1
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Hiemenz MC, Kaur J, Kuang Z, Huang RSP, Harries L, Metzger D, Schiavone K, Millis SZ, Lin DI, Lechpammer M, Decker B, Mata DA, Reddy A, Parke M, Lee EY, Cui X, Iwenofu OH, Buehler D, Henderson L, Baldwin EM, Boikos SA, Ramkissoon SH, Smith SC. POU2AF3-rearranged sarcomas: A novel tumor defined by fusions of EWSR1 or FUS to a gene formerly designated COLCA2. Genes Chromosomes Cancer 2023; 62:460-470. [PMID: 36862145 DOI: 10.1002/gcc.23136] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/30/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023] Open
Abstract
Gene fusions involving EWSR1 or FUS as the 5' partner have been reported in a diverse array of sarcomas. Here, we characterize the histopathology and genomics of six tumors harboring a gene fusion between EWSR1 or FUS and POU2AF3, an understudied, putative colorectal cancer predisposition gene. Striking morphologic features reminiscent of synovial sarcoma were observed including a biphasic appearance with variable fusiform to epithelioid cytomorphology and staghorn-type vasculature. RNA sequencing demonstrated variable breakpoints in EWSR1/FUS along with similar breakpoints in POU2AF3 that encompassed a 3' portion of this gene. For cases in which additional information was available, the behavior of these neoplasms was aggressive with local spread and/or distant metastases. Although further studies are needed to confirm the functional significance of our findings, POU2AF3 fusions to EWSR1 or FUS may define a novel type of POU2AF3-rearranged sarcomas with aggressive, malignant behavior.
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Affiliation(s)
| | | | - Zheng Kuang
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | | | - Dana Metzger
- Foundation Medicine, Cambridge, Massachusetts, USA
| | | | | | | | | | | | | | | | - Matthew Parke
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Eun Y Lee
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Xiaoyan Cui
- Department of Pathology and Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - O Hans Iwenofu
- Department of Pathology and Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Darya Buehler
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Les Henderson
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Erin M Baldwin
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sosipatros A Boikos
- Department of Hematology and Oncology, Georgetown Lombardi Comprehensive Cancer Center, Washington DC, USA
| | - Shakti H Ramkissoon
- Foundation Medicine, Cambridge, Massachusetts, USA
- Department of Pathology, Wake Forest School of Medicine and Wake Forest Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Steven C Smith
- Departments of Pathology and Surgery and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
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2
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ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen. Cell Rep 2023; 42:111909. [PMID: 36640339 PMCID: PMC10023214 DOI: 10.1016/j.celrep.2022.111909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
ATM gene mutation carriers are predisposed to estrogen-receptor-positive breast cancer (BC). ATM prevents BC oncogenesis by activating p53 in every cell; however, much remains unknown about tissue-specific oncogenesis after ATM loss. Here, we report that ATM controls the early transcriptional response to estrogens. This response depends on topoisomerase II (TOP2), which generates TOP2-DNA double-strand break (DSB) complexes and rejoins the breaks. When TOP2-mediated ligation fails, ATM facilitates DSB repair. After estrogen exposure, TOP2-dependent DSBs arise at the c-MYC enhancer in human BC cells, and their defective repair changes the activation profile of enhancers and induces the overexpression of many genes, including the c-MYC oncogene. CRISPR/Cas9 cleavage at the enhancer also causes c-MYC overexpression, indicating that this DSB causes c-MYC overexpression. Estrogen treatment induced c-Myc protein overexpression in mammary epithelial cells of ATM-deficient mice. In conclusion, ATM suppresses the c-Myc-driven proliferative effects of estrogens, possibly explaining such tissue-specific oncogenesis.
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3
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Polyploidy as an Adaptation against Loss of Heterozygosity in Cancer. Int J Mol Sci 2022; 23:ijms23158528. [PMID: 35955663 PMCID: PMC9369199 DOI: 10.3390/ijms23158528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022] Open
Abstract
Polyploidy is common in cancer cells and has implications for tumor progression and resistance to therapies, but it is unclear whether it is an adaptation of the tumor or the non-adaptive effect of genomic instability. I discuss the possibility that polyploidy reduces the deleterious effects of loss of heterozygosity, which arises as a consequence of mitotic recombination, and which in diploid cells leads instead to the rapid loss of complementation of recessive deleterious mutations. I use computational predictions of loss of heterozygosity to show that a population of diploid cells dividing by mitosis with recombination can be easily invaded by mutant polyploid cells or cells that divide by endomitosis, which reduces loss of complementation, or by mutant cells that occasionally fuse, which restores heterozygosity. A similar selective advantage of polyploidy has been shown for the evolution of different types of asexual reproduction in nature. This provides an adaptive explanation for cyclical ploidy, mitotic slippage and cell fusion in cancer cells.
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4
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Multiple Stochastic Parameters Influence Genome Dynamics in a Heterozygous Diploid Eukaryotic Model. J Fungi (Basel) 2022; 8:jof8070650. [PMID: 35887406 PMCID: PMC9323731 DOI: 10.3390/jof8070650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 12/10/2022] Open
Abstract
The heterozygous diploid genome of Candida albicans displays frequent genomic rearrangements, in particular loss-of-heterozygosity (LOH) events, which can be seen on all eight chromosomes and affect both laboratory and clinical strains. LOHs, which are often the consequence of DNA damage repair, can be observed upon stresses reminiscent of the host environment, and result in homozygous regions of various sizes depending on the molecular mechanisms at their origins. Recent studies have shed light on the biological importance of these frequent and ubiquitous LOH events in C. albicans. In diploid Saccharomyces cerevisiae, LOH facilitates the passage of recessive beneficial mutations through Haldane’s sieve, allowing rapid evolutionary adaptation. This also appears to be true in C. albicans, where the full potential of an adaptive mutation is often only observed upon LOH, as illustrated in the case of antifungal resistance and niche adaptation. To understand the genome-wide dynamics of LOH events in C. albicans, we constructed a collection of 15 strains, each one carrying a LOH reporter system on a different chromosome arm. This system involves the insertion of two fluorescent marker genes in a neutral genomic region on both homologs, allowing spontaneous LOH events to be detected by monitoring the loss of one of the fluorescent markers using flow cytometry. Using this collection, we observed significant LOH frequency differences between genomic loci in standard laboratory growth conditions; however, we further demonstrated that comparable heterogeneity was also observed for a given genomic locus between independent strains. Additionally, upon exposure to stress, three outcomes could be observed in C. albicans, where individual strains displayed increases, decreases, or no effect of stress in terms of LOH frequency. Our results argue against a general stress response triggering overall genome instability. Indeed, we showed that the heterogeneity of LOH frequency in C. albicans is present at various levels, inter-strain, intra-strain, and inter-chromosomes, suggesting that LOH events may occur stochastically within a cell, though the genetic background potentially impacts genome stability in terms of LOH throughout the genome in both basal and stress conditions. This heterogeneity in terms of genome stability may serve as an important adaptive strategy for the predominantly clonal human opportunistic pathogen C. albicans, by quickly generating a wide spectrum of genetic variation combinations potentially permitting subsistence in a rapidly evolving environment.
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5
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Maund SL, Sokol ES, Ang Houle A, Ross JS, Wilson TR. NTRK gene fusions are detected in both secretory and non-secretory breast cancers. Pathol Int 2022; 72:187-192. [PMID: 35102630 DOI: 10.1111/pin.13204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/01/2022] [Indexed: 01/01/2023]
Abstract
NTRK fusions represent a new biomarker-defined population that can be treated with TRK inhibitors. Although rare, NTRK fusions are detected across a wide range of solid tumors. Previous reports suggest that NTRK fusions are limited to the secretory subtype of breast cancer. Here we examined NTRK fusions in a large real world next-generation sequencing (NGS) dataset and confirmed secretory versus non-secretory status using H&E images. Of 23 NTRK fusion-positive cases, 11 were classified as secretory, 11 as non-secretory, and one as mixed status. The secretory subtype trended younger, was predominantly estrogen receptor (ER)-, had lower tumor mutational burden, and exhibited lower levels of genomic loss of heterozygosity. The non-secretory subtype was enriched for TP53 mutations. The secretory subtype was enriched for ETV6-NTRK3 fusions in 7 of 11 cases, and the non-secretory subtype had NTRK1 fusions in 7 of 11 cases, each with a different fusion partner. Our data suggests NTRK fusions are present in both secretory and non-secretory subtypes, and that comprehensive genomic profiling should be considered across all clinically advanced breast cancers to identify patients that could receive benefit from TRK inhibitors.
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Affiliation(s)
| | - Ethan S Sokol
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA.,Upstate Medical University, Syracuse, New York, USA
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6
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Long X, Xue H. Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability. Hum Genomics 2021; 15:19. [PMID: 33741065 PMCID: PMC7976700 DOI: 10.1186/s40246-021-00318-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/04/2021] [Indexed: 12/25/2022] Open
Abstract
Background Genetic variants, underlining phenotypic diversity, are known to distribute unevenly in the human genome. A comprehensive understanding of the distributions of different genetic variants is important for insights into genetic functions and disorders. Methods Herein, a sliding-window scan of regional densities of eight kinds of germline genetic variants, including single-nucleotide-polymorphisms (SNPs) and four size-classes of copy-number-variations (CNVs) in the human genome has been performed. Results The study has identified 44,379 hotspots with high genetic-variant densities, and 1135 hotspot clusters comprising more than one type of hotspots, accounting for 3.1% and 0.2% of the genome respectively. The hotspots and clusters are found to co-localize with different functional genomic features, as exemplified by the associations of hotspots of middle-size CNVs with histone-modification sites, work with balancing and positive selections to meet the need for diversity in immune proteins, and facilitate the development of sensory-perception and neuroactive ligand-receptor interaction pathways in the function-sparse late-replicating genomic sequences. Genetic variants of different lengths co-localize with retrotransposons of different ages on a “long-with-young” and “short-with-all” basis. Hotspots and clusters are highly associated with tumor suppressor genes and oncogenes (p < 10−10), and enriched with somatic tumor CNVs and the trait- and disease-associated SNPs identified by genome-wise association studies, exceeding tenfold enrichment in clusters comprising SNPs and extra-long CNVs. Conclusions In conclusion, the genetic-variant hotspots and clusters represent two-edged swords that spearhead both positive and negative genomic changes. Their strong associations with complex traits and diseases also open up a potential “Common Disease-Hotspot Variant” approach to the missing heritability problem. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00318-3.
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Affiliation(s)
- Xi Long
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China
| | - Hong Xue
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China. .,HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China. .,Centre for Cancer Genomics, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China.
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7
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Zhang X, Sjöblom T. Targeting Loss of Heterozygosity: A Novel Paradigm for Cancer Therapy. Pharmaceuticals (Basel) 2021; 14:ph14010057. [PMID: 33450833 PMCID: PMC7828287 DOI: 10.3390/ph14010057] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
Loss of heterozygosity (LOH) is a common genetic event in the development of cancer. In certain tumor types, LOH can affect more than 20% of the genome, entailing loss of allelic variation in thousands of genes. This reduction of heterozygosity creates genetic differences between tumor and normal cells, providing opportunities for development of novel cancer therapies. Here, we review and summarize (1) mutations associated with LOH on chromosomes which have been shown to be promising biomarkers of cancer risk or the prediction of clinical outcomes in certain types of tumors; (2) loci undergoing LOH that can be targeted for development of novel anticancer drugs as well as (3) LOH in tumors provides up-and-coming possibilities to understand the underlying mechanisms of cancer evolution and to discover novel cancer vulnerabilities which are worth a further investigation in the near future.
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8
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Ross JS, Sokol ES, Moch H, Mileshkin L, Baciarello G, Losa F, Beringer A, Thomas M, Elvin JA, Ngo N, Jin DX, Krämer A. Comprehensive Genomic Profiling of Carcinoma of Unknown Primary Origin: Retrospective Molecular Classification Considering the CUPISCO Study Design. Oncologist 2020; 26:e394-e402. [PMID: 33219618 PMCID: PMC7930409 DOI: 10.1002/onco.13597] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background Carcinoma of unknown primary origin (CUP) accounts for 2%–5% of newly diagnosed advanced malignancies, with chemotherapy as the standard of care. CUPISCO (NCT03498521) is an ongoing randomized trial using comprehensive genomic profiling (CGP) to assign patients with CUP to targeted or immunotherapy treatment arms based on genomic profiling. We performed a retrospective analysis of CUP cases referred for CGP to determine how many were potentially eligible for enrollment into an experimental CUPISCO arm. Materials and Methods Centrally reviewed adenocarcinoma and undifferentiated CUP specimens in the FoundationCore database were analyzed using the hybrid capture‐based FoundationOne CDx assay (mean coverage, >600×). Presence of genomic alterations, microsatellite instability (MSI), tumor mutational burden (TMB), genomic loss of heterozygosity (gLOH), and programmed death‐ligand 1 (PD‐L1) positivity were determined. Results A total of 96 of 303 patients (31.7%) could be matched to an experimental CUPISCO arm. Key genomic alterations included ERBB2 (7.3%), PIK3CA (6.3%), NF1 (5.6%), NF2 (4.6%), BRAF (4.3%), IDH1 (3.3%), PTEN, FGFR2, EGFR (3.6% each), MET (4.3%), CDK6 (3.0%), FBXW7, CDK4 (2.3% each), IDH2, RET, ROS1, NTRK (1.0% each), and ALK (0.7%). Median TMB was 3.75 mutations per megabase of DNA; 34 patients (11.6%) had a TMB ≥16 mutations per megabase. Three patients (1%) had high MSI, and 42 (14%) displayed high PD‐L1 expression (tumor proportion score ≥50%). gLOH could be assessed in 199 of 303 specimens; 19.6% had a score of >16%. Conclusions Thirty‐two percent of patients would have been eligible for targeted therapy in CUPISCO. Future studies, including additional biomarkers such as PD‐L1 positivity and gLOH, may identify a greater proportion potentially benefiting from CGP‐informed treatment. Clinical trial identification number. NCT03498521 Implications for Practice The findings of this retrospective analysis of carcinoma of unknown primary origin (CUP) cases validate the experimental treatment arms being used in the CUPISCO study (NCT03498521), an ongoing randomized trial using comprehensive genomic profiling to assign patients with CUP to targeted or immunotherapy treatment arms based on the presence of pathogenic genomic alterations. The findings also suggest that future studies including additional biomarkers and treatment arms, such as programmed death‐ligand 1 positivity and genomic loss of heterozygosity, may identify a greater proportion of patients with CUP potentially benefiting from comprehensive genomic profiling‐informed treatment. This article focuses on the ability of comprehensive genomic profiling to identify potentially targetable genetic alterations in cancers of unknown primary, based on the inclusion criteria for the CUPISCO clinical trial and aiming for more effective therapeutic options for patients.
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Affiliation(s)
- Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA.,SUNY Upstate Medical University, Syracuse, New York, New York, USA
| | - Ethan S Sokol
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Holger Moch
- University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Ferran Losa
- Hospital de Sant Joan Despí Moisès Broggi, Barcelona, Spain
| | | | | | - Julia A Elvin
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Nhu Ngo
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Dexter X Jin
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Alwin Krämer
- German Cancer Research Center (DKFZ) and University of Heidelberg, Heidelberg, Germany
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9
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Singh VK, Rastogi A, Hu X, Wang Y, De S. Mutational signature SBS8 predominantly arises due to late replication errors in cancer. Commun Biol 2020; 3:421. [PMID: 32747711 PMCID: PMC7400754 DOI: 10.1038/s42003-020-01119-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
Although a majority of somatic mutations in cancer are passengers, their mutational signatures provide mechanistic insights into mutagenesis and DNA repair processes. Mutational signature SBS8 is common in most cancers, but its etiology is debated. Incorporating genomic, epigenomic, and cellular process features for multiple cell-types we develop genome-wide composite epigenomic context-maps relevant for mutagenesis and DNA repair. Analyzing somatic mutation data from multiple cancer types in their epigenomic contexts, we show that SBS8 preferentially occurs in gene-poor, lamina-proximal, late replicating heterochromatin domains. While SBS8 is uncommon among mutations in non-malignant tissues, in tumor genomes its proportions increase with replication timing and speed, and checkpoint defects further promote this signature - suggesting that SBS8 probably arises due to uncorrected late replication errors during cancer progression. Our observations offer a potential reconciliation among different perspectives in the debate about the etiology of SBS8 and its relationship with other mutational signatures.
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Affiliation(s)
- Vinod Kumar Singh
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Arnav Rastogi
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Xiaoju Hu
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Yaqun Wang
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Subhajyoti De
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA.
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10
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Prusinski Fernung LE, Yang Q, Sakamuro D, Kumari A, Mas A, Al-Hendy A. Endocrine disruptor exposure during development increases incidence of uterine fibroids by altering DNA repair in myometrial stem cells. Biol Reprod 2019; 99:735-748. [PMID: 29688260 DOI: 10.1093/biolre/ioy097] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/20/2018] [Indexed: 12/20/2022] Open
Abstract
Despite the major negative impact uterine fibroids (UFs) have on female reproductive health, little is known about early events that initiate development of these tumors. Somatic fibroid-causing mutations in mediator complex subunit 12 (MED12), the most frequent genetic alterations in UFs (up to 85% of tumors), are implicated in transforming normal myometrial stem cells (MSCs) into tumor-forming cells, though the underlying mechanism(s) leading to these mutations remains unknown. It is well accepted that defective DNA repair increases the risk of acquiring tumor-driving mutations, though defects in DNA repair have not been explored in UF tumorigenesis. In the Eker rat UF model, a germline mutation in the Tsc2 tumor suppressor gene predisposes to UFs, which arise due to "second hits" in the normal allele of this gene. Risk for developing these tumors is significantly increased by early-life exposure to endocrine-disrupting chemicals (EDCs), suggesting increased UF penetrance is modulated by early drivers for these tumors. We analyzed DNA repair capacity using analyses of related gene and protein expression and DNA repair function in MSCs from adult rats exposed during uterine development to the model EDC diethylstilbestrol. Adult MSCs isolated from developmentally exposed rats demonstrated decreased DNA end-joining ability, higher levels of DNA damage, and impaired ability to repair DNA double-strand breaks relative to MSCs from age-matched, vehicle-exposed rats. These data suggest that early-life developmental EDC exposure alters these MSCs' ability to repair and reverse DNA damage, providing a driver for acquisition of mutations that may promote the development of these tumors in adult life.
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Affiliation(s)
| | - Qiwei Yang
- Department of Obstetrics and Gynecology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Daitoku Sakamuro
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, Georgia, USA
| | - Alpana Kumari
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, Georgia, USA
| | - Aymara Mas
- Reproductive Medicine Research Group, La Fe Health Research Institute, Valencia, Spain.,Igenomix, Paterna, Valencia, Spain.,Department of Obstetrics and Gynecology, Valencia University and INCLIVA, Valencia, Spain
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, University of Illinois at Chicago, Chicago, Illinois, USA
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11
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Bach DH, Zhang W, Sood AK. Chromosomal Instability in Tumor Initiation and Development. Cancer Res 2019; 79:3995-4002. [PMID: 31350294 PMCID: PMC7694409 DOI: 10.1158/0008-5472.can-18-3235] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/26/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022]
Abstract
Chromosomal instability (CIN) is one of the major forms of genomic instability in various human cancers and is recognized as a common hallmark of tumorigenesis and heterogeneity. However, some malignant tumors show a paucity of chromosomal alterations, suggesting that tumor progression and evolution can occur in the absence of CIN. It is unclear whether CIN is stable between precursor lesions, primary tumor, and metastases or if it evolves during these steps. In this review, we describe the influence of CIN on the various steps in tumor initiation and development. Given the recognized significant effects of CIN in cancer, CIN-targeted therapeutics could have a major impact on improving clinical outcomes.
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Affiliation(s)
- Duc-Hiep Bach
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
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12
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McCabe MJ, Pinese M, Chan CL, Sheriff N, Thompson TJ, Grady J, Wong M, Gauthier MEA, Puttick C, Gayevskiy V, Hajdu E, Wong SQ, Barrett W, Earls P, Lukeis R, Cheng YY, Lin RCY, Thomas DM, Watkins DN, Dinger ME, McCormack AI, Cowley MJ. Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003764. [PMID: 30936196 PMCID: PMC6549567 DOI: 10.1101/mcs.a003764] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/11/2019] [Indexed: 12/22/2022] Open
Abstract
Adrenocortical carcinoma is a rare malignancy with a poor prognosis and few treatment options. Molecular characterization of this cancer remains limited. We present a case of an adrenocortical carcinoma (ACC) in a 37-yr-old female, with dual lung metastases identified 1 yr following commencement of adjuvant mitotane therapy. As standard therapeutic regimens are often unsuccessful in ACC, we undertook a comprehensive genomic study into this case to identify treatment options and monitor disease progress. We performed targeted and whole-genome sequencing of germline, primary tumor, and both metastatic tumors from this patient and monitored recurrence over 2 years using liquid biopsy for ctDNA and steroid hormone measurements. Sequencing revealed the primary and metastatic tumors were hyperhaploid, with extensive loss of heterozygosity but few structural rearrangements. Loss-of-function mutations were identified in MSH2, TP53, RB1, and PTEN, resulting in tumors with mismatch repair signatures and microsatellite instability. At the cellular level, tumors were populated by mitochondria-rich oncocytes. Longitudinal ctDNA mutation and hormone profiles were unable to detect micrometastatic disease, consistent with clinical indicators of disease remission. The molecular signatures in our ACC case suggested immunotherapy in the event of disease progression; however, the patient remains free of cancer. The extensive molecular analysis presented here could be applied to other rare and/or poorly stratified cancers to identify novel or repurpose existing therapeutic options, thereby broadly improving diagnoses, treatments, and prognoses.
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Affiliation(s)
- Mark J McCabe
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2010, Australia
| | - Mark Pinese
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Chia-Ling Chan
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Nisa Sheriff
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Department of Endocrinology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Tanya J Thompson
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - John Grady
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Marie Wong
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Marie-Emilie A Gauthier
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Clare Puttick
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Elektra Hajdu
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Stephen Q Wong
- Molecular and Translational Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Wade Barrett
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Peter Earls
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Robyn Lukeis
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Yuen Y Cheng
- Asbestos Diseases Research Institute, The University of Sydney, Sydney, New South Wales 2139, Australia
| | - Ruby C Y Lin
- Asbestos Diseases Research Institute, The University of Sydney, Sydney, New South Wales 2139, Australia.,Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, New South Wales 2145, Australia
| | - David M Thomas
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - D Neil Watkins
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2010, Australia
| | - Ann I McCormack
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2010, Australia.,Department of Endocrinology, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2010, Australia.,Computational Biology Group, Children's Cancer Institute, Kensington, New South Wales 2031, Australia
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13
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Origin Firing Regulations to Control Genome Replication Timing. Genes (Basel) 2019; 10:genes10030199. [PMID: 30845782 PMCID: PMC6470937 DOI: 10.3390/genes10030199] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 12/19/2022] Open
Abstract
Complete genome duplication is essential for genetic homeostasis over successive cell generations. Higher eukaryotes possess a complex genome replication program that involves replicating the genome in units of individual chromatin domains with a reproducible order or timing. Two types of replication origin firing regulations ensure complete and well-timed domain-wise genome replication: (1) the timing of origin firing within a domain must be determined and (2) enough origins must fire with appropriate positioning in a short time window to avoid inter-origin gaps too large to be fully copied. Fundamental principles of eukaryotic origin firing are known. We here discuss advances in understanding the regulation of origin firing to control firing time. Work with yeasts suggests that eukaryotes utilise distinct molecular pathways to determine firing time of distinct sets of origins, depending on the specific requirements of the genomic regions to be replicated. Although the exact nature of the timing control processes varies between eukaryotes, conserved aspects exist: (1) the first step of origin firing, pre-initiation complex (pre-IC formation), is the regulated step, (2) many regulation pathways control the firing kinase Dbf4-dependent kinase, (3) Rif1 is a conserved mediator of late origin firing and (4) competition between origins for limiting firing factors contributes to firing timing. Characterization of the molecular timing control pathways will enable us to manipulate them to address the biological role of replication timing, for example, in cell differentiation and genome instability.
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14
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Jia P, Zhao Z. Impacts of somatic mutations on gene expression: an association perspective. Brief Bioinform 2017; 18:413-425. [PMID: 27127206 DOI: 10.1093/bib/bbw037] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 12/28/2022] Open
Abstract
Assessing the functional impacts of somatic mutations in cancer genomes is critical for both identifying driver mutations and developing molecular targeted therapies. Currently, it remains a fundamental challenge to distinguish the patterns through which mutations execute their biological effects and to infer biological mechanisms underlying these patterns. To this end, we systematically studied the association between somatic mutations in protein-coding regions and expression profiles, which represents an indirect measurement of impacts. We defined mutation features (mutation type, cluster and status) and built linear regression models to assess mutation associations with mRNA expression and protein expression. Our results presented a comprehensive landscape of the associations between mutation features and expression profile in multiple cancer types, including 62 genes showing mutation type associated expression changes, 21 genes showing mutation cluster associations and 51 genes showing mutation status associations. We revealed four characteristics of the patterns that mutations impact on expression. First, we showed that mutation type (truncation versus amino acid-altering mutations) was the most important determinant of expression levels. Second, we detected mutation clusters in well-studied oncogenes that were associated with gene expression. Third, we found both similarities and differences in association patterns existed within and across cancer types. Fourth, although many of the observed associations stay stable at both mRNA and protein expression levels, there are also novel associations uniquely observed at the protein level, which warrant future investigation. Taken together, our findings provided implications for cancer driver gene prioritization and insights into the functional consequences of somatic mutations.
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15
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Nuclear topology modulates the mutational landscapes of cancer genomes. Nat Struct Mol Biol 2017; 24:1000-1006. [PMID: 28967881 PMCID: PMC5744871 DOI: 10.1038/nsmb.3474] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/28/2017] [Indexed: 01/18/2023]
Abstract
Nuclear organization of genomic DNA affects DNA damage and repair processes, and yet its impact on mutational landscapes in cancer genomes remains unclear. Here we analyzed genome-wide somatic mutations from 366 samples of 6 cancer types. We found that lamina-associated regions, which are typically localized at the nuclear periphery, displayed higher somatic mutation frequencies compared to the inter-lamina regions at the nuclear core. This effect remained even after adjusting for features such as GC%, chromatin, and replication timing. Furthermore, mutational signatures differed between the nuclear core and periphery, indicating differences in the patterns of DNA damage and/or DNA repair processes. For instance, smoking and UV-related signatures were more enriched in the nuclear periphery. Substitutions at certain motifs were also more common in the nuclear periphery. Taken together, we found that the nuclear architecture influences mutational landscapes in cancer genomes beyond the effects already captured by chromatin and replication timing.
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16
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Blumenfeld B, Ben-Zimra M, Simon I. Perturbations in the Replication Program Contribute to Genomic Instability in Cancer. Int J Mol Sci 2017; 18:E1138. [PMID: 28587102 PMCID: PMC5485962 DOI: 10.3390/ijms18061138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 12/14/2022] Open
Abstract
Cancer and genomic instability are highly impacted by the deoxyribonucleic acid (DNA) replication program. Inaccuracies in DNA replication lead to the increased acquisition of mutations and structural variations. These inaccuracies mainly stem from loss of DNA fidelity due to replication stress or due to aberrations in the temporal organization of the replication process. Here we review the mechanisms and impact of these major sources of error to the replication program.
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Affiliation(s)
- Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Micha Ben-Zimra
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
- Pharmacology and Experimental Therapeutics Unit, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
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17
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Lee JK, Choi YL, Kwon M, Park PJ. Mechanisms and Consequences of Cancer Genome Instability: Lessons from Genome Sequencing Studies. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 11:283-312. [PMID: 26907526 DOI: 10.1146/annurev-pathol-012615-044446] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During tumor evolution, cancer cells can accumulate numerous genetic alterations, ranging from single nucleotide mutations to whole-chromosomal changes. Although a great deal of progress has been made in the past decades in characterizing genomic alterations, recent cancer genome sequencing studies have provided a wealth of information on the detailed molecular profiles of such alterations in various types of cancers. Here, we review our current understanding of the mechanisms and consequences of cancer genome instability, focusing on the findings uncovered through analysis of exome and whole-genome sequencing data. These analyses have shown that most cancers have evidence of genome instability, and the degree of instability is variable within and between cancer types. Importantly, we describe some recent evidence supporting the idea that chromosomal instability could be a major driving force in tumorigenesis and cancer evolution, actively shaping the genomes of cancer cells to maximize their survival advantage.
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Affiliation(s)
- June-Koo Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea;
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, South Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology (SAIHST), Sungkyunkwan University School of Medicine, Seoul 06351, South Korea;
| | - Mijung Kwon
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115;
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115;
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18
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Xue J, Yang G, Ding H, Wang P, Wang C. Role of NSC319726 in ovarian cancer based on the bioinformatics analyses. Onco Targets Ther 2016; 8:3757-65. [PMID: 26719703 PMCID: PMC4689271 DOI: 10.2147/ott.s86343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim This study aimed to explore the molecular mechanisms of NSC319726 in ovarian cancer by bioinformatics analyses. Methods Gene expression profile GSE35972 was downloaded from the Gene Expression Omnibus database. The data set contains six samples, including three samples of TOV112D cells untreated and three samples of TOV112D cells treated with NSC319726. The differentially expressed genes (DEGs) between untreated and treated samples were analyzed using the limma package. Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed using the signaling pathway impact analysis package, followed by the functional annotation of DEGs and protein–protein interaction network construction. Finally, the subnetwork was identified, and Gene Ontology functional enrichment analysis was performed on the DEGs enriched in the subnetwork. Results A total of 120 upregulated and 126 downregulated DEGs were identified. Six Kyoto Encyclopedia of Genes and Genomes pathways were significantly perturbed by DEGs, and the pathway of oocyte meiosis was identified as the most perturbed one. Oocyte meiosis was enriched by eight downregulated DEGs, such as ribosomal protein S6 kinase, 90 kDa, and polypeptide 6 (RPS6KA6). After functional annotation, eight transcription factors were upregulated (such as B-cell CLL/lymphoma 6 [BCL6]), and three transcription factors were downregulated. Seven tumor suppressor genes, such as forkhead box O3 (FOXO3), were upregulated. Additionally, in the protein–protein interaction network and subnetwork, cyclin B1 (CCNB1) and cell division cycle 20 (CDC20) were hub genes, which were also involved in the functions related to mitotic cell cycle. Conclusion NSC319726 may play an efficient role against ovarian cancer via targeting genes, such as RPS6KA6, BCL6, FOXO3, CCNB1, and CDC20, which are involved in oocyte meiosis pathway.
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Affiliation(s)
- Ji Xue
- Department of Chinese Medicine, The Second Hospital of Jilin University, People's Republic of China
| | - Guang Yang
- Department of Chinese Medicine, The Second Hospital of Jilin University, People's Republic of China
| | - Hong Ding
- Department of Chinese Medicine, The Second Hospital of Jilin University, People's Republic of China
| | - Pu Wang
- The Clinical Medical College of Jilin University (Grade 2013), People's Republic of China
| | - Changhong Wang
- Department of Chinese Medicine, China-Japan Union Hospital of Jilin University, Changchun City, People's Republic of China
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19
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Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR. APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions. Cell Rep 2015; 13:1103-1109. [PMID: 26527001 DOI: 10.1016/j.celrep.2015.09.077] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 08/11/2015] [Accepted: 09/25/2015] [Indexed: 10/22/2022] Open
Abstract
An antiviral component of the human innate immune system-the APOBEC cytidine deaminases-was recently identified as a prominent source of mutations in cancers. Here, we investigated the distribution of APOBEC-induced mutations across the genomes of 119 breast and 24 lung cancer samples. While the rate of most mutations is known to be elevated in late-replicating regions that are characterized by reduced chromatin accessibility and low gene density, we observed a marked enrichment of APOBEC mutations in early-replicating regions. This unusual mutagenesis profile may be associated with a higher propensity to form single-strand DNA substrates for APOBEC enzymes in early-replicating regions and should be accounted for in statistical analyses of cancer genome mutation catalogs aimed at understanding the mechanisms of carcinogenesis as well as highlighting genes that are significantly mutated in cancer.
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Affiliation(s)
- Marat D Kazanov
- Research and Training Center on Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow 127051, Russia
| | - Steven A Roberts
- National Institute of Environmental Health Sciences, Durham, NC 27709, USA; School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Paz Polak
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John Stamatoyannopoulos
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Leszek J Klimczak
- National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Dmitry A Gordenin
- National Institute of Environmental Health Sciences, Durham, NC 27709, USA.
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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20
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Managing Single-Stranded DNA during Replication Stress in Fission Yeast. Biomolecules 2015; 5:2123-39. [PMID: 26393661 PMCID: PMC4598791 DOI: 10.3390/biom5032123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 01/27/2023] Open
Abstract
Replication fork stalling generates a variety of responses, most of which cause an increase in single-stranded DNA. ssDNA is a primary signal of replication distress that activates cellular checkpoints. It is also a potential source of genome instability and a substrate for mutation and recombination. Therefore, managing ssDNA levels is crucial to chromosome integrity. Limited ssDNA accumulation occurs in wild-type cells under stress. In contrast, cells lacking the replication checkpoint cannot arrest forks properly and accumulate large amounts of ssDNA. This likely occurs when the replication fork polymerase and helicase units are uncoupled. Some cells with mutations in the replication helicase (mcm-ts) mimic checkpoint-deficient cells, and accumulate extensive areas of ssDNA to trigger the G2-checkpoint. Another category of helicase mutant (mcm4-degron) causes fork stalling in early S-phase due to immediate loss of helicase function. Intriguingly, cells realize that ssDNA is present, but fail to detect that they accumulate ssDNA, and continue to divide. Thus, the cellular response to replication stalling depends on checkpoint activity and the time that replication stress occurs in S-phase. In this review we describe the signs, signals, and symptoms of replication arrest from an ssDNA perspective. We explore the possible mechanisms for these effects. We also advise the need for caution when detecting and interpreting data related to the accumulation of ssDNA.
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21
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Kumar Y, Yang J, Hu T, Chen L, Xu Z, Xu L, Hu XX, Tang G, Wang JM, Li Y, Poon WS, Wan W, Zhang L, Mat WK, Pun FW, Lee P, Cheong THY, Ding X, Ng SK, Tsang SY, Chen JF, Zhang P, Li S, Wang HY, Xue H. Massive interstitial copy-neutral loss-of-heterozygosity as evidence for cancer being a disease of the DNA-damage response. BMC Med Genomics 2015. [PMID: 26208496 PMCID: PMC4515014 DOI: 10.1186/s12920-015-0104-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background The presence of loss-of-heterozygosity (LOH) mutations in cancer cell genomes is commonly encountered. Moreover, the occurrences of LOHs in tumor suppressor genes play important roles in oncogenesis. However, because the causative mechanisms underlying LOH mutations in cancer cells yet remain to be elucidated, enquiry into the nature of these mechanisms based on a comprehensive examination of the characteristics of LOHs in multiple types of cancers has become a necessity. Methods We performed next-generation sequencing on inter-Alu sequences of five different types of solid tumors and acute myeloid leukemias, employing the AluScan platform which entailed amplification of such sequences using multiple PCR primers based on the consensus sequences of Alu elements; as well as the whole genome sequences of a lung-to-liver metastatic cancer and a primary liver cancer. Paired-end sequencing reads were aligned to the reference human genome to identify major and minor alleles so that the partition of LOH products between homozygous-major vs. homozygous-minor alleles could be determined at single-base resolution. Strict filtering conditions were employed to avoid false positives. Measurements of LOH occurrences in copy number variation (CNV)-neutral regions were obtained through removal of CNV-associated LOHs. Results We found: (a) average occurrence of copy-neutral LOHs amounting to 6.9 % of heterologous loci in the various cancers; (b) the mainly interstitial nature of the LOHs; and (c) preference for formation of homozygous-major over homozygous-minor, and transitional over transversional, LOHs. Conclusions The characteristics of the cancer LOHs, observed in both AluScan and whole genome sequencings, point to the formation of LOHs through repair of double-strand breaks by interhomolog recombination, or gene conversion, as the consequence of a defective DNA-damage response, leading to a unified mechanism for generating the mutations required for oncogenesis as well as the progression of cancer cells. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0104-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yogesh Kumar
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Jianfeng Yang
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Taobo Hu
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Lei Chen
- Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China.
| | - Zhi Xu
- Department of Oncology, Nanjing First Hospital, and Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Lin Xu
- Jiangsu Key Laboratory of Cancer Molecular Biology and Translational Medicine, Jiangsu Cancer Hospital, Nanjing, China.
| | - Xiao-Xia Hu
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China.
| | - Gusheng Tang
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China.
| | - Jian-Min Wang
- Department of Hematology, Changhai Hospital, Second Military Medical University, Shanghai, China.
| | - Yi Li
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China.
| | - Wai-Sang Poon
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China.
| | - Weiqing Wan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.
| | - Wai-Kin Mat
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Frank W Pun
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Peggy Lee
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Timothy H Y Cheong
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Xiaofan Ding
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Siu-Kin Ng
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Shui-Ying Tsang
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Jin-Fei Chen
- Department of Oncology, Nanjing First Hospital, and Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Peng Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, and Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Shao Li
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, and Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Hong-Yang Wang
- Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China.
| | - Hong Xue
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
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22
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Koren A, Handsaker RE, Kamitaki N, Karlić R, Ghosh S, Polak P, Eggan K, McCarroll SA. Genetic variation in human DNA replication timing. Cell 2014; 159:1015-1026. [PMID: 25416942 PMCID: PMC4359889 DOI: 10.1016/j.cell.2014.10.025] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
Abstract
Genomic DNA replicates in a choreographed temporal order that impacts the distribution of mutations along the genome. We show here that DNA replication timing is shaped by genetic polymorphisms that act in cis upon megabase-scale DNA segments. In genome sequences from proliferating cells, read depth along chromosomes reflected DNA replication activity in those cells. We used this relationship to analyze variation in replication timing among 161 individuals sequenced by the 1000 Genomes Project. Genome-wide association of replication timing with genetic variation identified 16 loci at which inherited alleles associate with replication timing. We call these "replication timing quantitative trait loci" (rtQTLs). rtQTLs involved the differential use of replication origins, exhibited allele-specific effects on replication timing, and associated with gene expression variation at megabase scales. Our results show replication timing to be shaped by genetic polymorphism and identify a means by which inherited polymorphism regulates the mutability of nearby sequences.
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Affiliation(s)
- Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rosa Karlić
- Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, 10000 Zagreb, Croatia
| | - Sulagna Ghosh
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, The Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Paz Polak
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Cancer Center and Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, The Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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23
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Aghili L, Foo J, DeGregori J, De S. Patterns of somatically acquired amplifications and deletions in apparently normal tissues of ovarian cancer patients. Cell Rep 2014; 7:1310-9. [PMID: 24794429 DOI: 10.1016/j.celrep.2014.03.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/06/2014] [Accepted: 03/28/2014] [Indexed: 12/20/2022] Open
Abstract
Little is understood about the occurrence of somatic genomic alterations in normal tissues and their significance in the context of disease. Here, we identified potential somatic copy number alterations (pSCNAs) in apparently normal ovarian tissue and peripheral blood of 423 ovarian cancer patients. There were, on average, two to four pSCNAs per sample detectable at a tissue-level resolution, although some individuals had orders of magnitude more. Accordingly, we estimated the lower bound of the rate of pSCNAs per cell division. Older individuals and BRCA mutation carriers had more pSCNAs than others. pSCNAs significantly overlapped with Alu and G-quadruplexes, and the affected genes were enriched for signaling and regulation. Some of the amplification/deletion hotspots in pan-cancer genomes were hot spots of pSCNAs in normal tissues as well, suggesting that those regions might be inherently unstable. Prevalence of pSCNA in peripheral blood predicted survival, implying that mutations in normal tissues might have consequences for cancer patients.
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Affiliation(s)
- Leila Aghili
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jasmine Foo
- School of Mathematics, University of Minnesota, Minneapolis, MN 55455, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO 80045, USA
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO 80045, USA; Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA.
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24
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Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair. Proc Natl Acad Sci U S A 2014; 111:E924-32. [PMID: 24556991 DOI: 10.1073/pnas.1400236111] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
DNA nicks are the most common form of DNA damage, and if unrepaired can give rise to genomic instability. In human cells, nicks are efficiently repaired via the single-strand break repair pathway, but relatively little is known about the fate of nicks not processed by that pathway. Here we show that homology-directed repair (HDR) at nicks occurs via a mechanism distinct from HDR at double-strand breaks (DSBs). HDR at nicks, but not DSBs, is associated with transcription and is eightfold more efficient at a nick on the transcribed strand than at a nick on the nontranscribed strand. HDR at nicks can proceed by a pathway dependent upon canonical HDR factors RAD51 and BRCA2; or by an efficient alternative pathway that uses either ssDNA or nicked dsDNA donors and that is strongly inhibited by RAD51 and BRCA2. Nicks generated by either I-AniI or the CRISPR/Cas9(D10A) nickase are repaired by the alternative HDR pathway with little accompanying mutagenic end-joining, so this pathway may be usefully applied to genome engineering. These results suggest that alternative HDR at nicks may be stimulated in physiological contexts in which canonical RAD51/BRCA2-dependent HDR is compromised or down-regulated, which occurs frequently in tumors.
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