia.
| | - Susan van Dijk
- Human Health Program, Health and Biosecurity, CSIRO, Sydney, Australia
| | - Melinda Phang
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Michael R Skilton
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Sydney Institute for Women, Children and Their Families, Sydney Local Health District, Sydney, Australia
| | - Peter L Molloy
- Human Health Program, Health and Biosecurity, CSIRO, Sydney, Australia
| | - Yalchin Oytam
- Clinical Insights and Analytics Unit, South Eastern Sydney Local Health District, Sydney, Australia
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41
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Braga CL, Acquarone M, Arona VDC, Osório BS, Barreto TG, Kian RM, Pereira JPAL, Silva MDMCD, Silva BA, de Oliveira GMM, Macedo Rocco PR, Silva PL, Alencar AKN. Can Epigenetics Help Solve the Puzzle Between Concomitant Cardiovascular Injury and Severity of Coronavirus Disease 2019? J Cardiovasc Pharmacol 2022; 79:431-443. [PMID: 34935698 DOI: 10.1097/fjc.0000000000001201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/29/2021] [Indexed: 01/08/2023]
Abstract
ABSTRACT The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 has significant implications in patients with concomitant cardiovascular disease (CVD) because they are the population at the greatest risk of death. The treatment of such patients and complications may represent a new challenge for the fields of cardiology and pharmacology. Thus, understanding the involvement of this viral infection in CVD might help to reduce the aggressiveness of SARS-CoV-2 in causing multiorgan infection and damage. SARS-CoV-2 disturbs the host epigenome and several epigenetic processes involved in the pathophysiology of COVID-19 that can directly affect the function and structure of the cardiovascular system (CVS). Hence, it would be relevant to identify epigenetic alterations that directly impact CVS physiology after SARS-CoV-2 infection. This could contribute to the view of this virus-induced CVS injury and direct forthcoming tackles for COVID-19 treatment to reduce mortality in patients with CVD. Targeting epigenetic marks could offer strong evidence for the development of novel antiviral therapies, especially in the context of COVID-19-related CVS damage. In this review, we address some of the main signaling pathways that are currently known as being involved in COVID-19 pathophysiology and the importance of this glint on epigenetics and some of its modifiers (epidrugs) to control the unregulated epitope activity in the context of SARS-CoV-2 infection, COVID-19, and underlying CVD.
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Affiliation(s)
- Cássia L Braga
- Laboratório de Investigação Pulmonar, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana Acquarone
- Faculdade de Medicina de Petrópolis, School Clinic, Petrópolis, Brazil
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor da C Arona
- Faculdade de Medicina de Petrópolis, School Clinic, Petrópolis, Brazil
| | - Brenno S Osório
- Faculdade de Medicina de Petrópolis, School Clinic, Petrópolis, Brazil
| | - Thiago G Barreto
- Faculdade de Medicina de Petrópolis, School Clinic, Petrópolis, Brazil
| | - Ruan M Kian
- Faculdade de Medicina de Petrópolis, School Clinic, Petrópolis, Brazil
| | | | - Marina de Moraes C da Silva
- Serviço de Radiologia do Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bagnólia A Silva
- Programa de Pós-graduação em Produtos Naturais e Sintéticos Bioativos, Departamento de Ciências Farmacêuticas, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Gláucia Maria M de Oliveira
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; and
| | - Patricia Rieken Macedo Rocco
- Laboratório de Investigação Pulmonar, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro Leme Silva
- Laboratório de Investigação Pulmonar, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Allan K N Alencar
- Laboratório de Investigação Pulmonar, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Faculdade de Medicina de Petrópolis, School Clinic, Petrópolis, Brazil
- Departamento de Ciências Fisiológicas, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
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42
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Li J, Ming Z, Yang L, Wang T, Liu G, Ma Q. Long noncoding RNA XIST: Mechanisms for X chromosome inactivation, roles in sex-biased diseases, and therapeutic opportunities. Genes Dis 2022; 9:1478-1492. [PMID: 36157489 PMCID: PMC9485286 DOI: 10.1016/j.gendis.2022.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022] Open
Abstract
Sexual dimorphism has been reported in various human diseases including autoimmune diseases, neurological diseases, pulmonary arterial hypertension, and some types of cancers, although the underlying mechanisms remain poorly understood. The long noncoding RNA (lncRNA) X-inactive specific transcript (XIST) is involved in X chromosome inactivation (XCI) in female placental mammals, a process that ensures the balanced expression dosage of X-linked genes between sexes. XIST is abnormally expressed in many sex-biased diseases. In addition, escape from XIST-mediated XCI and skewed XCI also contribute to sex-biased diseases. Therefore, its expression or modification can be regarded as a biomarker for the diagnosis and prognosis of many sex-biased diseases. Genetic manipulation of XIST expression can inhibit the progression of some of these diseases in animal models, and therefore XIST has been proposed as a potential therapeutic target. In this manuscript, we summarize the current knowledge about the mechanisms for XIST-mediated XCI and the roles of XIST in sex-biased diseases, and discuss potential therapeutic strategies targeting XIST.
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43
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Fang X, Butler KM, Abidi F, Gass J, Beisang A, Feyma T, Ryther RC, Standridge S, Heydemann P, Jones M, Haas R, Lieberman DN, Marsh E, Benke TA, Skinner S, Neul JL, Percy AK, Friez MJ, Caylor RC. Analysis of X-inactivation status in a Rett syndrome natural history study cohort. Mol Genet Genomic Med 2022; 10:e1917. [PMID: 35318820 PMCID: PMC9034674 DOI: 10.1002/mgg3.1917] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a rare neurodevelopmental disorder associated with pathogenic MECP2 variants. Because the MECP2 gene is subject to X-chromosome inactivation (XCI), factors including MECP2 genotypic variation, tissue differences in XCI, and skewing of XCI all likely contribute to the clinical severity of individuals with RTT. METHODS We analyzed the XCI patterns from blood samples of 320 individuals and their mothers. It includes individuals with RTT (n = 287) and other syndromes sharing overlapping phenotypes with RTT (such as CDKL5 Deficiency Disorder [CDD, n = 16]). XCI status in each proband/mother duo and the parental origin of the preferentially inactivated X chromosome were analyzed. RESULTS The average XCI ratio in probands was slightly increased compared to their unaffected mothers (73% vs. 69%, p = .0006). Among the duos with informative XCI data, the majority of individuals with classic RTT had their paternal allele preferentially inactivated (n = 180/220, 82%). In sharp contrast, individuals with CDD had their maternal allele preferentially inactivated (n = 10/12, 83%). Our data indicate a weak positive correlation between XCI skewing ratio and clinical severity scale (CSS) scores in classic RTT patients with maternal allele preferentially inactivated XCI (rs = 0.35, n = 40), but not in those with paternal allele preferentially inactivated XCI (rs = -0.06, n = 180). The most frequent MECP2 pathogenic variants were enriched in individuals with highly/moderately skewed XCI patterns, suggesting an association with higher levels of XCI skewing. CONCLUSION These results extend our understanding of the pathogenesis of RTT and other syndromes with overlapping clinical features by providing insight into the both XCI and the preferential XCI of parental alleles.
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Affiliation(s)
- Xiaolan Fang
- Greenwood Genetic CenterGreenwoodSouth CarolinaUSA
| | | | - Fatima Abidi
- Greenwood Genetic CenterGreenwoodSouth CarolinaUSA
| | - Jennifer Gass
- Florida Cancer Specialists & Research InstituteFort MyersFLUSA,Present address:
Florida Cancer Specialists & Research InstituteFort MyersFloridaUSA
| | - Arthur Beisang
- Gillette Children’s Specialty HealthcareSt. PaulMinnesotaUSA
| | - Timothy Feyma
- Gillette Children’s Specialty HealthcareSt. PaulMinnesotaUSA
| | - Robin C. Ryther
- Department of NeurologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Shannon Standridge
- Division of NeurologyCincinnati Children’s Hospital Medical CenterCincinnatiOhioUSA,Department of Pediatrics, College of MedicineUniversity of CincinnatiCincinnatiOhioUSA
| | | | - Mary Jones
- Oakland Children’s Hospital, UCSFOaklandCaliforniaUSA
| | - Richard Haas
- University of California San DiegoSan DiegoCaliforniaUSA
| | - David N Lieberman
- Department of NeurologyBoston Children’s HospitalBostonMassachusettsUSA
| | - Eric D. Marsh
- Children’s Hospital of Philadelphia and University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Tim A. Benke
- University of Colorado School of Medicine, Children’s Hospital Colorado‐AuroraDenverColoradoUSA
| | | | - Jeffrey L. Neul
- Vanderbilt Kennedy CenterVanderbilt University Medical CenterNashville TN
| | - Alan K. Percy
- The University of Alabama at BirminghamBirminghamAlabamaUSA
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44
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LaSalle JM. X Chromosome Inactivation Timing is Not e XACT: Implications for Autism Spectrum Disorders. Front Genet 2022; 13:864848. [PMID: 35356429 PMCID: PMC8959653 DOI: 10.3389/fgene.2022.864848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The etiology of autism spectrum disorders (ASD) is complex, involving different combinations of genetic and environmental factors. My lab's approach has been to investigate DNA methylation as a tractable genome-wide modification at the interface of these complex interactions, reflecting past and future events in the molecular pathogenesis of ASD. Since X-linked genes were enriched in DNA methylation differences discovered from cord blood from newborns later diagnosed with ASD, this has prompted me to review and revisit the recent advancements in the field of X chromosome inactivation (XCI), particularly in humans and other primates. In this Perspective, I compare XCI mechanisms in different mammalian species, including the finding of the noncoding transcript XACT associated with X chromosome erosion in human pluripotent stem cells and recent findings from non-human primate post-implantation embryos. I focus on the experimentally challenging peri- and post-implantation stages of human development when the timing of XCI is prolonged and imprecise in humans. Collectively, this research has raised some important unanswered questions involving biased sex ratios in human births and the male bias in the incidence of ASD.
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Affiliation(s)
- Janine M. LaSalle
- Department of Medical Microbiology and Immunology, Perinatal Origins of Disparities Center, MIND Institute, Genome Center, Environmental Health Sciences Center, University of California, Davis, Davis, CA, United States
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Rodrigues B, Gonçalves A, Sousa V, Maia N, Marques I, Vale-Fernandes E, Santos R, Nogueira AJA, Jorge P. Use of the FMR1 Gene Methylation Status to Assess the X-Chromosome Inactivation Pattern: A Stepwise Analysis. Genes (Basel) 2022; 13:419. [PMID: 35327973 PMCID: PMC8951761 DOI: 10.3390/genes13030419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
X-chromosome inactivation (XCI) is a developmental process to compensate the imbalance in the dosage of X-chromosomal genes in females. A skewing of the XCI pattern may suggest a carrier status for an X-linked disease or explain the presence of a severe phenotype. In these cases, it is important to determine the XCI pattern, conventionally using the gold standard Human Androgen-Receptor Assay (HUMARA), based on the analysis of the methylation status at a polymorphic CAG region in the first exon of the human androgen receptor gene (AR). The aim of this study was to evaluate whether the methylation status of the fragile mental retardation protein translational regulator gene (FMR1) can provide an XCI pattern similar to that obtained by HUMARA. A set of 48 female carriers of FMR1 gene normal-sized alleles was examined using two assays: HUMARA and a FMR1 methylation PCR (mPCR). Ranges were defined to establish the XCI pattern using the methylation pattern of the FMR1 gene by mPCR. Overall, a 77% concordance of the XCI patterns was obtained between the two assays, which led us to propose a set of key points and a stepwise analysis towards obtaining an accurate result for the XCI pattern and to minimize the underlying pitfalls.
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Affiliation(s)
- Bárbara Rodrigues
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - Ana Gonçalves
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - Vanessa Sousa
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
| | - Nuno Maia
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - Isabel Marques
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - Emídio Vale-Fernandes
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
- Centre for Medically Assisted Procreation/Public Gamete Bank, Centro Materno-Infantil do Norte Dr. Albino Aroso (CMIN), Centro Hospitalar Universitário do Porto (CHUPorto), 4050-651 Porto, Portugal
| | - Rosário Santos
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
| | - António J. A. Nogueira
- CESAM—Center for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Paula Jorge
- Molecular Genetics Unit, Centro de Genética Médica Dr. Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), 4099-028 Porto, Portugal; (B.R.); (A.G.); (V.S.); (N.M.); (I.M.); (R.S.)
- UMIB—Unit for Multidisciplinary Research in Biomedicine, ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal;
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-313 Porto, Portugal
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Choy M, Xue R, Wu Y, Fan W, Dong Y, Liu C. Role of N6-methyladenosine Modification in Cardiac Remodeling. Front Cardiovasc Med 2022; 9:774627. [PMID: 35224032 PMCID: PMC8866307 DOI: 10.3389/fcvm.2022.774627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Abstract
Cardiac remodeling is the critical process in heart failure due to many cardiovascular diseases including myocardial infarction, hypertension, cardiovascular disease and cardiomyopathy. However, treatments for heart failure focusing on cardiac remodeling show relatively limited effectiveness. In recent decades, epitranscriptomic modifications were found abundantly present throughout the progression of cardiac remodeling, and numerous types of biochemical modifications were identified. m6A modification is the methylation of the adenosine base at the nitrogen-6 position, and dysregulation of m6A modification has been implicated in a wide range of diseases. However, function of m6A modifications still remain largely unknown in cardiac diseases, especially cardiac remodeling. LncRNAs are also shown to play a vital role in the pathophysiology of cardiac remodeling and heart failure. The crosstalk between lncRNAs and m6A modification provides a novel prospective for exploring possible regulatory mechanism and therapeutic targets of cardiac remodeling. This review summarizes the role of m6A modification in cardiac remodeling in the current researches.
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Affiliation(s)
- ManTing Choy
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Ruicong Xue
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Yuzhong Wu
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Wendong Fan
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Yugang Dong
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Chen Liu
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- National Health Commission (NHC) Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Chen Liu
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Xu Z, Shi J, Zhang Y, Liu Y, Zhao J, Chen Q, Song C, Geng S, Xie W, Wu F, Bai Y, Yang Y, Li X. Zfp57 Exerts Maternal and Sexually Dimorphic Effects on Genomic Imprinting. Front Cell Dev Biol 2022; 10:784128. [PMID: 35252168 PMCID: PMC8895500 DOI: 10.3389/fcell.2022.784128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/04/2022] [Indexed: 12/05/2022] Open
Abstract
Zfp57 has both maternal and zygotic functions in mouse. It maintains genomic imprinting at most known imprinted regions and controls allelic expression of the target imprinted genes in mouse embryos. The DNA methylation imprint at many imprinting control regions (ICRs) is lost when both maternal and zygotic Zfp57 are absent in Zfp57 maternal–zygotic mutant mouse embryos. Interestingly, we found that DNA methylation at a few ICRs was partially lost without maternal Zfp57 in Zfp57 heterozygous mouse embryos derived from Zfp57 homozygous female mice. This suggests that maternal Zfp57 is essential for the maintenance of DNA methylation at a small subset of imprinted regions in mouse embryos. This maternal effect of Zfp57 was applied to allelic expression switch as well as expression levels of the corresponding imprinted genes. It is rather surprising that DNA methylation imprint was affected differently at Rasgrf1 and AK008011 imprinted regions in the female or male Zfp57 maternal–zygotic mutant embryos, with more significant loss of DNA methylation observed in the male mutant embryos. Loss of ZFP57 resulted in gender-specific differences in allelic expression switch and expression level changes of some imprinted genes in female or male mutant embryos. These results indicate maternal and sexually dimorphic effects of ZFP57 on genomic imprinting in mouse.
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Affiliation(s)
- Zhen Xu
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Jiajia Shi
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuhan Liu
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Junzheng Zhao
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Qian Chen
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Chenglin Song
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Shuhui Geng
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Feizhen Wu
- Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Yang Yang
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
| | - Xiajun Li
- School of Life Science and Technology, ShanghaiTech University, ShanghaiChina
- *Correspondence: Xiajun Li,
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48
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Faber MW, Vo TV. Long RNA-Mediated Chromatin Regulation in Fission Yeast and Mammals. Int J Mol Sci 2022; 23:968. [PMID: 35055152 PMCID: PMC8778201 DOI: 10.3390/ijms23020968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
As part of a complex network of genome control, long regulatory RNAs exert significant influences on chromatin dynamics. Understanding how this occurs could illuminate new avenues for disease treatment and lead to new hypotheses that would advance gene regulatory research. Recent studies using the model fission yeast Schizosaccharomyces pombe (S. pombe) and powerful parallel sequencing technologies have provided many insights in this area. This review will give an overview of key findings in S. pombe that relate long RNAs to multiple levels of chromatin regulation: histone modifications, gene neighborhood regulation in cis and higher-order chromosomal ordering. Moreover, we discuss parallels recently found in mammals to help bridge the knowledge gap between the study systems.
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Affiliation(s)
| | - Tommy V. Vo
- Department of Biochemistry and Molecular Biology, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA;
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49
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Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022; 23:231-249. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage compensation between cells of females (XX karyotype) and males (XY). XCI is essential for female embryos to survive through development and requires the accurate spatiotemporal regulation of many different factors to achieve remarkable chromosome-wide gene silencing. As a result of XCI, the active and inactive X chromosomes are functionally and structurally different, with the inactive X chromosome undergoing a major conformational reorganization within the nucleus. In this Review, we discuss the multiple layers of genetic and epigenetic regulation that underlie initiation of XCI during development and then maintain it throughout life, in light of the most recent findings in this rapidly advancing field. We discuss exciting new insights into the regulation of X inactive-specific transcript (XIST), the trigger and master regulator of XCI, and into the mechanisms and dynamics that underlie the silencing of nearly all X-linked genes. Finally, given the increasing interest in understanding the impact of chromosome organization on gene regulation, we provide an overview of the factors that are thought to reshape the 3D structure of the inactive X chromosome and of the relevance of such structural changes for XCI establishment and maintenance.
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50
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Mahadik K, Rougeulle C. Study of X Chromosome Activity Status in Human Naive Pluripotent Stem Cells Using RNA-FISH. Methods Mol Biol 2022; 2416:239-255. [PMID: 34870840 DOI: 10.1007/978-1-0716-1908-7_15] [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: 06/13/2023]
Abstract
X chromosome activity is a defining attribute of naive pluripotency, with naive pluripotency being a rare context in which both X chromosomes of females are active. RNA-fluorescence in situ hybridization (RNA-FISH) is a powerful tool to determine the transcriptional status of specific genes with allelic and single-cell resolution and has been widely used in the context of X chromosome inactivation, the process ensuring dosage compensation for X-linked genes between sexes in mammals. RNA-FISH using genomic or intronic probes allows the detection of newly synthesized transcripts at the site of transcription. This technique is invaluable for appreciating the putative heterogeneity in the expression profiles within cell populations. RNA-FISH has the added advantage of allowing the visualization of gene transcription in a spatial perspective. Here, we provide a detailed protocol describing the application of RNA-FISH to detect nascent X-linked transcripts in female naive human embryonic stem cells to assess their X chromosome status, along with another complementary technique, DNA-FISH.
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Affiliation(s)
- Kasturi Mahadik
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75006, Paris, France
| | - Claire Rougeulle
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75006, Paris, France.
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