1
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Fisher SA, Patrick K, Hoang T, Marcq E, Behrouzfar K, Young S, Miller TJ, Robinson BWS, Bueno R, Nowak AK, Lesterhuis WJ, Morahan G, Lake RA. The MexTAg collaborative cross: host genetics affects asbestos related disease latency, but has little influence once tumours develop. FRONTIERS IN TOXICOLOGY 2024; 6:1373003. [PMID: 38694815 PMCID: PMC11061428 DOI: 10.3389/ftox.2024.1373003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/02/2024] [Indexed: 05/04/2024] Open
Abstract
Objectives: This study combines two innovative mouse models in a major gene discovery project to assess the influence of host genetics on asbestos related disease (ARD). Conventional genetics studies provided evidence that some susceptibility to mesothelioma is genetic. However, the identification of host modifier genes, the roles they may play, and whether they contribute to disease susceptibility remain unknown. Here we report a study designed to rapidly identify genes associated with mesothelioma susceptibility by combining the Collaborative Cross (CC) resource with the well-characterised MexTAg mesothelioma mouse model. Methods: The CC is a powerful mouse resource that harnesses over 90% of common genetic variation in the mouse species, allowing rapid identification of genes mediating complex traits. MexTAg mice rapidly, uniformly, and predictably develop mesothelioma, but only after asbestos exposure. To assess the influence of host genetics on ARD, we crossed 72 genetically distinct CC mouse strains with MexTAg mice and exposed the resulting CC-MexTAg (CCMT) progeny to asbestos and monitored them for traits including overall survival, the time to ARD onset (latency), the time between ARD onset and euthanasia (disease progression) and ascites volume. We identified phenotype-specific modifier genes associated with these traits and we validated the role of human orthologues in asbestos-induced carcinogenesis using human mesothelioma datasets. Results: We generated 72 genetically distinct CCMT strains and exposed their progeny (2,562 in total) to asbestos. Reflecting the genetic diversity of the CC, there was considerable variation in overall survival and disease latency. Surprisingly, however, there was no variation in disease progression, demonstrating that host genetic factors do have a significant influence during disease latency but have a limited role once disease is established. Quantitative trait loci (QTL) affecting ARD survival/latency were identified on chromosomes 6, 12 and X. Of the 97-protein coding candidate modifier genes that spanned these QTL, eight genes (CPED1, ORS1, NDUFA1, HS1BP3, IL13RA1, LSM8, TES and TSPAN12) were found to significantly affect outcome in both CCMT and human mesothelioma datasets. Conclusion: Host genetic factors affect susceptibility to development of asbestos associated disease. However, following mesothelioma establishment, genetic variation in molecular or immunological mechanisms did not affect disease progression. Identification of multiple candidate modifier genes and their human homologues with known associations in other advanced stage or metastatic cancers highlights the complexity of ARD and may provide a pathway to identify novel therapeutic targets.
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Affiliation(s)
- Scott A. Fisher
- National Centre for Asbestos Related Diseases (NCARD), Perth, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Perth, WA, Australia
| | - Kimberley Patrick
- National Centre for Asbestos Related Diseases (NCARD), Perth, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Perth, WA, Australia
| | - Tracy Hoang
- National Centre for Asbestos Related Diseases (NCARD), Perth, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Perth, WA, Australia
| | - Elly Marcq
- Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
- Lab of Dendritic Cell Biology and Cancer Immunotherapy, VIB Center for Inflammation Research, Brussels, Belgium
- Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kiarash Behrouzfar
- National Centre for Asbestos Related Diseases (NCARD), Perth, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Perth, WA, Australia
| | - Sylvia Young
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Timothy J. Miller
- Medical School, The University of Western Australia, Perth, WA, Australia
| | - Bruce W. S. Robinson
- National Centre for Asbestos Related Diseases (NCARD), Perth, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Perth, WA, Australia
- Medical School, The University of Western Australia, Perth, WA, Australia
| | - Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Anna K. Nowak
- National Centre for Asbestos Related Diseases (NCARD), Perth, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Perth, WA, Australia
- Medical School, The University of Western Australia, Perth, WA, Australia
| | | | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Richard A. Lake
- National Centre for Asbestos Related Diseases (NCARD), Perth, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Perth, WA, Australia
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2
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Erenpreisa J, Vainshelbaum NM, Lazovska M, Karklins R, Salmina K, Zayakin P, Rumnieks F, Inashkina I, Pjanova D, Erenpreiss J. The Price of Human Evolution: Cancer-Testis Antigens, the Decline in Male Fertility and the Increase in Cancer. Int J Mol Sci 2023; 24:11660. [PMID: 37511419 PMCID: PMC10380301 DOI: 10.3390/ijms241411660] [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: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The increasing frequency of general and particularly male cancer coupled with the reduction in male fertility seen worldwide motivated us to seek a potential evolutionary link between these two phenomena, concerning the reproductive transcriptional modules observed in cancer and the expression of cancer-testis antigens (CTA). The phylostratigraphy analysis of the human genome allowed us to link the early evolutionary origin of cancer via the reproductive life cycles of the unicellulars and early multicellulars, potentially driving soma-germ transition, female meiosis, and the parthenogenesis of polyploid giant cancer cells (PGCCs), with the expansion of the CTA multi-families, very late during their evolution. CTA adaptation was aided by retrovirus domestication in the unstable genomes of mammals, for protecting male fertility in stress conditions, particularly that of humans, as compensation for the energy consumption of a large complex brain which also exploited retrotransposition. We found that the early and late evolutionary branches of human cancer are united by the immunity-proto-placental network, which evolved in the Cambrian and shares stress regulators with the finely-tuned sex determination system. We further propose that social stress and endocrine disruption caused by environmental pollution with organic materials, which alter sex determination in male foetuses and further spermatogenesis in adults, bias the development of PGCC-parthenogenetic cancer by default.
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Affiliation(s)
| | | | - Marija Lazovska
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Roberts Karklins
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Kristine Salmina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Dace Pjanova
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Juris Erenpreiss
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
- Clinic iVF-Riga, Zala 1, LV-1010 Riga, Latvia
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3
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Li C, Feng Y, Fu Z, Deng J, Gu Y, Wang H, Wu X, Huang Z, Zhu Y, Liu Z, Huang M, Wang T, Hu S, Yao B, Zeng Y, Zhou CJ, Brown SDM, Liu Y, Vidal-Puig A, Dong Y, Xu Y. Human-specific gene CT47 blocks PRMT5 degradation to lead to meiosis arrest. Cell Death Discov 2022; 8:345. [PMID: 35918318 PMCID: PMC9345867 DOI: 10.1038/s41420-022-01139-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Exploring the functions of human-specific genes (HSGs) is challenging due to the lack of a tractable genetic model system. Testosterone is essential for maintaining human spermatogenesis and fertility, but the underlying mechanism is unclear. Here, we identified Cancer/Testis Antigen gene family 47 (CT47) as an essential regulator of human-specific spermatogenesis by stabilizing arginine methyltransferase 5 (PRMT5). A humanized mouse model revealed that CT47 functions to arrest spermatogenesis by interacting with and regulating CT47/PRMT5 accumulation in the nucleus during the leptotene/zygotene-to-pachytene transition of meiosis. We demonstrate that testosterone induces nuclear depletion of CT47/PRMT5 and rescues leptotene-arrested spermatocyte progression in humanized testes. Loss of CT47 in human embryonic stem cells (hESCs) by CRISPR/Cas9 led to an increase in haploid cells but blocked the testosterone-induced increase in haploid cells when hESCs were differentiated into haploid spermatogenic cells. Moreover, CT47 levels were decreased in nonobstructive azoospermia. Together, these results established CT47 as a crucial regulator of human spermatogenesis by preventing meiosis initiation before the testosterone surge.
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Affiliation(s)
- Chao Li
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Yuming Feng
- Department of Reproductive Medical Center, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Zhenxin Fu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Junjie Deng
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Yue Gu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Hanben Wang
- State Key Laboratory of Reproductive Medicine (SKLRM), Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine (SKLRM), Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Zhengyun Huang
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Yichen Zhu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhiwei Liu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Moli Huang
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tao Wang
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, Suzhou, 215000, China
| | - Bing Yao
- Department of Reproductive Medical Center, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Yizhun Zeng
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA, USA
| | - Steve D M Brown
- Medical Research Council (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, UK
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, MDU MRC, Cambridge, UK
| | - Yingying Dong
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical School of Soochow University, Suzhou, Jiangsu, 215123, China.
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4
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Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O'Neill RJ, Phillippy AM, Miga KH, Timp W. Epigenetic patterns in a complete human genome. Science 2022; 376:eabj5089. [PMID: 35357915 PMCID: PMC9170183 DOI: 10.1126/science.abj5089] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.
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Affiliation(s)
- Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | - Michael E G Sauria
- Department of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Xavi Guitart
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Paul W Hook
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Savannah J Hoyt
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Roham Razaghi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nicolas Altemose
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Gina V Caldas
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Michael C Schatz
- Department of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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5
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Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome Biol 2018; 19:208. [PMID: 30486838 PMCID: PMC6260756 DOI: 10.1186/s13059-018-1590-2] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 11/16/2018] [Indexed: 01/06/2023] Open
Abstract
We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains 42,611 genes, of which 20,352 are potentially protein-coding and 22,259 are noncoding, and a total of 323,258 transcripts. These include 224 novel protein-coding genes and 116,156 novel transcripts. We detected over 30 million additional transcripts at more than 650,000 genomic loci, nearly all of which are likely nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells. The CHESS database is available at http://ccb.jhu.edu/chess .
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Affiliation(s)
- Mihaela Pertea
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Alaina Shumate
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Geo Pertea
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ales Varabyou
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Florian P Breitwieser
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yu-Chi Chang
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Anil K Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Present address: Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Departments of Biological Chemistry, Pathology, Neurology, and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Present address: Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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6
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Gordeeva O. Cancer-testis antigens: Unique cancer stem cell biomarkers and targets for cancer therapy. Semin Cancer Biol 2018; 53:75-89. [PMID: 30171980 DOI: 10.1016/j.semcancer.2018.08.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 08/15/2018] [Accepted: 08/17/2018] [Indexed: 02/07/2023]
Abstract
Cancer-testis antigens (CTAs) are considered as unique and promising cancer biomarkers and targets for cancer therapy. CTAs are multifunctional protein group with specific expression patterns in normal embryonic and adult cells and various types of cancer cells. CTAs are involved in regulating of the basic cellular processes during development, stem cell differentiation and carcinogenesis though the biological roles and cell functions of CTA families remain largely unclear. Analysis of CTA expression patterns in embryonic germ and somatic cells, pluripotent and multipotent stem cells, cancer stem cells and their cell descendants indicates that rearrangements of characteristic CTA profiles (aberrant expression) could be associated with cancer transformation and failure of the developmental program of cell lineage specification and germ line restriction. Therefore, aberrant CTA profiles can be used as panels of biomarkers for diagnoses and the selection of cancer treatment strategies. Moreover, immunogenic CTAs are prospective targets for cancer immunotherapy. Clinical trials testing broad range of cancer therapeutic vaccines against antigens of MAGEA and NY-ESO-1 families for treating various cancers have shown mixed clinical efficiency, safety and tolerability, suggesting the requirement of in-depth research of CTA expression in normal and cancer stem cells and extensive clinical trials for improving cancer immunotherapy technologies. This review focuses on recent advancement in study of CTAs in normal and cancer cells, particularly in normal and cancer stem cells, and provides a new insight into CTA expression patterns during normal and cancer stem cell lineage development. Additionally, new approaches in development of effective CTA-based therapies exclusively targeting cancer stem cells will be discussed.
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Affiliation(s)
- Olga Gordeeva
- Laboratory of Cell and Molecular Mechanisms of Histogenesis, Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, Moscow, 119334, Russia.
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7
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Iwamori T, Iwamori N, Matsumoto M, Ono E, Matzuk MM. Identification of KIAA1210 as a novel X-chromosome-linked protein that localizes to the acrosome and associates with the ectoplasmic specialization in testes. Biol Reprod 2018; 96:469-477. [PMID: 28203736 DOI: 10.1095/biolreprod.116.145458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/21/2016] [Accepted: 12/15/2016] [Indexed: 11/01/2022] Open
Abstract
Cell junctions are necessary for spermatogenesis, and there are numerous types of junctions in testis, such as blood–testis barrier, intercellular bridge, and ectoplasmic specialization (ES). The details of their functions and construction are still unknown. To identify a novel protein essential to the function of a cell junction, we enriched testis membrane protein and analyzed it using a proteomics approach. Here, we report a novel ES protein, which is encoded on the X chromosome and an ortholog of hypothetical human protein KIAA1210. KIAA1210 is expressed in testis predominantly, localized to the sex body in spermatocyte, acrosome, and near ES. Moreover, KIAA1210 possesses a topoisomerase 2 (TOP2)-associated protein PAT1 domain, a herpes simplex virus 1 (HSV-1) large tegument protein UL36 hypothetical domain, and a provisional DNA translocase FtsK domain. Using IP-proteomics with specific antibody to KIAA1210, we identified proteins including TOP2 isoforms as components of a complex with KIAA1210, in cell junctions in testis. The interaction between KIAA1210 and TOP2 was confirmed by two different proteomic analyses. Furthermore, immunofluorescence showed that KIAA1210 and TOP2B co-localize around the sex body in spermatocyte, apical ES, and residual bodies in elongated spermatids. Our findings suggest that KIAA1210 may be essential cell junction protein that interacts with TOP2B to regulate the dynamic change of chromatin structures during spermiogenesis.
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Affiliation(s)
- Tokuko Iwamori
- Department of Biomedicine, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Iwamori
- Department of Biomedicine, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaki Matsumoto
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Etsuro Ono
- Department of Biomedicine, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Martin M Matzuk
- Departments of Pathology and Immunology, Molecular and Cellular Biology, Molecular and Human Genetics, and Pharmacology, Center for Drug Discovery, and Center for Reproductive Medicine, Baylor College of Medicine, Houston, Texas, USA
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8
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Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol 2018; 36:338-345. [PMID: 29431738 PMCID: PMC5889714 DOI: 10.1038/nbt.4060] [Citation(s) in RCA: 1005] [Impact Index Per Article: 167.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 12/11/2017] [Indexed: 02/07/2023]
Abstract
We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ∼3 Mb). We developed a protocol to generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb). Incorporating an additional 5× coverage of these ultra-long reads more than doubled the assembly contiguity (NG50 ∼6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.
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Affiliation(s)
- Miten Jain
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California USA
| | - Josh Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Arthur C Rand
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California USA
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah, Salt Lake City, Utah USA
- USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah USA
| | - John R Tyson
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | - Andrew D Beggs
- Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, UK
| | - Alexander T Dilthey
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland USA
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California USA
| | - Sunir Malla
- DeepSeq, School of Life Sciences, University of Nottingham, UK
| | - Hannah Marriott
- DeepSeq, School of Life Sciences, University of Nottingham, UK
| | - Tom Nieto
- Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, UK
| | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Hugh E Olsen
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California USA
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, Utah USA
- USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland USA
| | | | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah USA
- USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah USA
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah USA
| | - Terrance P Snutch
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | - Louise Tee
- Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, UK
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland USA
| | - Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, UK
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9
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Dumbovic G, Forcales SV, Perucho M. Emerging roles of macrosatellite repeats in genome organization and disease development. Epigenetics 2017; 12:515-526. [PMID: 28426282 PMCID: PMC5687341 DOI: 10.1080/15592294.2017.1318235] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/01/2017] [Accepted: 04/06/2017] [Indexed: 11/24/2022] Open
Abstract
Abundant repetitive DNA sequences are an enigmatic part of the human genome. Despite increasing evidence on the functionality of DNA repeats, their biologic role is still elusive and under frequent debate. Macrosatellites are the largest of the tandem DNA repeats, located on one or multiple chromosomes. The contribution of macrosatellites to genome regulation and human health was demonstrated for the D4Z4 macrosatellite repeat array on chromosome 4q35. Reduced copy number of D4Z4 repeats is associated with local euchromatinization and the onset of facioscapulohumeral muscular dystrophy. Although the role other macrosatellite families may play remains rather obscure, their diverse functionalities within the genome are being gradually revealed. In this review, we will outline structural and functional features of coding and noncoding macrosatellite repeats, and highlight recent findings that bring these sequences into the spotlight of genome organization and disease development.
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Affiliation(s)
- Gabrijela Dumbovic
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona, Barcelona, Spain
| | - Sonia-V. Forcales
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona, Barcelona, Spain
| | - Manuel Perucho
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona, Barcelona, Spain
- Sanford-Burnham-Prebys Medical Discovery Institute (SBP), La Jolla, CA, USA
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10
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Zhang XY, Yan QX, Guo XY, Chen CR, Chen RQ, Cai ZM, Tang AF. Expression profile of SPACA5/ Spaca5 in spermatogenesis and transitional cell carcinoma of the bladder. Oncol Lett 2016; 12:3731-3738. [PMID: 27895724 PMCID: PMC5104159 DOI: 10.3892/ol.2016.5164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/19/2016] [Indexed: 11/05/2022] Open
Abstract
The majority of bladder cancer-associated mortalities are due to transitional cell carcinoma (TCC), which is the most prevalent and chemoresistant malignancy of the bladder. Sperm acrosome associated 5 (SPACA5)/Spaca5 is a sperm acrosome-associated, c-type lysozyme-like protein that has been recently identified, and has been designated as an attractive candidate antigen for cancer testis. In the present study, the expression profile of SPACA5/Spaca5 was analyzed in spermatogenesis and TCC of the bladder using diverse molecular and cellular biology methods. Using reverse transcription-polymerase chain reaction (RT-PCR) to analyze the multi-tissue distribution and temporal expression of SPACA5/Spaca5, the SPACA5/Spaca5 gene was determined to be generally not expressed in normal tissue, with the exception of the testis, and it could be detected at a low level on day 20 after birth in mouse testes and at a higher level on day 28. Immunohistochemistry staining revealed that the SPACA5/Spaca5 protein was exclusively observed in the elongated spermatid of the normal testes, and was ectopically expressed in the cytoplasm of TCC, while it was not expressed in normal bladder tissues. The frequency of SPACA5 messenger RNA was detected in 45% of TCC (9/20) by RT-quantitative PCR. Furthermore, SPACA5 protein was more frequently detected in high-grade than in low-grade tumors (61.54 vs. 30.00%, P=0.035). Accordingly, high SPACA5 staining scores were observed to be significantly associated with high-grade tumors (n=65, R=0.279, P=0.027). Collectively, our findings indicated that SPACA5/Spaca5 may be important in male spermatogenesis and may be used as a potential target for specific immunotherapy in patients suffering from TCC.
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Affiliation(s)
- Xiao-Yue Zhang
- Department of Science and Education, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518035, P.R. China
| | - Qiu-Xia Yan
- Center for Reproductive Medicine of Obstetrics and Gynecology, The People's Hospital of Qingyuan, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong 511518, P.R. China
| | - Xiao-Yan Guo
- Center for Reproductive Medicine of Obstetrics and Gynecology, The People's Hospital of Qingyuan, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong 511518, P.R. China
| | - Cai-Rong Chen
- Center for Reproductive Medicine of Obstetrics and Gynecology, The People's Hospital of Qingyuan, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong 511518, P.R. China
| | - Run-Qiang Chen
- Center for Reproductive Medicine of Obstetrics and Gynecology, The People's Hospital of Qingyuan, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong 511518, P.R. China
| | - Zhi-Ming Cai
- Department of Science and Education, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518035, P.R. China
| | - Ai-Fa Tang
- Department of Science and Education, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518035, P.R. China
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11
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Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 2016. [PMID: 27887629 DOI: 10.1186/s13059–016–1103–0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
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Affiliation(s)
- Miten Jain
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Hugh E Olsen
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.
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12
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Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 2016; 17:239. [PMID: 27887629 PMCID: PMC5124260 DOI: 10.1186/s13059-016-1103-0] [Citation(s) in RCA: 678] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
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Affiliation(s)
- Miten Jain
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Hugh E Olsen
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.
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13
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Kozlov AP. Expression of evolutionarily novel genes in tumors. Infect Agent Cancer 2016; 11:34. [PMID: 27437030 PMCID: PMC4949931 DOI: 10.1186/s13027-016-0077-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023] Open
Abstract
The evolutionarily novel genes originated through different molecular mechanisms are expressed in tumors. Sometimes the expression of evolutionarily novel genes in tumors is highly specific. Moreover positive selection of many human tumor-related genes in primate lineage suggests their involvement in the origin of new functions beneficial to organisms. It is suggested to consider the expression of evolutionarily young or novel genes in tumors as a new biological phenomenon, a phenomenon of TSEEN (tumor specifically expressed, evolutionarily novel) genes.
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Affiliation(s)
- A. P. Kozlov
- The Biomedical Center and Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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14
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Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nat Methods 2015; 12:351-6. [PMID: 25686389 PMCID: PMC4907500 DOI: 10.1038/nmeth.3290] [Citation(s) in RCA: 371] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/20/2015] [Indexed: 12/31/2022]
Abstract
The Oxford Nanopore MinION sequences individual DNA molecules using an array of pores that read nucleotide identities based on ionic current steps. We evaluated and optimized MinION performance using M13 genomic dsDNA. Using expectation-maximization (EM) we obtained robust maximum likelihood (ML) estimates for read insertion, deletion and substitution error rates (4.9%, 7.8%, and 5.1% respectively). We found that 99% of high-quality ‘2D’ MinION reads mapped to reference at a mean identity of 85%. We present a MinION-tailored tool for single nucleotide variant (SNV) detection that uses ML parameter estimates and marginalization over many possible read alignments to achieve precision and recall of up to 99%. By pairing our high-confidence alignment strategy with long MinION reads, we resolved the copy number for a cancer/testis gene family (CT47) within an unresolved region of human chromosome Xq24.
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Affiliation(s)
- Miten Jain
- 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Ian T Fiddes
- 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Karen H Miga
- 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Hugh E Olsen
- 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Benedict Paten
- 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Mark Akeson
- 1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
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15
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Li W, Freudenberg J, Miramontes P. Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome. BMC Bioinformatics 2014; 15:2. [PMID: 24386976 PMCID: PMC3927684 DOI: 10.1186/1471-2105-15-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 12/17/2013] [Indexed: 11/10/2022] Open
Abstract
Background The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a longer read is more likely to be uniquely mapped to the reference genome, a quantitative analysis of the influence of read lengths on mappability has been lacking. To address this question, we evaluate the k-mer distribution of the human reference genome. The k-mer frequency is determined for k ranging from 20 bp to 1000 bp. Results We observe that the proportion of non-singletons k-mers decreases slowly with increasing k, and can be fitted by piecewise power-law functions with different exponents at different ranges of k. A slower decay at greater values for k indicates more limited gains in mappability for read lengths between 200 bp and 1000 bp. The frequency distributions of k-mers exhibit long tails with a power-law-like trend, and rank frequency plots exhibit a concave Zipf’s curve. The most frequent 1000-mers comprise 172 regions, which include four large stretches on chromosomes 1 and X, containing genes of biomedical relevance. Comparison with other databases indicates that the 172 regions can be broadly classified into two types: those containing LINE transposable elements and those containing segmental duplications. Conclusion Read mappability as measured by the proportion of singletons increases steadily up to the length scale around 200 bp. When read length increases above 200 bp, smaller gains in mappability are expected. Moreover, the proportion of non-singletons decreases with read lengths much slower than linear. Even a read length of 1000 bp would not allow the unique alignment of reads for many coding regions of human genes. A mix of techniques will be needed for efficiently producing high-quality data that cover the complete human genome.
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Affiliation(s)
- Wentian Li
- The Robert S, Boas Center for Genomics and Human Genetic, The Feinstein Institute for Medical Research, North Shore LIJ Health System, 350 Community Drive, Manhasset, USA.
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16
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The novelty of human cancer/testis antigen encoding genes in evolution. Int J Genomics 2013; 2013:105108. [PMID: 23691492 PMCID: PMC3652184 DOI: 10.1155/2013/105108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/16/2013] [Accepted: 02/13/2013] [Indexed: 01/10/2023] Open
Abstract
In order to be inherited in progeny generations, novel genes should originate in germ cells. Here, we suggest that the testes may play a special “catalyst” role in the birth and evolution of new genes. Cancer/testis antigen encoding genes (CT genes) are predominantly expressed both in testes and in a variety of tumors. By the criteria of evolutionary novelty, the CT genes are, indeed, novel genes. We performed homology searches for sequences similar to human CT in various animals and established that most of the CT genes are either found in humans only or are relatively recent in their origin. A majority of all human CT genes originated during or after the origin of Eutheria. These results suggest relatively recent origin of human CT genes and align with the hypothesis of the special role of the testes in the evolution of the gene families.
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17
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Schaap M, Lemmers RJLF, Maassen R, van der Vliet PJ, Hoogerheide LF, van Dijk HK, Baştürk N, de Knijff P, van der Maarel SM. Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions. BMC Genomics 2013; 14:143. [PMID: 23496858 PMCID: PMC3599962 DOI: 10.1186/1471-2164-14-143] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 02/25/2013] [Indexed: 11/27/2022] Open
Abstract
Background Macrosatellite repeats (MSRs), usually spanning hundreds of kilobases of genomic DNA, comprise a significant proportion of the human genome. Because of their highly polymorphic nature, MSRs represent an extreme example of copy number variation, but their structure and function is largely understudied. Here, we describe a detailed study of six autosomal and two X chromosomal MSRs among 270 HapMap individuals from Central Europe, Asia and Africa. Copy number variation, stability and genetic heterogeneity of the autosomal macrosatellite repeats RS447 (chromosome 4p), MSR5p (5p), FLJ40296 (13q), RNU2 (17q) and D4Z4 (4q and 10q) and X chromosomal DXZ4 and CT47 were investigated. Results Repeat array size distribution analysis shows that all of these MSRs are highly polymorphic with the most genetic variation among Africans and the least among Asians. A mitotic mutation rate of 0.4-2.2% was observed, exceeding meiotic mutation rates and possibly explaining the large size variability found for these MSRs. By means of a novel Bayesian approach, statistical support for a distinct multimodal rather than a uniform allele size distribution was detected in seven out of eight MSRs, with evidence for equidistant intervals between the modes. Conclusions The multimodal distributions with evidence for equidistant intervals, in combination with the observation of MSR-specific constraints on minimum array size, suggest that MSRs are limited in their configurations and that deviations thereof may cause disease, as is the case for facioscapulohumeral muscular dystrophy. However, at present we cannot exclude that there are mechanistic constraints for MSRs that are not directly disease-related. This study represents the first comprehensive study of MSRs in different human populations by applying novel statistical methods and identifies commonalities and differences in their organization and function in the human genome.
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Affiliation(s)
- Mireille Schaap
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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18
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Stouffs K, Lissens W. X chromosomal mutations and spermatogenic failure. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1864-72. [DOI: 10.1016/j.bbadis.2012.05.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 02/24/2012] [Accepted: 05/14/2012] [Indexed: 01/11/2023]
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19
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Hegyi H, Tompa P. Increased structural disorder of proteins encoded on human sex chromosomes. ACTA ACUST UNITED AC 2012; 8:229-36. [DOI: 10.1039/c1mb05285c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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20
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Epigenetic regulation of the X-chromosomal macrosatellite repeat encoding for the cancer/testis gene CT47. Eur J Hum Genet 2011; 20:185-91. [PMID: 21811308 DOI: 10.1038/ejhg.2011.150] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Macrosatellite repeats (MSRs) present an extreme example of copy number variation, yet their epigenetic regulation in normal and malignant cells is largely understudied. The CT47 cancer/testis antigen located on human Xq24 is organized as an array of 4.8 kb large units. CT47 is expressed in the testis and in certain types of cancer, but not in non-malignant somatic tissue. We used CT47 as a model to study a possible correlation between copy number variation, epigenetic regulation and transcription originating from MSRs in normal and malignant cells. In lymphoblastoid cell lines and primary fibroblasts, CT47 expression was absent, consistent with the observed heterochromatic structure and DNA hypermethylation of the CT47 promoter. Heterochromatinization of CT47 occurs early during development as human embryonic stem cells show high levels of DNA methylation and repressive chromatin modifications in the absence of CT47 expression. In small-cell lung carcinoma cell lines with low levels of CT47 transcripts, we observed reduced levels of histone 3 lysine 9 trimethylation (H3K9me3) and trimethylated lysine 27 of histone H3 (H3K27me3) without concomitant increase in euchromatic histone modifications. DNA methylation levels in the promoter region of CT47 are also significantly reduced in these cells. This supports a model in which during oncogenic transformation, there is a relative loss of repressive chromatin markers resulting in leaky expression of CT47. We conclude that some MSRs, like CT47 and the autosomal MSRs TAF11-Like, PRR20, ZAV and D4Z4, the latter being involved in facioscapulohumeral muscular dystrophy, seem to be governed by common regulatory mechanisms with their abundant expression mostly being restricted to the germ line.
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21
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Tremblay DC, Moseley S, Chadwick BP. Variation in array size, monomer composition and expression of the macrosatellite DXZ4. PLoS One 2011; 6:e18969. [PMID: 21544201 PMCID: PMC3081327 DOI: 10.1371/journal.pone.0018969] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 03/25/2011] [Indexed: 11/18/2022] Open
Abstract
Macrosatellites are some of the most polymorphic regions of the human genome, yet many remain uncharacterized despite the association of some arrays with disease susceptibility. This study sought to explore the polymorphic nature of the X-linked macrosatellite DXZ4. Four aspects of DXZ4 were explored in detail, including tandem repeat copy number variation, array instability, monomer sequence polymorphism and array expression. DXZ4 arrays contained between 12 and 100 3.0 kb repeat units with an average array containing 57. Monomers were confirmed to be arranged in uninterrupted tandem arrays by restriction digest analysis and extended fiber FISH, and therefore DXZ4 encompasses 36–288 kb of Xq23. Transmission of DXZ4 through three generations in three families displayed a high degree of meiotic instability (8.3%), consistent with other macrosatellite arrays, further highlighting the unstable nature of these sequences in the human genome. Subcloning and sequencing of complete DXZ4 monomers identified numerous single nucleotide polymorphisms and alleles for the three microsatellite repeats located within each monomer. Pairwise comparisons of DXZ4 monomer sequences revealed that repeat units from an array are more similar to one another than those originating from different arrays. RNA fluorescence in situ hybridization revealed significant variation in DXZ4 expression both within and between cell lines. DXZ4 transcripts could be detected originiating from both the active and inactive X chromosome. Expression levels of DXZ4 varied significantly between males, but did not relate to the size of the array, nor did inheritance of the same array result in similar expression levels. Collectively, these studies provide considerable insight into the polymorphic nature of DXZ4, further highlighting the instability and variation potential of macrosatellites in the human genome.
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Affiliation(s)
- Deanna C. Tremblay
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Shawn Moseley
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Brian P. Chadwick
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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22
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Tremblay DC, Alexander G, Moseley S, Chadwick BP. Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome. BMC Genomics 2010; 11:632. [PMID: 21078170 PMCID: PMC3018141 DOI: 10.1186/1471-2164-11-632] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 11/15/2010] [Indexed: 11/13/2022] Open
Abstract
Background Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease facioscapulohumeral muscular dystrophy. Nevertheless, many other macrosatellite arrays in the human genome remain poorly characterized. Results Here we describe the organization, tandem repeat copy number variation, transmission stability and expression of four macrosatellite arrays in the human genome: the TAF11-Like array located on chromosomes 5p15.1, the SST1 arrays on 4q28.3 and 19q13.12, the PRR20 array located on chromosome 13q21.1, and the ZAV array at 9q32. All are polymorphic macrosatellite arrays that at least for TAF11-Like and SST1 show evidence of meiotic instability. With the exception of the SST1 array that is ubiquitously expressed, all are expressed at high levels in the testis and to a lesser extent in the brain. Conclusions Our results extend the number of characterized macrosatellite arrays in the human genome and provide the foundation for formulation of hypotheses to begin assessing their functional role in the human genome.
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Affiliation(s)
- Deanna C Tremblay
- Department of Biological Sciences, Florida State University, King Life Science Building, Tallahassee, FL 32306-4295, USA
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23
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Abstract
Advocates of chimpanzee research claim the genetic similarity of humans and chimpanzees make them an indispensable research tool to combat human diseases. Given that cancer is a leading cause of human death worldwide, one might expect that if chimpanzees were needed for, or were productive in, cancer research, then they would have been widely used. This comprehensive literature analysis reveals that chimpanzees have scarcely been used in any form of cancer research, and that chimpanzee tumours are extremely rare and biologically different from human cancers. Often, chimpanzee citations described peripheral use of chimpanzee cells and genetic material in predominantly human genomic studies. Papers describing potential new cancer therapies noted significant concerns regarding the chimpanzee model. Other studies described interventions that have not been pursued clinically. Finally, available evidence indicates that chimpanzees are not essential in the development of therapeutic monoclonal antibodies. It would therefore be unscientific to claim that chimpanzees are vital to cancer research. On the contrary, it is reasonable to conclude that cancer research would not suffer, if the use of chimpanzees for this purpose were prohibited in the US. Genetic differences between humans and chimpanzees, make them an unsuitable model for cancer, as well as other human diseases.
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Affiliation(s)
- Jarrod Bailey
- New England Anti-Vivisection Society, Boston, MA 02108-5100, USA.
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24
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Chadwick BP. Macrosatellite epigenetics: the two faces of DXZ4 and D4Z4. Chromosoma 2009; 118:675-81. [PMID: 19690880 DOI: 10.1007/s00412-009-0233-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 07/23/2009] [Accepted: 07/30/2009] [Indexed: 01/08/2023]
Abstract
Almost half of the human genome consists of repetitive DNA. Understanding what role these elements have in setting up chromatin states that underlie gene and chromosome function in complex genomes is paramount. The function of some types of repetitive DNA is obvious by virtue of their location, such as the alphoid arrays that define active centromeres. However, there are many other types of repetitive DNA whose evolutionary origins and current roles in genome biology remain unknown. One type of repetitive DNA that falls into this class is the macrosatellites. The relevance of these sequences to disease is clearly demonstrated by the 4q macrosatellite (D4Z4), whereupon contraction in the size of the array is associated with the onset of facioscapulohumeral muscular dystrophy. Here, I describe recent findings relating to the chromatin organization of D4Z4 and that of the X-linked macrosatellite DXZ4, highlighting the fact that these enigmatic sequences share more than a similar name.
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Affiliation(s)
- Brian P Chadwick
- Department of Biological Science, Florida State University, 3090 King Life Sciences Building, Tallahassee, FL 32306, USA.
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Chen YT, Hsu M, Lee P, Shin SJ, Mhawech-Fauceglia P, Odunsi K, Altorki NK, Song CJ, Jin BQ, Simpson AJ, Old LJ. Cancer/testis antigen CT45: analysis of mRNA and protein expression in human cancer. Int J Cancer 2009; 124:2893-8. [PMID: 19296537 DOI: 10.1002/ijc.24296] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CT45 is a cancer/testis gene that we previously identified by massively parallel signature sequencing. Encoded by a multigene family on chromosome X, CT45 showed restricted mRNA expression to normal testis and various cancers. In this study, monoclonal antibodies were generated against recombinant CT45 protein, and CT45 protein expression in normal and tumor tissues was evaluated by immunohistochemical analysis. In adult normal tissue, CT45 expression was restricted to testicular germ cells, detected as a nuclear protein mainly at the stage of primary spermatocytes. In tumors, CT45 protein expression correlated with the mRNA levels detected by quantitative RT-PCR, and most lung cancer and ovarian cancers with CT45 mRNA at levels >1% of testicular expression were CT45 protein-positive. In positive cases, CT45 showed expression patterns that ranged from diffuse strong staining to heterogeneous and patchy expression. In lung cancer, CT45 expression was least frequent in adenocarcinoma, more frequent in squamous cell carcinoma and neuroendocrine tumors. Using tissue microarrays, 376 lung cancer, 219 ovarian cancer and 155 breast cancer were evaluated for CT45 protein expression. The expression frequency was highest in ovarian cancer (37%), followed by lung cancer (13%) and lowest in breast cancer (<5%). Given the focal nature of CT45 expression in many cases, these numbers represented the minimal frequency of expression in these tumor types. In summary, the expression frequency and characteristics of CT45 expression are similar to other CT cancer vaccine targets currently in clinical trials, e.g., NY-ESO-1 and MAGE-A, suggesting CT45 as a potentially useful cancer target.
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Affiliation(s)
- Yao-Tseng Chen
- Departments of Pathology and Surgery, Weill Cornell Medical College, New York, NY 10065, USA.
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Metlapally R, Michaelides M, Bulusu A, Li YJ, Schwartz M, Rosenberg T, Hunt DM, Moore AT, Züchner S, Rickman CB, Young TL. Evaluation of the X-linked high-grade myopia locus (MYP1) with cone dysfunction and color vision deficiencies. Invest Ophthalmol Vis Sci 2008; 50:1552-8. [PMID: 19098318 DOI: 10.1167/iovs.08-2455] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE X-linked high myopia with mild cone dysfunction and color vision defects has been mapped to chromosome Xq28 (MYP1 locus). CXorf2/TEX28 is a nested, intercalated gene within the red-green opsin cone pigment gene tandem array on Xq28. The authors investigated whether TEX28 gene alterations were associated with the Xq28-linked myopia phenotype. Genomic DNA from five pedigrees (with high myopia and either protanopia or deuteranopia) that mapped to Xq28 were screened for TEX28 copy number variations (CNVs) and sequence variants. METHODS To examine for CNVs, ultra-high resolution array-comparative genomic hybridization (array-CGH) assays were performed comparing the subject genomic DNA with control samples (two pairs from two pedigrees). Opsin or TEX28 gene-targeted quantitative real-time gene expression assays (comparative CT method) were performed to validate the array-CGH findings. All exons of TEX28, including intron/exon boundaries, were amplified and sequenced using standard techniques. RESULTS Array-CGH findings revealed predicted duplications in affected patient samples. Although only three copies of TEX28 were previously reported within the opsin array, quantitative real-time analysis of the TEX28 targeted assay of affected male or carrier female individuals in these pedigrees revealed either fewer (one) or more (four or five) copies than did related and control unaffected individuals. Sequence analysis of TEX28 did not reveal any variants associated with the disease status. CONCLUSIONS CNVs have been proposed to play a role in disease inheritance and susceptibility as they affect gene dosage. TEX28 gene CNVs appear to be associated with the MYP1 X-linked myopia phenotypes.
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Warburton PE, Hasson D, Guillem F, Lescale C, Jin X, Abrusan G. Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 2008; 9:533. [PMID: 18992157 PMCID: PMC2588610 DOI: 10.1186/1471-2164-9-533] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Accepted: 11/07/2008] [Indexed: 01/26/2023] Open
Abstract
Background Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence. Results Using Tandem Repeats Finder (TRF), tandem repeat arrays greater than 10 kb in total size were identified, and classified into simple sequence e.g. GAATG, classical satellites e.g. alpha satellite DNA, and locus specific VNTR arrays. Analysis of these large sequenced regions revealed that several "simple sequence" arrays actually showed complex domain and/or higher order repeat organization. Using additional methods, we further identified a total of 96 additional arrays with tandem repeat units greater than 2 kb (the detection limit of TRF), 53 of which contained genes or repeated exons. The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized. Several novel megasatellite tandem DNA families were observed that are characterized by repeating patterns of interspersed transposable elements that have expanded presumably by unequal crossing over. One of these families is found on 11 different chromosomes in >25 arrays, and represents one of the largest most widespread megasatellite DNA families. Conclusion This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families.
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Affiliation(s)
- Peter E Warburton
- Deptartment of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA.
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Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics 2008; 9:466. [PMID: 18842134 PMCID: PMC2584115 DOI: 10.1186/1471-2164-9-466] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 10/08/2008] [Indexed: 02/06/2023] Open
Abstract
Background Evolution via point mutations is a relatively slow process and is unlikely to completely explain the differences between primates and other mammals. By contrast, 45% of the human genome is composed of retroposed elements, many of which were inserted in the primate lineage. A subset of retroposed mRNAs (retrocopies) shows strong evidence of expression in primates, often yielding functional retrogenes. Results To identify and analyze the relatively recently evolved retrogenes, we carried out BLASTZ alignments of all human mRNAs against the human genome and scored a set of features indicative of retroposition. Of over 12,000 putative retrocopy-derived genes that arose mainly in the primate lineage, 726 with strong evidence of transcript expression were examined in detail. These mRNA retroposition events fall into three categories: I) 34 retrocopies and antisense retrocopies that added potential protein coding space and UTRs to existing genes; II) 682 complete retrocopy duplications inserted into new loci; and III) an unexpected set of 13 retrocopies that contributed out-of-frame, or antisense sequences in combination with other types of transposed elements (SINEs, LINEs, LTRs), even unannotated sequence to form potentially novel genes with no homologs outside primates. In addition to their presence in human, several of the gene candidates also had potentially viable ORFs in chimpanzee, orangutan, and rhesus macaque, underscoring their potential of function. Conclusion mRNA-derived retrocopies provide raw material for the evolution of genes in a wide variety of ways, duplicating and amending the protein coding region of existing genes as well as generating the potential for new protein coding space, or non-protein coding RNAs, by unexpected contributions out of frame, in reverse orientation, or from previously non-protein coding sequence.
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Affiliation(s)
- Robert Baertsch
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.
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Stevenson BJ, Iseli C, Panji S, Zahn-Zabal M, Hide W, Old LJ, Simpson AJ, Jongeneel CV. Rapid evolution of cancer/testis genes on the X chromosome. BMC Genomics 2007; 8:129. [PMID: 17521433 PMCID: PMC1890293 DOI: 10.1186/1471-2164-8-129] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 05/23/2007] [Indexed: 11/15/2022] Open
Abstract
Background Cancer/testis (CT) genes are normally expressed only in germ cells, but can be activated in the cancer state. This unusual property, together with the finding that many CT proteins elicit an antigenic response in cancer patients, has established a role for this class of genes as targets in immunotherapy regimes. Many families of CT genes have been identified in the human genome, but their biological function for the most part remains unclear. While it has been shown that some CT genes are under diversifying selection, this question has not been addressed before for the class as a whole. Results To shed more light on this interesting group of genes, we exploited the generation of a draft chimpanzee (Pan troglodytes) genomic sequence to examine CT genes in an organism that is closely related to human, and generated a high-quality, manually curated set of human:chimpanzee CT gene alignments. We find that the chimpanzee genome contains homologues to most of the human CT families, and that the genes are located on the same chromosome and at a similar copy number to those in human. Comparison of putative human:chimpanzee orthologues indicates that CT genes located on chromosome X are diverging faster and are undergoing stronger diversifying selection than those on the autosomes or than a set of control genes on either chromosome X or autosomes. Conclusion Given their high level of diversifying selection, we suggest that CT genes are primarily responsible for the observed rapid evolution of protein-coding genes on the X chromosome.
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Affiliation(s)
- Brian J Stevenson
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Christian Iseli
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Sumir Panji
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, 7535, South Africa
| | - Monique Zahn-Zabal
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Winston Hide
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, 7535, South Africa
| | - Lloyd J Old
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - Andrew J Simpson
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - C Victor Jongeneel
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
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Luo C, Xiao X, Liu D, Chen S, Li M, Xu A, Liu J, Gao S, Wu S, He D. CABYR Is a Novel Cancer-Testis Antigen in Lung Cancer. Clin Cancer Res 2007; 13:1288-97. [PMID: 17317841 DOI: 10.1158/1078-0432.ccr-06-1742] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Cancer-testis (CT) antigens are often expressed in a proportion of tumors of various types. Their restricted normal tissue expression and immunogenicity make them potential targets for immunotherapy. CABYR is a calcium-binding tyrosine phosphorylation-regulated fibrous sheath protein initially reported to be testis specific and subsequently shown to be present in brain tumors. This study was to determine whether CABYR is a novel CT antigen in lung cancer. EXPERIMENTAL DESIGN mRNA expression of CABYR-a/b (combination of CABYR-a and CABYR-b) and CABYR-c was examined in 36 lung cancer specimens, 14 cancer cell lines, and 1 normal cell line by conventional and real-time reverse transcription-PCR. Protein expression of CABYR was analyzed in 50 lung cancer tissues by immunohistochemistry. Antibodies specific to CABYR were analyzed in sera from 174 lung cancer patients and 60 healthy donors by ELISA and Western blot. RESULTS mRNA expression of CABYR-a/b and CABYR-c was observed, respectively, in 13 and 15 of 36 lung cancer tissues as well as in 3 and 5 of 14 cancer cell lines, whereas neither of them was observed in adjacent noncancerous tissues or the normal cell line. Protein expression of CABYR-a/b and CABYR-c was observed, respectively, in 20 and 19 of 50 lung cancer tissues. IgG antibodies specific to CABYR-a/b and CABYR-c were detected, respectively, in 11% and 9% of sera from lung cancer patients but not from the 60 healthy donors. CONCLUSION CABYR is a novel CT antigen in lung cancer and may be a promising target for immunotherapy for lung cancer patients.
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Affiliation(s)
- Chonglin Luo
- Key laboratory of Cell Proliferation and Regulation of Ministry of Education, Beijing Normal University, China
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