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Gao Y, Yang X, Chen H, Tan X, Yang Z, Deng L, Wang B, Kong S, Li S, Cui Y, Lei C, Wang Y, Pan Y, Ma S, Sun H, Zhao X, Shi Y, Yang Z, Wu D, Wu S, Zhao X, Shi B, Jin L, Hu Z, Lu Y, Chu J, Ye K, Xu S. A pangenome reference of 36 Chinese populations. Nature 2023; 619:112-121. [PMID: 37316654 PMCID: PMC10322713 DOI: 10.1038/s41586-023-06173-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/05/2023] [Indexed: 06/16/2023]
Abstract
Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form, but populations of Asian ancestry are underrepresented. Here we present data from the first phase of the Chinese Pangenome Consortium, including a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With an average 30.65× high-fidelity long-read sequence coverage, an average contiguity N50 of more than 35.63 megabases and an average total size of 3.01 gigabases, the CPC core assemblies add 189 million base pairs of euchromatic polymorphic sequences and 1,367 protein-coding gene duplications to GRCh38. We identified 15.9 million small variants and 78,072 structural variants, of which 5.9 million small variants and 34,223 structural variants were not reported in a recently released pangenome reference1. The Chinese Pangenome Consortium data demonstrate a remarkable increase in the discovery of novel and missing sequences when individuals are included from underrepresented minority ethnic groups. The missing reference sequences were enriched with archaic-derived alleles and genes that confer essential functions related to keratinization, response to ultraviolet radiation, DNA repair, immunological responses and lifespan, implying great potential for shedding new light on human evolution and recovering missing heritability in complex disease mapping.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinjiang Tan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoqing Yang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, China
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Baonan Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Shuang Kong
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Songyang Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Yuhang Cui
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Chang Lei
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yimin Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sen Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hao Sun
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, China
| | - Xiaohan Zhao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Yingbing Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyi Yang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, International Joint Center of Genomics of Jiangsu Province School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xingming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Ministry of Education Key (MOE) Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science Fudan University, Shanghai, China
| | - Binyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
| | - Jiayou Chu
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, China.
| | - Kai Ye
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, International Joint Center of Genomics of Jiangsu Province School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Carron J, Della Coletta R, Lourenço GJ. Pseudogene Transcripts in Head and Neck Cancer: Literature Review and In Silico Analysis. Genes (Basel) 2021; 12:genes12081254. [PMID: 34440428 PMCID: PMC8391979 DOI: 10.3390/genes12081254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/25/2022] Open
Abstract
Once considered nonfunctional, pseudogene transcripts are now known to provide valuable information for cancer susceptibility, including head and neck cancer (HNC), a serious health problem worldwide, with about 50% unimproved overall survival over the last decades. The present review focuses on the role of pseudogene transcripts involved in HNC risk and prognosis. We combined current literature and in silico analyses from The Cancer Genome Atlas (TCGA) database to identify the most deregulated pseudogene transcripts in HNC and their genetic variations. We then built a co-expression network and performed gene ontology enrichment analysis to better understand the pseudogenes’ interactions and pathways in HNC. In the literature, few pseudogenes have been studied in HNC. Our in silico analysis identified 370 pseudogene transcripts associated with HNC, where SPATA31D5P, HERC2P3, SPATA31C2, MAGEB6P1, SLC25A51P1, BAGE2, DNM1P47, SPATA31C1, ZNF733P and OR2W5 were found to be the most deregulated and presented several genetic alterations. NBPF25P, HSP90AB2P, ZNF658B and DPY19L2P3 pseudogenes were predicted to interact with 12 genes known to participate in HNC, DNM1P47 was predicted to interact with the TP53 gene, and HLA-H pseudogene was predicted to interact with HLA-A and HLA-B genes. The identified pseudogenes were associated with cancer biology pathways involving cell communication, response to stress, cell death, regulation of the immune system, regulation of gene expression, and Wnt signaling. Finally, we assessed the prognostic values of the pseudogenes with the Kaplan–Meier Plotter database, and found that expression of SPATA31D5P, SPATA31C2, BAGE2, SPATA31C1, ZNF733P and OR2W5 pseudogenes were associated with patients’ survival. Due to pseudogene transcripts’ potential for cancer diagnosis, progression, and as therapeutic targets, our study can guide new research to HNC understanding and development of new target therapies.
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Affiliation(s)
- Juliana Carron
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, São Paulo, Brazil;
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, São Paulo, Brazil;
- Correspondence: ; Tel.: +55-19-3521-9120
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Morris BJ, Willcox BJ, Donlon TA. Genetic and epigenetic regulation of human aging and longevity. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1718-1744. [PMID: 31109447 PMCID: PMC7295568 DOI: 10.1016/j.bbadis.2018.08.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/02/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023]
Abstract
Here we summarize the latest data on genetic and epigenetic contributions to human aging and longevity. Whereas environmental and lifestyle factors are important at younger ages, the contribution of genetics appears more important in reaching extreme old age. Genome-wide studies have implicated ~57 gene loci in lifespan. Epigenomic changes during aging profoundly affect cellular function and stress resistance. Dysregulation of transcriptional and chromatin networks is likely a crucial component of aging. Large-scale bioinformatic analyses have revealed involvement of numerous interaction networks. As the young well-differentiated cell replicates into eventual senescence there is drift in the highly regulated chromatin marks towards an entropic middle-ground between repressed and active, such that genes that were previously inactive "leak". There is a breakdown in chromatin connectivity such that topologically associated domains and their insulators weaken, and well-defined blocks of constitutive heterochromatin give way to generalized, senescence-associated heterochromatin, foci. Together, these phenomena contribute to aging.
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Affiliation(s)
- Brian J Morris
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, University of Sydney, New South Wales 2006, Australia; Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Kuakini Medical Center Campus, Honolulu, HI 96813, United States.
| | - Bradley J Willcox
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Kuakini Medical Center Campus, Honolulu, HI 96813, United States.
| | - Timothy A Donlon
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI 96817, United States; Departments of Cell & Molecular Biology and Pathology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, United States.
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