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Unlocking the secrets of structural variants in a healthy tissue. Nat Genet 2024; 56:1047-1048. [PMID: 38839886 DOI: 10.1038/s41588-024-01757-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
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2
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Grimes K, Jeong H, Amoah A, Xu N, Niemann J, Raeder B, Hasenfeld P, Stober C, Rausch T, Benito E, Jann JC, Nowak D, Emini R, Hoenicka M, Liebold A, Ho A, Shuai S, Geiger H, Sanders AD, Korbel JO. Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells. Nat Genet 2024; 56:1134-1146. [PMID: 38806714 PMCID: PMC11176070 DOI: 10.1038/s41588-024-01754-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single-cell genomes from 19 human donors of increasing age, and discovered the heterogeneous mSV landscapes of hematopoietic stem and progenitor cells. While mSVs are continuously acquired throughout life, expanded subclones in our cohort are confined to individuals >60. Cells already harboring mSVs are more likely to acquire additional somatic structural variants, including megabase-scale segmental aneuploidies. Capitalizing on comprehensive single-cell micrococcal nuclease digestion with sequencing reference data, we conducted high-resolution cell-typing for eight hematopoietic stem and progenitor cells. Clonally expanded mSVs disrupt normal cellular function by dysregulating diverse cellular pathways, and enriching for myeloid progenitors. Our findings underscore the contribution of mSVs to the cellular and molecular phenotypes associated with the aging hematopoietic system, and establish a foundation for deciphering the molecular links between mSVs, aging and disease susceptibility in normal tissues.
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Affiliation(s)
- Karen Grimes
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hyobin Jeong
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Amanda Amoah
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Nuo Xu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Julian Niemann
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Benjamin Raeder
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patrick Hasenfeld
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Catherine Stober
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tobias Rausch
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eva Benito
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Johann-Christoph Jann
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany
| | - Ramiz Emini
- Department of Cardiothoracic and Vascular Surgery, Ulm University Hospital, Ulm, Germany
| | - Markus Hoenicka
- Department of Cardiothoracic and Vascular Surgery, Ulm University Hospital, Ulm, Germany
| | - Andreas Liebold
- Department of Cardiothoracic and Vascular Surgery, Ulm University Hospital, Ulm, Germany
| | - Anthony Ho
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Shimin Shuai
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Ashley D Sanders
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.
- Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Qin Y, Touch K, Sha M, Sun Y, Zhang S, Wu J, Wu Y, Feng L, Chen S, Xiao J. The chromosomal characteristics of spontaneous abortion and its potential associated copy number variants and genes. J Assist Reprod Genet 2024; 41:1285-1296. [PMID: 38668959 PMCID: PMC11143157 DOI: 10.1007/s10815-024-03119-4] [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: 09/27/2023] [Accepted: 04/02/2024] [Indexed: 06/01/2024] Open
Abstract
PURPOSE This study aimed to investigate the correlation between chromosomal abnormalities in spontaneous abortion with clinical features and seek copy number variations (CNVs) and genes that might be connected to spontaneous abortion. METHODS Over 7 years, we used CNV-seq and STR analysis to study POCs, comparing chromosomal abnormalities with clinical features and identifying critical CNVs and genes associated with spontaneous abortion. RESULTS Total chromosomal variants in the POCs were identified in 66.8% (2169/3247) of all cases, which included 45.2% (1467/3247) numerical abnormalities and 21.6% (702/3247) copy number variants (CNVs). Chromosome number abnormalities, especially aneuploidy abnormalities, were more pronounced in the group of mothers aged ≥ 35 years, the early miscarriage group, and the chorionic villi group. We further analyzed 212 pathogenic and likely pathogenic CNVs in 146 POCs as well as identified 8 statistically significant SORs through comparison with both a healthy population and a group of non-spontaneously aborted fetuses. Our analysis suggests that these CNVs may play a crucial role in spontaneous abortion. Furthermore, by utilizing the RVIS score and MGI database, we identified 86 genes associated with spontaneous abortion, with particular emphasis on PARP6, ISLR, ULK3, FGFRL1, TBC1D14, SCRIB, and PLEC. CONCLUSION We found variability in chromosomal abnormalities across clinical features, identifying eight crucial copy number variations (CNVs) and multiple key genes that may be linked to spontaneous abortion. This research enhances the comprehension of genetic factors contributing to spontaneous abortion.
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Affiliation(s)
- Yu Qin
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Koksear Touch
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Menghan Sha
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanan Sun
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Shunran Zhang
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Jianli Wu
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Yuanyuan Wu
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Ling Feng
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Suhua Chen
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China.
| | - Juan Xiao
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China.
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Alves Abrantes JJP, Veríssimo de Azevedo JC, Fernandes FL, Duarte Almeida V, Custódio De Oliveira LA, Ferreira de Oliveira MT, Galvão De Araújo JM, Lanza DCF, Bezerra FL, Andrade VS, Araújo de Medeiros Fernandes TA, Fernandes JV. Viruses as a potential environmental trigger of type 1 diabetes mellitus (Review). Biomed Rep 2024; 20:81. [PMID: 38628629 PMCID: PMC11019645 DOI: 10.3892/br.2024.1770] [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: 06/14/2023] [Accepted: 09/07/2023] [Indexed: 04/19/2024] Open
Abstract
The etiopathogenesis of type 1 diabetes mellitus (T1DM) is a complex multifactorial process that involves an intricate network of genetic, epigenetic, immunological, and environmental factors. Despite the advances in recent years, some aspects of the mechanisms involved in triggering the disease are still unclear. Infections with certain viruses have been suggested as possible environmental triggers for the autoimmune process that leads to selective and progressive destruction of pancreatic β-cells and insufficiency of insulin production, which is its hallmark. In this review, advances in knowledge and evidence that suggest the participation of certain viruses in the mechanisms of disease initiation and progression are described. It has been accepted that environmental factors, including viruses, can initiate and possibly sustain, accelerate, or slow down the autoimmune process and consequently damage insulin-producing pancreatic β-cells. Although the role of these agents, especially human enteroviruses, has been exhaustively studied as the most likely triggers of the activation of autoimmunity that destroys pancreatic islets and leads to T1DM, certain doubts remain. Clinical epidemiological and experimental studies in humans and animals provide consistent and increasing evidence that persistent viral infections, especially with human enteroviruses and rotavirus infections, are associated with an increased risk of the disease in individuals genetically predisposed to autoimmunity.
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Affiliation(s)
| | | | - Fernando Liberalino Fernandes
- Department of Biomedical Sciences, Rio Grande do Norte State University, Mossoró, Rio Grande do Norte 59607-360, Brazil
| | - Valéria Duarte Almeida
- Department of Biomedical Sciences, Rio Grande do Norte State University, Mossoró, Rio Grande do Norte 59607-360, Brazil
| | | | | | - Josélio Maria Galvão De Araújo
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte 59078-970, Brazil
| | - Daniel Carlos Ferreira Lanza
- Laboratory of Applied Molecular Biology, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte 59078-970, Brazil
| | - Fabiana Lima Bezerra
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte 59078-970, Brazil
| | - Vania Sousa Andrade
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte 59078-970, Brazil
| | | | - José Veríssimo Fernandes
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte 59078-970, Brazil
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Tsuchiya J, Maki Y, Ayano M, Kikuchi T, Watanabe Y, Ohtake K, Fujita R, Hayashi M, Yamamoto J, Wang Y, Anzai A, Kubo T, Sano S. A Novel Method for Acquired Sex Chromosome Mosaicism. Adv Biol (Weinh) 2024:e2300512. [PMID: 38684458 DOI: 10.1002/adbi.202300512] [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: 09/23/2023] [Revised: 03/19/2024] [Indexed: 05/02/2024]
Abstract
The phenomenon of sex chromosome loss from hematopoietic cells is an emerging indicator of biological aging. While many methods to detect this loss have been developed, enhancing the field, these existing methods often suffer from being labor-intensive, expensive, and not sufficiently sensitive. To bridge this gap, a novel and more efficient technique is developed, named the SinChro assay. This method employs multiplexed single-cell droplet PCR, designed to detect cells with sex chromosome loss at single-cell resolution. Through the SinChro assay, the age-dependent increase in Y chromosome loss in male blood is successfully mapped. The age-dependent loss of the X chromosome in female blood is also identified, a finding that has been challenging with existing methods. The advent of the SinChro assay marks a significant breakthrough in the study of age-related sex mosaicism. Its utility extends beyond blood analysis, applicable to a variety of tissues, and it holds the potential to deepen the understanding of biological aging and related diseases.
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Affiliation(s)
| | - Yoshinori Maki
- Laboratory of Cardiovascular Mosaicism, National Cerebral and Cardiovascular Center, Osaka, 564-8565, Japan
- Hikone Central Hospital, Shiga, 522-0054, Japan
| | | | - Taiki Kikuchi
- Laboratory of Cardiovascular Mosaicism, National Cerebral and Cardiovascular Center, Osaka, 564-8565, Japan
- Department of Obstetrics and Gynecology, Osaka Metropolitan University, Osaka, 584-8585, Japan
| | - Yosuke Watanabe
- Laboratory of Cardiovascular Mosaicism, National Cerebral and Cardiovascular Center, Osaka, 564-8565, Japan
- Department of Cardiovascular Medicine, Faculty of Medicine, University of Yamanashi, Yamanashi, 409-3898, Japan
| | - Kiyoshi Ohtake
- Department of Clinical Laboratory, Tokyo Takanawa Hospital, Tokyo, 108-0074, Japan
| | - Rumi Fujita
- Department of Clinical Laboratory, Tokyo Takanawa Hospital, Tokyo, 108-0074, Japan
| | | | - Junji Yamamoto
- Department of Surgery, Tokyo Takanawa Hospital, Tokyo, 108-0074, Japan
| | - Ying Wang
- Department of Cardiology, The Second Affiliated Hospital of Army Medical University, Chongqing, 400037, China
| | - Atsushi Anzai
- Laboratory of Cardiovascular Mosaicism, National Cerebral and Cardiovascular Center, Osaka, 564-8565, Japan
- Department of Cardiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | | | - Soichi Sano
- Laboratory of Cardiovascular Mosaicism, National Cerebral and Cardiovascular Center, Osaka, 564-8565, Japan
- Hikone Central Hospital, Shiga, 522-0054, Japan
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Gutiérrez-Hurtado IA, Sánchez-Méndez AD, Becerra-Loaiza DS, Rangel-Villalobos H, Torres-Carrillo N, Gallegos-Arreola MP, Aguilar-Velázquez JA. Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men's Health. Int J Mol Sci 2024; 25:4230. [PMID: 38673816 PMCID: PMC11050192 DOI: 10.3390/ijms25084230] [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: 03/05/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Until a few years ago, it was believed that the gradual mosaic loss of the Y chromosome (mLOY) was a normal age-related process. However, it is now known that mLOY is associated with a wide variety of pathologies in men, such as cardiovascular diseases, neurodegenerative disorders, and many types of cancer. Nevertheless, the mechanisms that generate mLOY in men have not been studied so far. This task is of great importance because it will allow focusing on possible methods of prophylaxis or therapy for diseases associated with mLOY. On the other hand, it would allow better understanding of mLOY as a possible marker for inferring the age of male samples in cases of human identification. Due to the above, in this work, a comprehensive review of the literature was conducted, presenting the most relevant information on the possible molecular mechanisms by which mLOY is generated, as well as its implications for men's health and its possible use as a marker to infer age.
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Affiliation(s)
- Itzae Adonai Gutiérrez-Hurtado
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
| | - Astrid Desireé Sánchez-Méndez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán 47820, Jalisco, Mexico
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Martha Patricia Gallegos-Arreola
- División de Genética, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Jalisco, Mexico
| | - José Alonso Aguilar-Velázquez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
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Deng S, Gong H, Zhang D, Zhang M, He X. A statistical method for quantifying progenitor cells reveals incipient cell fate commitments. Nat Methods 2024; 21:597-608. [PMID: 38379073 DOI: 10.1038/s41592-024-02189-7] [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: 03/04/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024]
Abstract
Quantifying the number of progenitor cells that found an organ, tissue or cell population is of fundamental importance for understanding the development and homeostasis of a multicellular organism. Previous efforts rely on marker genes that are specifically expressed in progenitors. This strategy is, however, often hindered by the lack of ideal markers. Here we propose a general statistical method to quantify the progenitors of any tissues or cell populations in an organism, even in the absence of progenitor-specific markers, by exploring the cell phylogenetic tree that records the cell division history during development. The method, termed targeting coalescent analysis (TarCA), computes the probability that two randomly sampled cells of a tissue coalesce within the tissue-specific monophyletic clades. The inverse of this probability then serves as a measure of the progenitor number of the tissue. Both mathematic modeling and computer simulations demonstrated the high accuracy of TarCA, which was then validated using real data from nematode, fruit fly and mouse, all with related cell phylogenetic trees. We further showed that TarCA can be used to identify lineage-specific upregulated genes during embryogenesis, revealing incipient cell fate commitments in mouse embryos.
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Affiliation(s)
- Shanjun Deng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Han Gong
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Di Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Mengdong Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xionglei He
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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8
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Mattisson J, Halvardson J, Davies H, Bruhn-Olszewska B, Olszewski P, Danielsson M, Bjurling J, Lindberg A, Zaghlool A, Rychlicka-Buniowska E, Dumanski JP, Forsberg LA. Loss of chromosome Y in regulatory T cells. BMC Genomics 2024; 25:243. [PMID: 38443832 PMCID: PMC10913415 DOI: 10.1186/s12864-024-10168-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Mosaic loss of chromosome Y (LOY) in leukocytes is the most prevalent somatic aneuploidy in aging humans. Men with LOY have increased risks of all-cause mortality and the major causes of death, including many forms of cancer. It has been suggested that the association between LOY and disease risk depends on what type of leukocyte is affected with Y loss, with prostate cancer patients showing higher levels of LOY in CD4 + T lymphocytes. In previous studies, Y loss has however been observed at relatively low levels in this cell type. This motivated us to investigate whether specific subsets of CD4 + T lymphocytes are particularly affected by LOY. Publicly available, T lymphocyte enriched, single-cell RNA sequencing datasets from patients with liver, lung or colorectal cancer were used to study how LOY affects different subtypes of T lymphocyte. To validate the observations from the public data, we also generated a single-cell RNA sequencing dataset comprised of 23 PBMC samples and 32 CD4 + T lymphocytes enriched samples. RESULTS Regulatory T cells had significantly more LOY than any other studied T lymphocytes subtype. Furthermore, LOY in regulatory T cells increased the ratio of regulatory T cells compared with other T lymphocyte subtypes, indicating an effect of Y loss on lymphocyte differentiation. This was supported by developmental trajectory analysis of CD4 + T lymphocytes culminating in the regulatory T cells cluster most heavily affected by LOY. Finally, we identify dysregulation of 465 genes in regulatory T cells with Y loss, many involved in the immunosuppressive functions and development of regulatory T cells. CONCLUSIONS Here, we show that regulatory T cells are particularly affected by Y loss, resulting in an increased fraction of regulatory T cells and dysregulated immune functions. Considering that regulatory T cells plays a critical role in the process of immunosuppression; this enrichment for regulatory T cells with LOY might contribute to the increased risk for cancer observed among men with Y loss in leukocytes.
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Affiliation(s)
- Jonas Mattisson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Paweł Olszewski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Josefin Bjurling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Lindberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Jan P Dumanski
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- The Beijer Laboratory, Uppsala University, Uppsala, Sweden
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9
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Stańkowska W, Sarkisyan D, Bruhn-Olszewska B, Duzowska K, Bieńkowski M, Jąkalski M, Wójcik-Zalewska M, Davies H, Drężek-Chyła K, Pęksa R, Harazin-Lechowska A, Ambicka A, Przewoźnik M, Adamczyk A, Sasim K, Makarewicz W, Matuszewski M, Biernat W, Järhult JD, Lipcsey M, Hultström M, Frithiof R, Jaszczyński J, Ryś J, Genovese G, Piotrowski A, Filipowicz N, Dumanski JP. Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium. Cancers (Basel) 2024; 16:961. [PMID: 38473323 DOI: 10.3390/cancers16050961] [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: 11/30/2023] [Revised: 01/15/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Bladder urothelial carcinoma (BLCA) is the 10th most common cancer with a low survival rate and strong male bias. We studied the field cancerization in BLCA using multi-sample- and multi-tissue-per-patient protocol for sensitive detection of autosomal post-zygotic chromosomal alterations and loss of chromosome Y (LOY). We analysed 277 samples of histologically normal urothelium, 145 tumors and 63 blood samples from 52 males and 15 females, using the in-house adapted Mosaic Chromosomal Alterations (MoChA) pipeline. This approach allows identification of the early aberrations in urothelium from BLCA patients. Overall, 45% of patients exhibited at least one alteration in at least one normal urothelium sample. Recurrence analysis resulted in 16 hotspots composed of either gains and copy number neutral loss of heterozygosity (CN-LOH) or deletions and CN-LOH, encompassing well-known and new BLCA cancer driver genes. Conservative assessment of LOY showed 29%, 27% and 18% of LOY-cells in tumors, blood and normal urothelium, respectively. We provide a proof of principle that our approach can characterize the earliest alterations preconditioning normal urothelium to BLCA development. Frequent LOY in blood and urothelium-derived tissues suggest its involvement in BLCA.
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Affiliation(s)
- Wiktoria Stańkowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Daniil Sarkisyan
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Katarzyna Duzowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Marcin Jąkalski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Magdalena Wójcik-Zalewska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Kinga Drężek-Chyła
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Karol Sasim
- Clinic of Urology and Oncological Urology, Specialist Hospital of Kościerzyna, Piechowskiego 36, 83-400 Kościerzyna, Poland
| | - Wojciech Makarewicz
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Piechowskiego 36, 83-400 Kościerzyna, Poland
| | - Marcin Matuszewski
- Department and Clinic of Urology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Miklós Lipcsey
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
- Hedenstierna Laboratory, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Michael Hultström
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Robert Frithiof
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Janusz Jaszczyński
- Department of Urology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Giulio Genovese
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
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10
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Wilson PC, Verma A, Yoshimura Y, Muto Y, Li H, Malvin NP, Dixon EE, Humphreys BD. Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease. Genome Biol 2024; 25:36. [PMID: 38287344 PMCID: PMC10823641 DOI: 10.1186/s13059-024-03173-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and chronic kidney disease. RESULTS The likelihood of a cell having LOY varies depending on its location in the nephron. Cortical epithelial cell types have a greater proportion of LOY than medullary or glomerular cell types, which may reflect their proliferative history. Proximal tubule cells are the most abundant cell type in the cortex and are susceptible to hypoxic injury. A subset of these cells acquires a pro-inflammatory transcription and chromatin accessibility profile associated with expression of HAVCR1, VCAM1, and PROM1. These injured epithelial cells have the greatest proportion of LOY and their presence predicts future kidney function decline. Moreover, proximal tubule cells with LOY are more likely to harbor additional large chromosomal gains and express pro-survival pathways. Spatial transcriptomics localizes injured proximal tubule cells to a pro-fibrotic microenvironment where they adopt a secretory phenotype and likely communicate with infiltrating immune cells. CONCLUSIONS We hypothesize that LOY is an indicator of increased DNA damage and potential marker of cellular senescence that can be applied to single-cell datasets in other tissues.
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Affiliation(s)
- Parker C Wilson
- Division of Diagnostic Innovation, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Amit Verma
- Division of Diagnostic Innovation, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole P Malvin
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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11
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Minow MAA, Marand AP, Schmitz RJ. Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. Annu Rev Genet 2023; 57:297-319. [PMID: 37562412 PMCID: PMC10775913 DOI: 10.1146/annurev-genet-022123-110824] [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: 08/12/2023]
Abstract
The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.
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Affiliation(s)
- Mark A A Minow
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
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12
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Burr R, Leshchiner I, Costantino CL, Blohmer M, Sundaresan T, Cha J, Seeger K, Guay S, Danysh BP, Gore I, Jacobs RA, Slowik K, Utro F, Rhrissorrakrai K, Levovitz C, Barth JL, Dubash T, Chirn B, Parida L, Sequist LV, Lennerz JK, Mino-Kenudson M, Maheswaran S, Naxerova K, Getz G, Haber DA. Germline mutations and developmental mosaicism underlying EGFR-mutant lung cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.28.23296274. [PMID: 37808694 PMCID: PMC10557804 DOI: 10.1101/2023.09.28.23296274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
While the development of multiple primary tumors in smokers with lung cancer can be attributed to carcinogen-induced field cancerization, the occurrence of multiple primary tumors in individuals with EGFR-mutant lung cancer who lack known environmental exposures remains unexplained. We identified ten patients with early-stage, resectable non-small cell lung cancer who presented with multiple anatomically distinct EGFR-mutant tumors. We analyzed the phylogenetic relationships among multiple tumors from each patient using whole exome sequencing (WES) and hypermutable poly-guanine (poly-G) repeat genotyping, as orthogonal methods for lineage tracing. In two patients, we identified germline EGFR variants, which confer moderately enhanced signaling when modeled in vitro. In four other patients, developmental mosaicism is supported by the poly-G lineage tracing and WES, indicating a common non-germline cell-of-origin. Thus, developmental mosaicism and germline variants define two distinct mechanisms of genetic predisposition to multiple EGFR-mutant primary tumors, with implications for understanding their etiology and clinical management.
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Affiliation(s)
- Risa Burr
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Ignaty Leshchiner
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina L Costantino
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Blohmer
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Justin Cha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karsen Seeger
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Sara Guay
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Brian P Danysh
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ira Gore
- St Vincent’s Hospital, Birmingham, AL, USA
| | - Raquel A Jacobs
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kara Slowik
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Taronish Dubash
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Brian Chirn
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kamila Naxerova
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
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13
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Úbeda F, Wild G. Microchimerism as a source of information on future pregnancies. Proc Biol Sci 2023; 290:20231142. [PMID: 37608718 PMCID: PMC10445024 DOI: 10.1098/rspb.2023.1142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
Small numbers of fetal cells cross the placenta during pregnancy turning mothers into microchimeras. Fetal cells from all previous pregnancies accumulate forming the mother's fetal microchiome. What is significant about microchimeric cells is that they have been linked to health problems including reproductive and autoimmune diseases. Three decades after the discovery of fetal microchimerism, the function of these cells remains a mystery. Here, we contend that the role of microchimeric cells is to inform the fetus about the likelihood that its genes are present in future pregnancies. We argue that, when genes are more likely than average to be in future maternal siblings, fetuses will send a fixed number of cells that will not elicit a maternal immune response against them. However, when genes are less likely to be in future maternal siblings, fetuses will send an ever-increasing number of cells that will elicit an ever-stronger maternal immune response. Our work can explain the observed clinical association between microchimeric cells and pre-eclampsia. However, our work predicts that this association should be stronger in women with a genetically diverse microchiome. If supported by medical tests, our work would allow establishing the likelihood of pregnancy or autoimmune problems advising medical interventions.
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Affiliation(s)
- Francisco Úbeda
- Department of Biological Sciences, Royal Holloway, University of London, Egham TW20 0EX, UK
| | - Geoff Wild
- Department of Mathematics, The University of Western Ontario, London, Ontario, Canada N6A 5B7
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14
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Leshchyk A, Xiang Q, Andersen SL, Gurinovich A, Song Z, Lee JH, Christensen K, Yashin A, Wojczynski M, Schwander K, Perls TT, Monti S, Sebastiani P. Mosaic Chromosomal Alterations and Human Longevity. J Gerontol A Biol Sci Med Sci 2023; 78:1561-1568. [PMID: 36988570 PMCID: PMC10460554 DOI: 10.1093/gerona/glad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 03/30/2023] Open
Abstract
Mosaic chromosomal alterations (mCAs) are structural alterations associated with aging, cancer, cardiovascular disease, infectious diseases, and mortality. The distribution of mCAs in centenarians and individuals with familial longevity is poorly understood. We used MOsaic CHromosomal Alteration (MoChA) to discover mCAs in 2050 centenarians, offspring, and 248 controls from the New England Centenarian Study (NECS) and in 3 642 subjects with familial longevity and 920 spousal controls from the Long-Life Family Study (LLFS). We analyzed study-specific associations of somatic mCAs with age, familial longevity, the incidence of age-related diseases, and mortality and aggregated the results by meta-analysis. We show that the accumulation of mCAs > 100 KB increased to 102 years and plateaued at older ages. Centenarians and offspring accumulated fewer autosomal mCAs compared with controls (relative risk 0.637, p = .0147). Subjects with the APOE E4 allele had a 35.3% higher risk of accumulating autosomal mCAs (p = .002). Males were at higher risk for mCAs compared to females (male relative risk 1.36, p = 5.15e-05). mCAs were associated with increased hazard for cancer (hazard ratio 1.2) and dementia (hazard ratio 1.259) at a 10% false discovery rate. We observed a borderline significant association between mCAs and risk for mortality (hazard ratio 1.07, p = .0605). Our results show that the prevalence of individuals with mCAs does not continue to increase at ages >102 years and factors promoting familial longevity appear to confer protections from mCAs. These results suggest that limited mCA accumulation could be an important mechanism for extreme human longevity that needs to be investigated.
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Affiliation(s)
- Anastasia Leshchyk
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Department of Medicine, Computational Biomedicine Section, Boston University, Boston, Massachusetts, USA
| | - Qingyan Xiang
- Department of Biostatistics, Boston University, Boston, Massachusetts, USA
| | - Stacy L Andersen
- Department of Medicine, Section of Geriatrics, Boston University, Boston, Massachusetts, USA
| | - Anastasia Gurinovich
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts, USA
| | - Zeyuan Song
- Department of Biostatistics, Boston University, Boston, Massachusetts, USA
| | - Joseph H Lee
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Kaare Christensen
- Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Anatoliy Yashin
- Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Mary Wojczynski
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Karen Schwander
- Division of Biostatistics, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Thomas T Perls
- Department of Medicine, Section of Geriatrics, Boston University, Boston, Massachusetts, USA
| | - Stefano Monti
- Department of Medicine, Computational Biomedicine Section, Boston University, Boston, Massachusetts, USA
| | - Paola Sebastiani
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Medicine, Tufts University, Boston, Massachusetts, USA
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15
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Lutshumba J, Wilcock DM, Monson NL, Stowe AM. Sex-based differences in effector cells of the adaptive immune system during Alzheimer's disease and related dementias. Neurobiol Dis 2023; 184:106202. [PMID: 37330146 PMCID: PMC10481581 DOI: 10.1016/j.nbd.2023.106202] [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: 01/19/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Neurological conditions such as Alzheimer's disease (AD) and related dementias (ADRD) present with many challenges due to the heterogeneity of the related disease(s), making it difficult to develop effective treatments. Additionally, the progression of ADRD-related pathologies presents differently between men and women. With two-thirds of the population affected with ADRD being women, ADRD has presented itself with a bias toward the female population. However, studies of ADRD generally do not incorporate sex-based differences in investigating the development and progression of the disease, which is detrimental to understanding and treating dementia. Additionally, recent implications for the adaptive immune system in the development of ADRD bring in new factors to be considered as part of the disease, including sex-based differences in immune response(s) during ADRD development. Here, we review the sex-based differences of pathological hallmarks of ADRD presentation and progression, sex-based differences in the adaptive immune system and how it changes with ADRD, and the importance of precision medicine in the development of a more targeted and personalized treatment for this devastating and prevalent neurodegenerative condition.
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Affiliation(s)
- Jenny Lutshumba
- Department of Neurology, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Donna M Wilcock
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States of America; Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Nancy L Monson
- Department of Neurology and Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Ann M Stowe
- Department of Neurology, College of Medicine, University of Kentucky, Lexington, KY, United States of America; Center for Advanced Translational Stroke Science, University of Kentucky, Lexington, KY, United States of America.
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16
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Xu X, Zhou R, Duan Q, Miao Y, Zhang T, Wang M, Jones OD, Xu M. Circulating macrophages as the mechanistic link between mosaic loss of Y-chromosome and cardiac disease. Cell Biosci 2023; 13:135. [PMID: 37488646 PMCID: PMC10364353 DOI: 10.1186/s13578-023-01075-7] [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: 11/23/2022] [Accepted: 06/19/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Genetics evidences have long linked mosaic loss of Y-chromosome (mLOY) in peripheral leukocytes with a wide range of male age-associated diseases. However, a lack of cellular and molecular mechanistic explanations for this link has limited further investigation into the relationship between mLOY and male age-related disease. Excitingly, Sano et al. have provided the first piece of evidence directly linking mLOY to cardiac fibrosis through mLOY enriched profibrotic transforming growth factor β1 (TGF-β1) regulons in hematopoietic macrophages along with suppressed interleukin-1β (IL-1β) proinflammatory regulons. The results of this novel finding can be extrapolated to other disease related to mLOY, such as cancer, cardiac disease, and age-related macular degeneration. RESULTS Sano et al. used a CRISPR-Cas9 gRNAs gene editing induced Y-chromosome ablation mouse model to assess results of a UK biobank prospective analysis implicating the Y-chromosome in male age-related disease. Using this in vivo model, Sano et al. showed that hematopoietic mLOY accelerated cardiac fibrosis and heart failure in male mice through profibrotic pathways. This process was linked to monocyte-macrophage differentiation during hematopoietic development. Mice confirmed to have mLOY in leukocytes, by loss of Y-chromosome genes Kdm5d, Uty, Eif2s3y, and Ddx3y, at similar percentages to the human population were shown to have accelerated rates of interstitial and perivascular fibrosis and abnormal echocardiograms. These mice also recovered poorly from the transverse aortic constriction (TAC) model of heart failure and developed left ventricular dysfunction at higher rates. This was attributed to aberrant proliferation of cardiac MEF-SK4 + fibroblasts promoted by mLOY macrophages enriched in profibrotic regulons and lacking in proinflammatory regulons. These pro-fibrotic macrophages localized to heart and eventually resulted in cardiac fibrosis via enhanced TGF-β1 and suppressed IL-1β signaling. Furthermore, treatment of mLOY mice with TGFβ1 neutralizing antibody was able to improve their cardiac function. This study by Sano et al. was able to provide a causative link between the known association between mLOY and male cardiac disease morbidity and mortality for the first time, and thereby provide a new target for improving human health. CONCLUSIONS Using a CRISPR-Cas9 induced Y-chromosome ablation mouse model, Sano et al. has proven mosaic loss of Y-chromosome in peripheral myeloid cells to have a causative effect on male mobility and mortality due to male age-related cardiac disease. They traced the mechanism of this effect to hyper-expression of the profibrotic TGF-β1 and reduced pro-inflammatory IL-1β signaling, attenuation of which could provide another potential strategy in improving outcomes against age-related diseases in men.
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Affiliation(s)
- Xuehong Xu
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences and University Hospital Medical Center, 620 West Chang'an, Chang'an District, Xi'an, 710119, China.
| | - Rong Zhou
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences and University Hospital Medical Center, 620 West Chang'an, Chang'an District, Xi'an, 710119, China
| | - Qinchun Duan
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences and University Hospital Medical Center, 620 West Chang'an, Chang'an District, Xi'an, 710119, China
| | - Yuanlin Miao
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences and University Hospital Medical Center, 620 West Chang'an, Chang'an District, Xi'an, 710119, China
| | - Tingting Zhang
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences and University Hospital Medical Center, 620 West Chang'an, Chang'an District, Xi'an, 710119, China
| | - Mofei Wang
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences and University Hospital Medical Center, 620 West Chang'an, Chang'an District, Xi'an, 710119, China
| | - Odell D Jones
- University of Pennsylvania School of Medicine ULAR, Philadelphia, PA, 19144, USA
| | - MengMeng Xu
- Department of Pediatrics, Morgan Stanley Children's Hospital, Columbia University, 3959 Broadway, New York, NY, 10032, USA.
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17
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Allen JB, Ludtka C, James BD. Sex as a Biological Variable in Tissue Engineering and Regenerative Medicine. Annu Rev Biomed Eng 2023; 25:311-331. [PMID: 37104652 PMCID: PMC10312304 DOI: 10.1146/annurev-bioeng-092222-030857] [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: 04/29/2023]
Abstract
Although sex differences have been noted in cellular function and behavior, therapy efficacy, and disease incidence and outcomes, the adoption of sex as a biological variable in tissue engineering and regenerative medicine remains limited. Furthering the development of personalized, precision medicine requires considering biological sex at the bench and in the clinic. This review provides the basis for considering biological sex when designing tissue-engineered constructs and regenerative therapies by contextualizing sex as a biological variable within the tissue engineering triad of cells, matrices, and signals. To achieve equity in biological sex within medicine requires a cultural shift in science and engineering research, with active engagement by researchers, clinicians, companies, policymakers, and funding agencies.
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Affiliation(s)
- Josephine B Allen
- Department of Materials Science and Engineering, University of Florida, Gainesville, Florida, USA;
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, USA;
| | - Christopher Ludtka
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, USA;
| | - Bryan D James
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA;
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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18
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Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Salazar MA, Hentges LD, Mickute G, Clark K, Sopp P, Davies JOJ, Hughes JR, Vyas P. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell 2023; 30:722-740.e11. [PMID: 37146586 DOI: 10.1016/j.stem.2023.04.012] [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: 10/04/2022] [Revised: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.
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Affiliation(s)
- Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angus Groom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Simone G Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - E Ravza Gür
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Batchimeg Usukhbayar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Mirian Angulo Salazar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lance D Hentges
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gerda Mickute
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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19
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Rockweiler NB, Ramu A, Nagirnaja L, Wong WH, Noordam MJ, Drubin CW, Huang N, Miller B, Todres EZ, Vigh-Conrad KA, Zito A, Small KS, Ardlie KG, Cohen BA, Conrad DF. The origins and functional effects of postzygotic mutations throughout the human life span. Science 2023; 380:eabn7113. [PMID: 37053313 DOI: 10.1126/science.abn7113] [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: 12/16/2021] [Accepted: 03/17/2023] [Indexed: 04/15/2023]
Abstract
Postzygotic mutations (PZMs) begin to accrue in the human genome immediately after fertilization, but how and when PZMs affect development and lifetime health remain unclear. To study the origins and functional consequences of PZMs, we generated a multitissue atlas of PZMs spanning 54 tissue and cell types from 948 donors. Nearly half the variation in mutation burden among tissue samples can be explained by measured technical and biological effects, and 9% can be attributed to donor-specific effects. Through phylogenetic reconstruction of PZMs, we found that their type and predicted functional impact vary during prenatal development, across tissues, and through the germ cell life cycle. Thus, methods for interpreting effects across the body and the life span are needed to fully understand the consequences of genetic variants.
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Affiliation(s)
- Nicole B Rockweiler
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Wing H Wong
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michiel J Noordam
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Casey W Drubin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ni Huang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian Miller
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Ellen Z Todres
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Katinka A Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Antonino Zito
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | | | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR 97239, USA
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20
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Truty R, Rojahn S, Ouyang K, Kautzer C, Kennemer M, Pineda-Alvarez D, Johnson B, Stafford A, Basel-Salmon L, Saitta S, Slavotinek A, Chandrasekharappa SC, Suarez CJ, Burnett L, Nussbaum RL, Aradhya S. Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals. Am J Hum Genet 2023; 110:551-564. [PMID: 36933558 PMCID: PMC10119133 DOI: 10.1016/j.ajhg.2023.02.013] [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: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.
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Affiliation(s)
- Rebecca Truty
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Karen Ouyang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | | | | | - Britt Johnson
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital and Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlos Jose Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; School of Medicine, University of California - San Francisco, San Francisco, CA, USA
| | - Swaroop Aradhya
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA.
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21
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Pereira QC, dos Santos TW, Fortunato IM, Ribeiro ML. The Molecular Mechanism of Polyphenols in the Regulation of Ageing Hallmarks. Int J Mol Sci 2023; 24:ijms24065508. [PMID: 36982583 PMCID: PMC10049696 DOI: 10.3390/ijms24065508] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 03/16/2023] Open
Abstract
Ageing is a complex process characterized mainly by a decline in the function of cells, tissues, and organs, resulting in an increased risk of mortality. This process involves several changes, described as hallmarks of ageing, which include genomic instability, telomere attrition, epigenetic changes, loss of proteostasis, dysregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell depletion, and altered intracellular communication. The determining role that environmental factors such as diet and lifestyle play on health, life expectancy, and susceptibility to diseases, including cancer and neurodegenerative diseases, is wellestablished. In view of the growing interest in the beneficial effects of phytochemicals in the prevention of chronic diseases, several studies have been conducted, and they strongly suggest that the intake of dietary polyphenols may bring numerous benefits due to their antioxidant and anti-inflammatory properties, and their intake has been associated with impaired ageing in humans. Polyphenol intake has been shown to be effective in ameliorating several age-related phenotypes, including oxidative stress, inflammatory processes, impaired proteostasis, and cellular senescence, among other features, which contribute to an increased risk of ageing-associated diseases. This review aims to address, in a general way, the main findings described in the literature about the benefits of polyphenols in each of the hallmarks of ageing, as well as the main regulatory mechanisms responsible for the observed antiageing effects.
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Affiliation(s)
- Quélita Cristina Pereira
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University Medical School, Braganca Paulista 12916-900, SP, Brazil
| | - Tanila Wood dos Santos
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University Medical School, Braganca Paulista 12916-900, SP, Brazil
| | - Isabela Monique Fortunato
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University Medical School, Braganca Paulista 12916-900, SP, Brazil
| | - Marcelo Lima Ribeiro
- Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University Medical School, Braganca Paulista 12916-900, SP, Brazil
- Lymphoma Translational Group, Josep Carreras Leukemia Research Institute, 08916 Badalona, Spain
- Correspondence:
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22
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The emergence of genotypic divergence and future precision medicine applications. HANDBOOK OF CLINICAL NEUROLOGY 2023; 192:87-99. [PMID: 36796950 DOI: 10.1016/b978-0-323-85538-9.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genotypic divergence is a term adapted from population genetics and intimately linked to evolution. We use divergence here to emphasize the differences that set individuals apart in any cohort. The history of genetics is filled with descriptions of genotypic differences, but causal inference of interindividual biological variation has been scarce. We suggest that the practice of precision medicine requires a divergent approach, an approach dependent on the causal interpretation of previous convergent (and preliminary) knowledge in the field. This knowledge has relied on convergent descriptive syndromology (lumping), which has overemphasized a reductionistic gene determinism on the quest of seeking associations without causal understanding. Regulatory variants with small effect and somatic mutations are some of the modifying factors that lead to incomplete penetrance and intrafamilial variable expressivity often observed in apparently monogenic clinical disorders. A truly divergent approach to precision medicine requires splitting, that is, the consideration of different layers of genetic phenomena that interact causally in a nonlinear fashion. This chapter reviews convergences and divergences in genetics and genomics, aiming to discuss what can be causally understood to approximate the as-yet utopian lands of Precision Medicine for patients with neurodegenerative disorders.
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23
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Grave-to-cradle: human embryonic lineage tracing from the postmortem body. Exp Mol Med 2023; 55:13-21. [PMID: 36599930 PMCID: PMC9898511 DOI: 10.1038/s12276-022-00912-y] [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: 04/04/2022] [Revised: 09/02/2022] [Accepted: 10/13/2022] [Indexed: 01/06/2023] Open
Abstract
Curiosity concerning the process of human creation has been around for a long time. Relevant questions seemed to be resolved with the knowledge of how cells divide after fertilization obtained through in vitro fertilization experiments. However, we still do not know how human life is created at the cellular level. Recently, the value of cadavers as a resource from which to obtain "normal" cells and tissues has been established, and human research using postmortem bodies has attracted growing scientific attention. As the human genome can be analyzed at the level of nucleotides through whole-genome sequencing, individual cells in a postmortem body can be traced back to determine what developmental processes have transpired from fertilization. These retrospective lineage tracing studies have answered several unsolved questions on how humans are created. This review covers the methodologies utilized in lineage tracing research in a historical context and the conceptual basis for reconstructing the division history of cells in a retrospective manner using postzygotic somatic variants in postmortem tissue. We further highlight answers that postmortem research could potentially address and discuss issues that wait to be solved in the future.
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24
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Evans MA, Walsh K. Clonal hematopoiesis, somatic mosaicism, and age-associated disease. Physiol Rev 2023; 103:649-716. [PMID: 36049115 PMCID: PMC9639777 DOI: 10.1152/physrev.00004.2022] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 12/15/2022] Open
Abstract
Somatic mosaicism, the occurrence of multiple genetically distinct cell clones within the same tissue, is an evitable consequence of human aging. The hematopoietic system is no exception to this, where studies have revealed the presence of expanded blood cell clones carrying mutations in preleukemic driver genes and/or genetic alterations in chromosomes. This phenomenon is referred to as clonal hematopoiesis and is remarkably prevalent in elderly individuals. While clonal hematopoiesis represents an early step toward a hematological malignancy, most individuals will never develop blood cancer. Somewhat unexpectedly, epidemiological studies have found that clonal hematopoiesis is associated with an increase in the risk of all-cause mortality and age-related disease, particularly in the cardiovascular system. Studies using murine models of clonal hematopoiesis have begun to shed light on this relationship, suggesting that driver mutations in mature blood cells can causally contribute to aging and disease by augmenting inflammatory processes. Here we provide an up-to-date review of clonal hematopoiesis within the context of somatic mosaicism and aging and describe recent epidemiological studies that have reported associations with age-related disease. We will also discuss the experimental studies that have provided important mechanistic insight into how driver mutations promote age-related disease and how this knowledge could be leveraged to treat individuals with clonal hematopoiesis.
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Affiliation(s)
- Megan A Evans
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
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25
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Mosaic loss of chromosome Y in peripheral blood cells is associated with age-related macular degeneration in men. Cell Biosci 2022; 12:73. [PMID: 35642040 PMCID: PMC9153148 DOI: 10.1186/s13578-022-00811-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Age-related macular degeneration (AMD) is the leading cause of severe vision loss in patients over 55 years old in the industrialized world. In the past 20 years, approximately 288 million patents have been affected by this disease. Despite this high prevalence, the molecular mechanism for AMD remains unclear, and there remains no effective treatment for this disease. The mosaic loss of Y chromosome (mLOY) has been identified as a common phenomenon in multiple age-related disease (i.e., oncogenesis and cardiovascular disease) has recently been identified by genome-wide analysis to be linked to AMD as well. As the Y chromosome mainly possesses three genomic functions, sister chromatin cohesion, cell cycle mitosis, and apoptotic signaling, here we characterize the Y chromosome euchromatic genes and non-chromosome AMD genes in relevance to cellular proliferation and apoptotic signaling of leukocytes. Results Using STRING, a publically available database of all protein–protein interaction, Grassmann et al. found the genes on the Y chromosome is mainly believed to take part in three major cellular genomic functions- sister chromatin cohesion, cell cycle mitosis, and apoptotic signaling. Based on data from the Ensembl Genome database, we focus on our discussion on coding genes found in the euchromatins but not the PAR1 and PAR2 regions of the Y chromosomes. All 14 known euchromatic genes on the Y chromosome short arm and all 31 known euchromatic genes on the Y chromosome long arm (Yq) are directly or indirectly involved in the cell cycle (meiosis and mitosis) and proliferation. We sorted non-Y chromosome AMD associated genes into these three categories to identify signaling pathways that may compound with cellular dysregulation due to mLOY. Of the genes associated with AMD, complement pathway genes such as C2, C9 and CFH/ARMD4 are associated with proliferation, receptor-mediated endocytosis genes such as APOE, DAB2 and others associated with apoptotic signaling. Because nucleated cells found in peripheral circulation are mainly composed of leukocytes with reduced expression of CD99, a protein essential for leukocytes adhesion, translocation, and function, mLOY in these cells likely affect retinal degeneration through altered immunological surveillance. In fact, there is precedence that circulating macrophage can stabilize and modify the cardiac rhythm and contractility post ischemic damage. Therefore, the most likely mechanism through which peripheral mLOY affects AMD development in men is through the role affected leukocytes play in retinal proliferation and apoptosis. Conclusions mLOY in peripheral blood is newly discovered in AMD by Grassmann et al. as it is a common phenomenon in oncogenesis and cardiac dysfunction. Here the recent data conclude the possible mechanism for the newly identified link between mLOY and AMD, and provide support that mLOY in circulating macrophage-monocyte of affected male patients promotes AMD by targeting the retina and causing macular degeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00811-9.
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26
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Jeong H, Grimes K, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO. Functional analysis of structural variants in single cells using Strand-seq. Nat Biotechnol 2022:10.1038/s41587-022-01551-4. [PMID: 36424487 DOI: 10.1038/s41587-022-01551-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 10/07/2022] [Indexed: 11/27/2022]
Abstract
Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.
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Affiliation(s)
- Hyobin Jeong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
| | - Karen Grimes
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Kerstin K Rauwolf
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Peter-Martin Bruch
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Tobias Rausch
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Patrick Hasenfeld
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Eva Benito
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tobias Roider
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | | | - David Porubsky
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarbrücken, Germany.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sophie A Herbst
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Büşra Erarslan-Uysal
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Johann-Christoph Jann
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Ashley D Sanders
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany. .,Charité-Universitätsmedizin, Berlin, Germany.
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany. .,Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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27
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Dvir E, Shohat S, Flint J, Shifman S. Identification of genetic mechanisms for tissue-specific genetic effects based on CRISPR screens. Genetics 2022; 222:iyac134. [PMID: 36063051 PMCID: PMC9630981 DOI: 10.1093/genetics/iyac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/26/2022] [Indexed: 11/12/2022] Open
Abstract
A major challenge in genetic studies of complex diseases is to determine how the action of risk genes is restricted to a tissue or cell type. Here, we investigate tissue specificity of gene action using CRISPR screens from 786 cancer cell lines originating from 24 tissues. We find that the expression pattern of the gene across tissues explains only a minority of cases of tissue-specificity (9%), while gene amplification and the expression levels of paralogs account for 39.5% and 15.5%, respectively. In addition, the transfer of small molecules to mutant cells explains tissue-specific gene action in blood. The tissue-specific genes we found are not specific just for human cancer cell lines: we found that the tissue-specific genes are intolerant to functional mutations in the human population and are associated with human diseases more than genes that are essential across all cell types. Our findings offer important insights into genetic mechanisms for tissue specificity of human diseases.
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Affiliation(s)
- Elad Dvir
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shahar Shohat
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jonathan Flint
- Department of Psychiatry and Biobehavioral Sciences, Brain Research Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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28
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Mertens J, Regin M, De Munck N, Couvreu de Deckersberg E, Belva F, Sermon K, Tournaye H, Blockeel C, Van de Velde H, Spits C. Mitochondrial DNA variants segregate during human preimplantation development into genetically different cell lineages that are maintained postnatally. Hum Mol Genet 2022; 31:3629-3642. [PMID: 35285472 PMCID: PMC9616571 DOI: 10.1093/hmg/ddac059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 06/30/2024] Open
Abstract
Humans present remarkable diversity in their mitochondrial DNA (mtDNA) in terms of variants across individuals as well as across tissues and even cells within one person. We have investigated the timing of the first appearance of this variant-driven mosaicism. For this, we deep-sequenced the mtDNA of 254 oocytes from 85 donors, 158 single blastomeres of 25 day-3 embryos, 17 inner cell mass and trophectoderm samples of 7 day-5 blastocysts, 142 bulk DNA and 68 single cells of different adult tissues. We found that day-3 embryos present blastomeres that carry variants only detected in that cell, showing that mtDNA mosaicism arises very early in human development. We classified the mtDNA variants based on their recurrence or uniqueness across different samples. Recurring variants had higher heteroplasmic loads and more frequently resulted in synonymous changes or were located in non-coding regions than variants unique to one oocyte or single embryonic cell. These differences were maintained through development, suggesting that the mtDNA mosaicism arising in the embryo is maintained into adulthood. We observed a decline in potentially pathogenic variants between day 3 and day 5 of development, suggesting early selection. We propose a model in which closely clustered mitochondria carrying specific mtDNA variants in the ooplasm are asymmetrically distributed throughout the cell divisions of the preimplantation embryo, resulting in the earliest form of mtDNA mosaicism in human development.
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Affiliation(s)
- Joke Mertens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Neelke De Munck
- Brussels IVF, Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Florence Belva
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Herman Tournaye
- Brussels IVF, Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
- Research Group Biology of the Testis, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
- Department of Obstetrics, Gynaecology, Perinatology and Reproduction, Institute of Professional Education, Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Moscow 119992, Russia
| | - Christophe Blockeel
- Brussels IVF, Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
| | - Hilde Van de Velde
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
- Brussels IVF, Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
- Research Group Reproduction and Immunology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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30
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Vihinen M. Individual Genetic Heterogeneity. Genes (Basel) 2022; 13:genes13091626. [PMID: 36140794 PMCID: PMC9498725 DOI: 10.3390/genes13091626] [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: 08/12/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden
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31
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Cobo I, Tanaka TN, Chandra Mangalhara K, Lana A, Yeang C, Han C, Schlachetzki J, Challcombe J, Fixsen BR, Sakai M, Li RZ, Fields H, Mokry M, Tsai RG, Bejar R, Prange K, de Winther M, Shadel GS, Glass CK. DNA methyltransferase 3 alpha and TET methylcytosine dioxygenase 2 restrain mitochondrial DNA-mediated interferon signaling in macrophages. Immunity 2022; 55:1386-1401.e10. [PMID: 35931086 PMCID: PMC9718507 DOI: 10.1016/j.immuni.2022.06.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 12/15/2022]
Abstract
Deleterious somatic mutations in DNA methyltransferase 3 alpha (DNMT3A) and TET mehtylcytosine dioxygenase 2 (TET2) are associated with clonal expansion of hematopoietic cells and higher risk of cardiovascular disease (CVD). Here, we investigated roles of DNMT3A and TET2 in normal human monocyte-derived macrophages (MDM), in MDM isolated from individuals with DNMT3A or TET2 mutations, and in macrophages isolated from human atherosclerotic plaques. We found that loss of function of DNMT3A or TET2 resulted in a type I interferon response due to impaired mitochondrial DNA integrity and activation of cGAS signaling. DNMT3A and TET2 normally maintained mitochondrial DNA integrity by regulating the expression of transcription factor A mitochondria (TFAM) dependent on their interactions with RBPJ and ZNF143 at regulatory regions of the TFAM gene. These findings suggest that targeting the cGAS-type I IFN pathway may have therapeutic value in reducing risk of CVD in patients with DNMT3A or TET2 mutations.
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Affiliation(s)
- Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiffany N Tanaka
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | | | - Addison Lana
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Calvin Yeang
- University of California San Diego, Sulpizio Cardiovascular Center, La Jolla, CA, USA
| | - Claudia Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Johannes Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jean Challcombe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bethany R Fixsen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Fields
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, 3584 EA Utrecht, the Netherlands
| | - Randy G Tsai
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Rafael Bejar
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Koen Prange
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Menno de Winther
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
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32
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Ceyhan-Birsoy O. Germline Testing for the Evaluation of Hereditary Cancer Predisposition. Clin Lab Med 2022; 42:497-506. [DOI: 10.1016/j.cll.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Cosenza MR, Rodriguez-Martin B, Korbel JO. Structural Variation in Cancer: Role, Prevalence, and Mechanisms. Annu Rev Genomics Hum Genet 2022; 23:123-152. [DOI: 10.1146/annurev-genom-120121-101149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | | | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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34
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Filipowicz N, Drężek K, Horbacz M, Wojdak A, Szymanowski J, Rychlicka-Buniowska E, Juhas U, Duzowska K, Nowikiewicz T, Stańkowska W, Chojnowska K, Andreou M, Ławrynowicz U, Wójcik M, Davies H, Śrutek E, Bieńkowski M, Milian-Ciesielska K, Zdrenka M, Ambicka A, Przewoźnik M, Harazin-Lechowska A, Adamczyk A, Kowalski J, Bała D, Wiśniewski D, Tkaczyński K, Kamecki K, Drzewiecka M, Wroński P, Siekiera J, Ratnicka I, Jankau J, Wierzba K, Skokowski J, Połom K, Przydacz M, Bełch Ł, Chłosta P, Matuszewski M, Okoń K, Rostkowska O, Hellmann A, Sasim K, Remiszewski P, Sierżęga M, Hać S, Kobiela J, Kaska Ł, Jankowski M, Hodorowicz-Zaniewska D, Jaszczyński J, Zegarski W, Makarewicz W, Pęksa R, Szpor J, Ryś J, Szylberg Ł, Piotrowski A, Dumanski JP. Comprehensive cancer-oriented biobanking resource of human samples for studies of post-zygotic genetic variation involved in cancer predisposition. PLoS One 2022; 17:e0266111. [PMID: 35390022 PMCID: PMC8989288 DOI: 10.1371/journal.pone.0266111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
The progress in translational cancer research relies on access to well-characterized samples from a representative number of patients and controls. The rationale behind our biobanking are explorations of post-zygotic pathogenic gene variants, especially in non-tumoral tissue, which might predispose to cancers. The targeted diagnoses are carcinomas of the breast (via mastectomy or breast conserving surgery), colon and rectum, prostate, and urinary bladder (via cystectomy or transurethral resection), exocrine pancreatic carcinoma as well as metastases of colorectal cancer to the liver. The choice was based on the high incidence of these cancers and/or frequent fatal outcome. We also collect age-matched normal controls. Our still ongoing collection originates from five clinical centers and after nearly 2-year cooperation reached 1711 patients and controls, yielding a total of 23226 independent samples, with an average of 74 donors and 1010 samples collected per month. The predominant diagnosis is breast carcinoma, with 933 donors, followed by colorectal carcinoma (383 donors), prostate carcinoma (221 donors), bladder carcinoma (81 donors), exocrine pancreatic carcinoma (15 donors) and metachronous colorectal cancer metastases to liver (14 donors). Forty percent of the total sample count originates from macroscopically healthy cancer-neighboring tissue, while contribution from tumors is 12%, which adds to the uniqueness of our collection for cancer predisposition studies. Moreover, we developed two program packages, enabling registration of patients, clinical data and samples at the participating hospitals as well as the central system of sample/data management at coordinating center. The approach used by us may serve as a model for dispersed biobanking from multiple satellite hospitals. Our biobanking resource ought to stimulate research into genetic mechanisms underlying the development of common cancers. It will allow all available "-omics" approaches on DNA-, RNA-, protein- and tissue levels to be applied. The collected samples can be made available to other research groups.
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Affiliation(s)
| | - Kinga Drężek
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Horbacz
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Agata Wojdak
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Jakub Szymanowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Bioenit Jakub Szymanowski, Gdańsk, Poland
| | | | - Ulana Juhas
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Tomasz Nowikiewicz
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | | | | | - Maria Andreou
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Magdalena Wójcik
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ewa Śrutek
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Jacek Kowalski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Dariusz Bała
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Dorian Wiśniewski
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Karol Tkaczyński
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Krzysztof Kamecki
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Marta Drzewiecka
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Paweł Wroński
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Jerzy Siekiera
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Izabela Ratnicka
- Department of Plastic Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Jerzy Jankau
- Department of Plastic Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Wierzba
- Department of Internal Medicine, Connective Tissue Diseases and Geriatrics, Medical University of Gdańsk, Gdańsk, Poland
| | - Jarosław Skokowski
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
- Department of Medical Laboratory Diagnostics-Biobank, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Połom
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Mikołaj Przydacz
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Łukasz Bełch
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Piotr Chłosta
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Marcin Matuszewski
- Department and Clinic of Urology, Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Okoń
- Department of Pathomorphology, Jagiellonian University Medical College, Kraków, Poland
| | - Olga Rostkowska
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Andrzej Hellmann
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Sasim
- Clinic of Urology and Oncological Urology, Specialist Hospital of Kościerzyna, Kościerzyna, Poland
| | - Piotr Remiszewski
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Marek Sierżęga
- Department of General, Oncological, and Gastrointestinal Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Stanisław Hać
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Jarosław Kobiela
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Łukasz Kaska
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Jankowski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Diana Hodorowicz-Zaniewska
- Department of General, Oncological, and Gastrointestinal Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Janusz Jaszczyński
- Department of Urology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Wojciech Zegarski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Makarewicz
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Kościerzyna, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Joanna Szpor
- Department of Pathomorphology, Jagiellonian University Medical College, Kraków, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
| | - Jan P. Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
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35
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Zhang Q, Zhao L, Yang Y, Li S, Liu Y, Chen C. Mosaic loss of chromosome Y promotes leukemogenesis and clonal hematopoiesis. JCI Insight 2022; 7:153768. [PMID: 35132955 PMCID: PMC8855789 DOI: 10.1172/jci.insight.153768] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/23/2021] [Indexed: 12/21/2022] Open
Abstract
Mosaic loss of chromosome Y (mLOY) in blood cells is one of the most frequent chromosome alterations in adult males. It is strongly associated with clonal hematopoiesis, hematopoietic malignancies, and other hematopoietic and nonhematopoietic diseases. However, whether there is a causal relationship between mLOY and human diseases is unknown. Here, we generated mLOY in murine hematopoietic stem and progenitor cells (HSPCs) with CRISPR/Cas9 genome editing. We found that mLOY led to dramatically increased DNA damage in HSPCs. Interestingly, HSPCs with mLOY displayed significantly enhanced reconstitution capacity and gave rise to clonal hematopoiesis in vivo. mLOY, which is associated with AML1-ETO translocation and p53 defects in patients with acute myeloid leukemia (AML), promoted AML in mice. Mechanistically, loss of KDM5D, a chromosome Y-specific histone 3 lysine 4 demethylase in both humans and mice, partially recapitulated mLOY in DNA damage and leukemogenesis. Thus, our study validates mLOY as a functional driver for clonal hematopoiesis and leukemogenesis.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Chromosomes, Human, Y/genetics
- Clonal Hematopoiesis/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Gene Editing
- Hematopoietic Stem Cells/metabolism
- Hematopoietic Stem Cells/pathology
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Mice
- Mice, Transgenic
- Models, Animal
- Mutation
- Neoplasms, Experimental
- Translocation, Genetic
- Tumor Cells, Cultured
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36
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Rydzanicz M, Glinkowski W, Walczak A, Koppolu A, Kostrzewa G, Gasperowicz P, Pollak A, Stawiński P, Płoski R. Postzygotic mosaicism of a novel PTPN11 mutation in monozygotic twins discordant for metachondromatosis. Am J Med Genet A 2022; 188:1482-1487. [PMID: 35112464 DOI: 10.1002/ajmg.a.62670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 01/05/2023]
Abstract
Genetic mosaicism caused by postzygotic mutations is of a great interest due to its role in human disease. Monozygotic twins arising from a single zygote are considered as genetically identical, and any differences likely to be caused by postzygotic events. Thus, phenotypically discordant monozygotic twins offer a unique opportunity to study genotype-phenotype correlation. Here, we present a three-generation family starting from a pair of monozygotic twins discordant for metachondromatosis due to postzygotic p.(Gln175His) variant in the PTPN11 gene. Both phenotypically discordant monozygotic twins harbor p.(Gln175His), however significant differences in mosaic ratio is observed not only between twins, but also within different tissue types within one individual. Phenotypic manifestation of p.(Gln175His) in examined family clearly depends on allele variant fraction (VAF). Individuals harboring constitutional mutation (VAF 50%) present typical metachondromatosis. Milder phenotype is observed in twin harboring high-level mosaicism in the tissue of ectodermal origin (VAF 45%), but not in a blood (VAF 5%). Finally, her twin sister harboring low-level mosaicism in blood (VAF 2%) and nonblood (VAF 12%) tissues is phenotypically normal. Our results provide insights into biological role of mosaicism in disease and further support the usefulness of nonblood tissues as an optimal source of DNA for the identification of postzygotic mutations in phenotypically discordant monozygotic twins.
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Affiliation(s)
| | - Wojciech Glinkowski
- Center of Excellence "TeleOrto" for Telediagnostics and Treatment of Disorders and Injuries of the Locomotor System, Department of Medical Informatics and Telemedicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Koppolu
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Gasperowicz
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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Human Genetic Diseases Linked to the Absence of NEMO: An Obligatory Somatic Mosaic Disorder in Male. Int J Mol Sci 2022; 23:ijms23031179. [PMID: 35163099 PMCID: PMC8835834 DOI: 10.3390/ijms23031179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/22/2023] Open
Abstract
De novo somatic mutations are well documented in diseases such as neoplasia but are rarely reported in rare diseases. Hovewer, severe genetic diseases that are not compatible with embryonic development are caused exclusively by deleterious mutations that could only be found as mosaic and not as inherited mutations. We will review here the paradigmatic case of Incontinentia Pigmenti, a rare X-linked dominant disease caused by deficiency of the NEMO (also called IKKgamma) protein, which plays a pivotal role in tissue homeostasis. The loss-of-function mutations of NEMO are embryonically lethal in males while females survive because of unbalanced X-inactivation due to NEMO wild type (WT) expressing cells survival despite of NEMO mutant expressing cells. The few surviving IP males are obligatory mosaic mutants with the typical clinical presentation of IP in female. Indeed, the IP pathogenesis in the female and most likely also in the male somatic mosaics is based on the cellular effects of an impaired NEMO activity, but in the context of the interaction of genetically different cells in the affected tissue, which might underline the inflammatory status.
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Kirsch-Volders M, Fenech M. Aneuploidy, inflammation and diseases. Mutat Res 2022; 824:111777. [PMID: 35358789 DOI: 10.1016/j.mrfmmm.2022.111777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 05/23/2023]
Abstract
This review discusses how numerical aneuploidy may trigger inflammation in somatic cells and its consequences. Therefore we: i) summarized current knowledge on the cellular and molecular pathological effects of aneuploidy; ii) considered which of these aspects are able to trigger inflammation; iii) determined the genetic and environmental factors which may modulate the link between aneuploidy and inflammation; iv) explored the rôle of diet in prevention of aneuploidy and inflammation; v) examined whether aneuploidy and inflammation are causes and/or consequences of diseases; vi) identified the knowledge gaps and research needed to translate these observations into improved health care and disease prevention. The relationships between aneuploidy, inflammation and diseases are complex, because they depend on which chromosomes are involved, the proportion of cells affected and which organs are aneuploid in the case of mosaic aneuploidy. Therefore, a systemic approach is recommended to understand the emergence of aneuploidy-driven diseases and to take preventive measures to protect individuals from exposure to aneugenic conditions.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Michael Fenech
- Genome Health Foundation, North Brighton, SA 5048, Australia; Clinical and Health Sciences, University of South Australia, SA 5000, Australia.
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Cobo I, Tanaka T, Glass CK, Yeang C. Clonal hematopoiesis driven by DNMT3A and TET2 mutations: role in monocyte and macrophage biology and atherosclerotic cardiovascular disease. Curr Opin Hematol 2022; 29:1-7. [PMID: 34654019 PMCID: PMC8639635 DOI: 10.1097/moh.0000000000000688] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Clonal hematopoiesis of indeterminate potential (CHIP), defined by the presence of somatic mutations in hematopoietic cells, is associated with advanced age and increased mortality due to cardiovascular disease. Gene mutations in DNMT3A and TET2 are the most frequently identified variants among patients with CHIP and provide selective advantage that spurs clonal expansion and myeloid skewing. Although DNMT3A and TET2 appear to have opposing enzymatic influence on DNA methylation, mounting data has characterized convergent inflammatory pathways, providing insights to how CHIP may mediate atherosclerotic cardiovascular disease (ASCVD). RECENT FINDINGS We review a multitude of studies that characterize aberrant inflammatory signaling as result of DNMT3A and TET2 deficiency in monocytes and macrophages, immune cells with prominent roles in atherosclerosis. Although specific DNA methylation signatures associated with these known epigenetic regulators have been identified, many studies have also characterized diverse modulatory functions of DNTM3A and TET2 that urge cell and context-specific experimental studies to further define how DNMT3A and TET2 may nonenzymatically activate inflammatory pathways with clinically meaningful consequences. SUMMARY CHIP, common in elderly individuals, provides an opportunity understand and potentially modify age-related chronic inflammatory ASCVD risk.
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Affiliation(s)
- Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California San Diego
| | - Tiffany Tanaka
- University of California San Diego, Moores Cancer Center
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego
| | - Calvin Yeang
- Sulpizio Cardiovascular Center, Division of Cardiology, University of California San Diego, La Jolla, California, USA
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40
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Guo L, Zhong MB, Zhang L, Zhang B, Cai D. Sex Differences in Alzheimer's Disease: Insights From the Multiomics Landscape. Biol Psychiatry 2022; 91:61-71. [PMID: 33896621 PMCID: PMC8996342 DOI: 10.1016/j.biopsych.2021.02.968] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) has complex etiologies, and the impact of sex on AD varies over the course of disease development. The literature provides some evidence of sex-specific contributions to AD. However, molecular mechanisms of sex-biased differences in AD remain elusive. Multiomics data in tandem with systems biology approaches offer a new avenue to dissect sex-stratified molecular mechanisms of AD and to develop sex-specific diagnostic and therapeutic strategies for AD. Single-cell transcriptomic datasets and cell deconvolution of bulk tissue transcriptomic data provide additional insights into brain cell type-specific impact on sex-biased differences in AD. In this review, we summarize the impact of sex chromosomes and sex hormones on AD, the impact of sex-biased differences during AD development, and the interplay between sex and a major AD genetic risk factor, the APOE ε4 genotype, through the multiomics landscape. Several sex-biased molecular pathways such as neuroinflammation and bioenergetic metabolism have been identified. The importance of sex chromosome and sex hormones, as well as the associated pathways in AD pathogenesis, is further strengthened by findings from omics studies. Future research efforts should integrate the multiomics data from different brain regions and different cell types using systems biology approaches, and leverage the knowledge into a holistic examination of sex differences in AD. Advances in systems biology technologies and increasingly available large-scale multiomics datasets will facilitate future studies dissecting such complex signaling mechanisms to better understand AD pathogenesis in both sexes, with the ultimate goals of developing efficacious sex- and APOE-stratified preventive and therapeutic interventions for AD.
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Affiliation(s)
- Lei Guo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Margaret B Zhong
- Department of Neuroscience, Barnard College of Columbia University, New York, New York
| | - Larry Zhang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York; Research and Development Service, James J. Peters VA Medical Center, Bronx, New York
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Dongming Cai
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York; Alzheimer Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, New York; Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York; Research and Development Service, James J. Peters VA Medical Center, Bronx, New York.
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41
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Yang H, Zhu G, Zhou W, Luo M, Zhang Y, Zhang Y, Shu C, Zhou Z. A systematic study of mosaicism in heritable thoracic aortic aneurysm and dissection. Genomics 2021; 114:196-201. [PMID: 34921932 DOI: 10.1016/j.ygeno.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/05/2021] [Accepted: 12/13/2021] [Indexed: 11/04/2022]
Abstract
Mosaicisms are often overlooked in routine molecular diagnosis. Although not common, they are of great significance for accurate diagnosis and genetic counseling. In this study, we systematically evaluated the frequency of mosaicisms in both asymptomatic parents and affected patients with thoracic aortic aneurysm and dissection (TAAD). Next-generation sequencing (NGS) data from 1085 patients was reanalyzed with a more lenient allele frequency to detect potential mosaic variants. In addition, parental mosaicisms were investigated in 80 TAAD families. Finally, a total of six mosaic variants were detected in our cohort. Three of them were identified in symptomatic patients and three were in asymptomatic parents. Notably, a low-level mosaic variant in TGFB2 was detected combined with a causative FBN1 variant in patient AD2001, which might partially explain the clinical heterogeneity in his family. Our study hinted that it is necessary and feasible to implement mosaicism analysis in routine molecular diagnosis.
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Affiliation(s)
- Hang Yang
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Guoyan Zhu
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Weizhen Zhou
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Mingyao Luo
- State Key Laboratory of Cardiovascular Disease, Center of Vascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Yujing Zhang
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Yinhui Zhang
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Chang Shu
- State Key Laboratory of Cardiovascular Disease, Center of Vascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Zhou Zhou
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China.
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Riaz M, Mattisson J, Polekhina G, Bakshi A, Halvardson J, Danielsson M, Ameur A, McNeil J, Forsberg LA, Lacaze P. A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells. Cell Biosci 2021; 11:205. [PMID: 34895331 PMCID: PMC8667399 DOI: 10.1186/s13578-021-00716-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background Mosaic loss of Y chromosome (LOY) is the most common somatic change that occurs in circulating white blood cells of older men. LOY in leukocytes is associated with increased risk for all-cause mortality and a range of common disease such as hematological and non-hematological cancer, Alzheimer’s disease, and cardiovascular events. Recent genome-wide association studies identified up to 156 germline variants associated with risk of LOY. The objective of this study was to use these variants to calculate a novel polygenic risk score (PRS) for LOY, and to assess the predictive performance of this score in a large independent population of older men. Results We calculated a PRS for LOY in 5131 men aged 70 years and older. Levels of LOY were estimated using microarrays and validated by whole genome sequencing. After adjusting for covariates, the PRS was a significant predictor of LOY (odds ratio [OR] = 1.74 per standard deviation of the PRS, 95% confidence intervals [CI] 1.62–1.86, p < 0.001). Men in the highest quintile of the PRS distribution had > fivefold higher risk of LOY than the lowest (OR = 5.05, 95% CI 4.05–6.32, p < 0.001). Adding the PRS to a LOY prediction model comprised of age, smoking and alcohol consumption significantly improved prediction (AUC = 0.628 [CI 0.61–0.64] to 0.695 [CI 0.67–0.71], p < 0.001). Conclusions Our results suggest that a PRS for LOY could become a useful tool for risk prediction and targeted intervention for common disease in men. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00716-z.
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Affiliation(s)
- Moeen Riaz
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Galina Polekhina
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Andrew Bakshi
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - John McNeil
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,The Beijer Laboratory, Uppsala University, Uppsala, Sweden.
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia.
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Liu B, Chen M, Yang Y, Huang Y, Qian Y, Dong M. Identification of of a PAX2 mutation from maternal mosaicism causes recurrent renal disorder in siblings. Clin Chim Acta 2021; 525:23-28. [PMID: 34906559 DOI: 10.1016/j.cca.2021.12.007] [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: 11/18/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND PAX2-related disorder is an autosomal dominant disorder characterized by renal and eye abnormalities. Some patients may present with isolated renal abnormalities without obvious ocular abnormalities. It is associated with mutations in paired box gene 2 (PAX2), which is one of the families of paired box transcription factor genes. Studies on mosaicism have been limited in PAX2-related disorder, as only three families with mosaic PAX2 mutations have been reported in the literature. METHODS The proband with multicystic dysplastic kidneys from a Chinese family was recruited in our study. Detailed clinical symptoms were enquired. Trio-based whole exome sequencing (WES), SNP array, sanger sequencing and droplet digital PCR (ddPCR) were used to characterize etiology in the proband. Prenatal diagnosis was performed through amniocentesis and prenatal ultrasound when the proband's mother was further pregnant at 20 weeks. RESULTS A heterozygous missense mutation in PAX2 (c.194 T > C) was identified in the proband. His asymptomatic mother has the same mutation with somatic mosaicism ratio of 22%. The mutation was also detected in the fetus. Prenatal ultrasound showed that bilateral hyperechogenic kidneys with decrease of renal size. CONCLUSIONS This is the first report on PAX2 mosaicism in a Chinese family. Identifying PAX2 mosaicism provides more evidence for estimating recurrence risk. Our findings have important implications on genetic counseling for patients with PAX2-related disorder and provide an effective diagnostic technology for mosaicism.
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Affiliation(s)
- Bei Liu
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Mengjia Chen
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yanmei Yang
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yingzhi Huang
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Yeqing Qian
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China
| | - Minyue Dong
- Women's Hospital School of Medicine Zhejiang University, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China; Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Hangzhou, Zhejiang 310006, PR China.
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Martín-Campos JM. Genetic Determinants of Plasma Low-Density Lipoprotein Cholesterol Levels: Monogenicity, Polygenicity, and "Missing" Heritability. Biomedicines 2021; 9:biomedicines9111728. [PMID: 34829957 PMCID: PMC8615680 DOI: 10.3390/biomedicines9111728] [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: 10/09/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Changes in plasma low-density lipoprotein cholesterol (LDL-c) levels relate to a high risk of developing some common and complex diseases. LDL-c, as a quantitative trait, is multifactorial and depends on both genetic and environmental factors. In the pregenomic age, targeted genes were used to detect genetic factors in both hyper- and hypolipidemias, but this approach only explained extreme cases in the population distribution. Subsequently, the genetic basis of the less severe and most common dyslipidemias remained unknown. In the genomic age, performing whole-exome sequencing in families with extreme plasma LDL-c values identified some new candidate genes, but it is unlikely that such genes can explain the majority of inexplicable cases. Genome-wide association studies (GWASs) have identified several single-nucleotide variants (SNVs) associated with plasma LDL-c, introducing the idea of a polygenic origin. Polygenic risk scores (PRSs), including LDL-c-raising alleles, were developed to measure the contribution of the accumulation of small-effect variants to plasma LDL-c. This paper discusses other possibilities for unexplained dyslipidemias associated with LDL-c, such as mosaicism, maternal effect, and induced epigenetic changes. Future studies should consider gene-gene and gene-environment interactions and the development of integrated information about disease-driving networks, including phenotypes, genotypes, transcription, proteins, metabolites, and epigenetics.
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Affiliation(s)
- Jesús Maria Martín-Campos
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau (IR-HSCSP)-Biomedical Research Institute Sant Pau (IIB-Sant Pau), C/Sant Quintí 77-79, 08041 Barcelona, Spain
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Lähnemann D, Köster J, Fischer U, Borkhardt A, McHardy AC, Schönhuth A. Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo. Nat Commun 2021; 12:6744. [PMID: 34795237 PMCID: PMC8602313 DOI: 10.1038/s41467-021-26938-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/22/2021] [Indexed: 01/14/2023] Open
Abstract
Accurate single cell mutational profiles can reveal genomic cell-to-cell heterogeneity. However, sequencing libraries suitable for genotyping require whole genome amplification, which introduces allelic bias and copy errors. The resulting data violates assumptions of variant callers developed for bulk sequencing. Thus, only dedicated models accounting for amplification bias and errors can provide accurate calls. We present ProSolo for calling single nucleotide variants from multiple displacement amplified (MDA) single cell DNA sequencing data. ProSolo probabilistically models a single cell jointly with a bulk sequencing sample and integrates all relevant MDA biases in a site-specific and scalable-because computationally efficient-manner. This achieves a higher accuracy in calling and genotyping single nucleotide variants in single cells in comparison to state-of-the-art tools and supports imputation of insufficiently covered genotypes, when downstream tools cannot handle missing data. Moreover, ProSolo implements the first approach to control the false discovery rate reliably and flexibly. ProSolo is implemented in an extendable framework, with code and usage at: https://github.com/prosolo/prosolo.
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Affiliation(s)
- David Lähnemann
- grid.7490.a0000 0001 2238 295XDepartment for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany ,grid.6738.a0000 0001 1090 0254Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany ,grid.411327.20000 0001 2176 9917Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany ,grid.14778.3d0000 0000 8922 7789Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany ,grid.5718.b0000 0001 2187 5445Algorithms for Reproducible Bioinformatics, Institute of Human Genetics, University of Duisburg-Essen, 45147 Essen, Germany
| | - Johannes Köster
- grid.5718.b0000 0001 2187 5445Algorithms for Reproducible Bioinformatics, Institute of Human Genetics, University of Duisburg-Essen, 45147 Essen, Germany ,grid.6054.70000 0004 0369 4183Genome Data Science, Life Sciences Group, Centrum Wiskunde & Informatica, 1098 XG Amsterdam, The Netherlands
| | - Ute Fischer
- grid.14778.3d0000 0000 8922 7789Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Arndt Borkhardt
- grid.14778.3d0000 0000 8922 7789Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Alice C. McHardy
- grid.7490.a0000 0001 2238 295XDepartment for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany ,grid.6738.a0000 0001 1090 0254Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany ,grid.411327.20000 0001 2176 9917Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Alexander Schönhuth
- Genome Data Science, Life Sciences Group, Centrum Wiskunde & Informatica, 1098 XG, Amsterdam, The Netherlands. .,Genome Data Science, Faculty of Technology, Bielefeld University, 33615, Bielefeld, Germany.
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Johansson M, Pedersen A, Cole JW, Lagging C, Lindgren A, Maguire JM, Rost NS, Söderholm M, Worrall BB, Stanne TM, Jern C. Genetic Predisposition to Mosaic Chromosomal Loss Is Associated With Functional Outcome After Ischemic Stroke. NEUROLOGY-GENETICS 2021; 7:e634. [PMID: 34786478 PMCID: PMC8589264 DOI: 10.1212/nxg.0000000000000634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/15/2021] [Indexed: 11/27/2022]
Abstract
Background and Objectives To test the hypothesis that a predisposition to acquired genetic alterations is associated with ischemic stroke outcome by investigating the association between a polygenic risk score (PRS) for mosaic loss of chromosome Y (mLOY) and outcome in a large international data set. Methods We used data from the genome-wide association study performed within the Genetics of Ischemic Stroke Functional Outcome network, which included 6,165 patients (3,497 men and 2,668 women) with acute ischemic stroke of mainly European ancestry. We assessed a weighted PRS for mLOY and examined possible associations with the modified Rankin Scale (mRS) score 3 months poststroke in logistic regression models. We investigated the whole study sample as well as men and women separately. Results Increasing PRS for mLOY was associated with poor functional outcome (mRS score >2) with an odds ratio (OR) of 1.11 (95% confidence interval [CI] 1.03–1.19) per 1 SD increase in the PRS after adjustment for age, sex, ancestry, stroke severity (NIH Stroke Scale), smoking, and diabetes mellitus. In sex-stratified analyses, we found a statistically significant association in women (adjusted OR 1.20, 95% CI 1.08–1.33). In men, the association was in the same direction (adjusted OR 1.04, 95% CI 0.95–1.14), and we observed no significant genotype-sex interaction. Discussion In this exploratory study, we found associations between genetic variants predisposing to mLOY and stroke outcome. The significant association in women suggests underlying mechanisms related to genomic instability that operate in both sexes. These findings need replication and mechanistic exploration.
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Affiliation(s)
- Malin Johansson
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Annie Pedersen
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - John W Cole
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Cecilia Lagging
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Arne Lindgren
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Jane M Maguire
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Natalia S Rost
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Martin Söderholm
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Bradford B Worrall
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Tara M Stanne
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Christina Jern
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
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47
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Lebedev IN, Zhigalina DI. From contemplation to classification of chromosomal mosaicism in human preimplantation embryos. J Assist Reprod Genet 2021; 38:2833-2848. [PMID: 34518954 PMCID: PMC8609036 DOI: 10.1007/s10815-021-02304-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022] Open
Abstract
Chromosomal mosaicism is a hallmark of early human embryo development. The last decade yielded an enormous amount of information about diversity and prevalence of mosaicism in preimplantation embryos due to progress in preimplantation genetic testing of aneuploidies (PGT-A) based exclusively on molecular karyotyping of trophectoderm biopsy. However, the inner cell mass karyotype is still missing for mosaic embryos affecting the success rate of assisted reproductive medicine. Here, a classification model of chromosomal mosaicism is proposed based on the analysis of the primary zygote karyotype, the timing and types of primary and secondary chromosome segregation errors, and the distribution of mosaic cell clones between different embryonic and extraembryonic compartments of the blastocyst. Five basic principles for mosaicism analysis are introduced, namely, the estimation of the primary zygote karyotype, the investigation of additional sample point, the requirement of the second time point analysis, the delineating of reciprocity of chromosome segregation, and comprehensive chromosome screening at the single-cell level. The suggested model allows the prediction of the inner cell mass karyotype of the blastocyst and its developmental potential based on information from trophectoderm biopsy and non-invasive PGT-A using blastocoele fluid sample or spent culture medium as additional sample and time points for analysis and considering the reciprocity as a basic process in chromosome segregation errors between daughter cells in postzygotic cell divisions.
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Affiliation(s)
- Igor N. Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050 Russia
| | - Daria I. Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050 Russia
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48
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Swiatczak B. Struggle within: evolution and ecology of somatic cell populations. Cell Mol Life Sci 2021; 78:6797-6806. [PMID: 34477897 PMCID: PMC11073125 DOI: 10.1007/s00018-021-03931-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/31/2021] [Accepted: 08/25/2021] [Indexed: 12/19/2022]
Abstract
The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable multicellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts at the cellular level. On the other hand, the example of clonal selection of lymphocytes indicates that certain forms of somatic mutation and selection are concordant with the organism-level fitness. Recent DNA sequencing and tissue physiology studies suggest that in addition to adaptive immune cells also neurons, epithelial cells, epidermal cells, hematopoietic stem cells and functional cells in solid bodily organs are subject to evolutionary forces during the lifetime of an organism. Here we refer to these recent studies and suggest that the expanding list of somatically evolving cells modifies idealized views of biological individuals as radically different from collectives.
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Affiliation(s)
- Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, 96 Jinzhai Rd., Hefei, 230026, China.
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49
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Hong Y, Zhang D, Zhou X, Chen A, Abliz A, Bai J, Wang L, Hu Q, Gong K, Guan X, Liu M, Zheng X, Lai S, Qu H, Zhao F, Hao S, Wu Z, Cai H, Hu S, Ma Y, Zhang J, Ke Y, Wang QF, Chen W, Zeng C. Common Postzygotic Mutational Signatures in Healthy Adult Tissues Related to Embryonic Hypoxia. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 20:177-191. [PMID: 34624550 PMCID: PMC9510933 DOI: 10.1016/j.gpb.2021.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 12/04/2022]
Abstract
Postzygotic mutations are acquired in normal tissues throughout an individual’s lifetime and hold clues for identifying mutagenic factors. Here, we investigated postzygotic mutation spectra of healthy individuals using optimized ultra-deep exome sequencing of the time-series samples from the same volunteer as well as the samples from different individuals. In blood, sperm, and muscle cells, we resolved three common types of mutational signatures. Signatures A and B represent clock-like mutational processes, and the polymorphisms of epigenetic regulation genes influence the proportion of signature B in mutation profiles. Notably, signature C, characterized by C>T transitions at GpCpN sites, tends to be a feature of diverse normal tissues. Mutations of this type are likely to occur early during embryonic development, supported by their relatively high allelic frequencies, presence in multiple tissues, and decrease in occurrence with age. Almost none of the public datasets for tumors feature this signature, except for 19.6% of samples of clear cell renal cell carcinoma with increased activation of the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Moreover, the accumulation of signature C in the mutation profile was accelerated in a human embryonic stem cell line with drug-induced activation of HIF-1α. Thus, embryonic hypoxia may explain this novel signature across multiple normal tissues. Our study suggests that hypoxic condition in an early stage of embryonic development is a crucial factor inducing C>T transitions at GpCpN sites; and individuals’ genetic background may also influence their postzygotic mutation profiles.
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Affiliation(s)
- Yaqiang Hong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dake Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xiangtian Zhou
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou 325035, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou 325035, China
| | - Aili Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Amir Abliz
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jian Bai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Liang Wang
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Qingtao Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Kenan Gong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Xiaonan Guan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Mengfei Liu
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xinchang Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujuan Lai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Fuxin Zhao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou 325035, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou 325035, China
| | - Shuang Hao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhen Wu
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Hong Cai
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Shaoyan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou 215025, China
| | - Yue Ma
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Junting Zhang
- Skull Base and Brainstem Tumor Division, Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China; China National Clinical Research Center for Neurological Diseases, Beijing 100050, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (MOE), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Qian-Fei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Collaborative Innovation Center for Genetics and Development, Shanghai 200438, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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50
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Aging and Cancer: The Waning of Community Bonds. Cells 2021; 10:cells10092269. [PMID: 34571918 PMCID: PMC8468626 DOI: 10.3390/cells10092269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer often arises in the context of an altered tissue landscape. We argue that a major contribution of aging towards increasing the risk of neoplastic disease is conveyed through effects on the microenvironment. It is now firmly established that aged tissues are prone to develop clones of altered cells, most of which are compatible with a normal histological appearance. Such increased clonogenic potential results in part from a generalized decrease in proliferative fitness, favoring the emergence of more competitive variant clones. However, specific cellular genotypes can emerge with reduced cooperative and integrative capacity, leading to disruption of tissue architecture and paving the way towards progression to overt neoplastic phenotypes.
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