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Farnoosh G, Saeedi-Boroujeni A, Jalali A, Keikhaei B, Mahmoudian-Sani MR. Polymorphisms in genes involved in breast cancer among Iranian patients. Per Med 2021; 18:153-169. [PMID: 33565318 DOI: 10.2217/pme-2020-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review gives a summary of the important genetic polymorphisms in breast cancer with a focus on people in Iran. Several single nucleotide polymorphisms were considered as breast cancer susceptibility polymorphisms within genes (STK15, ERRs, ESR1, p53, SEP15, AURKA, SHBG, SRC, FAS, VEGF, XRCC1, GST, NFκB1, XPC, XRCC3, sirtuin-3, NKG2D). Cytosine-adenine repeat (IGF-I), rs3877899, G-2548A, GGC (eRF3a/GSPT1), IVS2nt-124A/G have shown an increased risk of breast cancers and a decreased risk has been observed in 4G/5G (PAI-1), rs6505162, tri-nucleotide (GCG TGFBR1). We observed that the signaling pathways and antioxidant related genes are the main molecular processes associated with breast cancer progression. Further studies on types of polymorphisms in breast cancer could validate the prognostic value of biomarkers.
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Affiliation(s)
- Gholamreza Farnoosh
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Saeedi-Boroujeni
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Immunology Today, Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Akram Jalali
- Department of Molecular Medicine & Genetics, School of Medicine Hamadan University of Medical Sciences
| | - Bijan Keikhaei
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad-Reza Mahmoudian-Sani
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Barba D, León-Sosa A, Lugo P, Suquillo D, Torres F, Surre F, Trojman L, Caicedo A. Breast cancer, screening and diagnostic tools: All you need to know. Crit Rev Oncol Hematol 2020; 157:103174. [PMID: 33249359 DOI: 10.1016/j.critrevonc.2020.103174] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/18/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is one of the most frequent malignancies among women worldwide. Methods for screening and diagnosis allow health care professionals to provide personalized treatments that improve the outcome and survival. Scientists and physicians are working side-by-side to develop evidence-based guidelines and equipment to detect cancer earlier. However, the lack of comprehensive interdisciplinary information and understanding between biomedical, medical, and technology professionals makes innovation of new screening and diagnosis tools difficult. This critical review gathers, for the first time, information concerning normal breast and cancer biology, established and emerging methods for screening and diagnosis, staging and grading, molecular and genetic biomarkers. Our purpose is to address key interdisciplinary information about these methods for physicians and scientists. Only the multidisciplinary interaction and communication between scientists, health care professionals, technical experts and patients will lead to the development of better detection tools and methods for an improved screening and early diagnosis.
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Affiliation(s)
- Diego Barba
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Instituto de Investigaciones en Biomedicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador
| | - Ariana León-Sosa
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Instituto de Investigaciones en Biomedicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador
| | - Paulina Lugo
- Hospital de los Valles HDLV, Quito, Ecuador; Fundación Ayuda Familiar y Comunitaria AFAC, Quito, Ecuador
| | - Daniela Suquillo
- Instituto de Investigaciones en Biomedicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Ingeniería en Procesos Biotecnológicos, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Fernando Torres
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Hospital de los Valles HDLV, Quito, Ecuador
| | - Frederic Surre
- University of Glasgow, James Watt School of Engineering, Glasgow, G12 8QQ, United Kingdom
| | - Lionel Trojman
- LISITE, Isep, 75006, Paris, France; Universidad San Francisco de Quito USFQ, Colegio de Ciencias e Ingenierías Politécnico - USFQ, Instituto de Micro y Nanoelectrónica, IMNE, USFQ, Quito, Ecuador
| | - Andrés Caicedo
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Instituto de Investigaciones en Biomedicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Sistemas Médicos SIME, Universidad San Francisco de Quito USFQ, Quito, Ecuador.
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Bagshaw AT. Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes. Genome Biol Evol 2017; 9:2428-2443. [PMID: 28957459 PMCID: PMC5622345 DOI: 10.1093/gbe/evx164] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2017] [Indexed: 02/06/2023] Open
Abstract
Microsatellite repeat DNA is best known for its length mutability, which is implicated in several neurological diseases and cancers, and often exploited as a genetic marker. Less well-known is the body of work exploring the widespread and surprisingly diverse functional roles of microsatellites. Recently, emerging evidence includes the finding that normal microsatellite polymorphism contributes substantially to the heritability of human gene expression on a genome-wide scale, calling attention to the task of elucidating the mechanisms involved. At present, these are underexplored, but several themes have emerged. I review evidence demonstrating roles for microsatellites in modulation of transcription factor binding, spacing between promoter elements, enhancers, cytosine methylation, alternative splicing, mRNA stability, selection of transcription start and termination sites, unusual structural conformations, nucleosome positioning and modification, higher order chromatin structure, noncoding RNA, and meiotic recombination hot spots.
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Azad AK, Bairati I, Qiu X, Girgis H, Cheng L, Waggott D, Cheng D, Mirshams M, Ho J, Fortin A, Vigneault E, Huang SH, O'Sullivan B, Waldron J, Boutros PC, Goldstein D, Meyer F, Xu W, Liu G. A genome-wide association study of non-HPV-related head and neck squamous cell carcinoma identifies prognostic genetic sequence variants in the MAP-kinase and hormone pathways. Cancer Epidemiol 2016; 42:173-80. [PMID: 27173062 DOI: 10.1016/j.canep.2016.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/26/2016] [Accepted: 05/02/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Carcinomas of the oral cavity, pharynx and larynx are referred to as head and neck cancers (HNC); together they account for 2-3% of all newly diagnosed cancers in North America. Between 40-50% of HNC are early diagnosed at stages I-II. The 5-year and 10-year relative survival rates are 61% and 50%, respectively. Germline genetic sequence variants (GSV) have become increasingly found to have prognostic implications in a variety of cancers. Identifying these variants may have important clinical and biological implications. METHODS We conducted a genome-wide association study (GWAS) in 531 Stage I-II radiation-treated HNC patients (originally recruited for α-tocopherol/β-carotene placebo-controlled secondary prevention study) and used a replication cohort of 566 HNC patients of all stages, of mostly non-HPV-related cancers. Survival rates were estimated by the Kaplan-Meier method. Cox proportional hazards models adjusted for potential clinical factors and principal components were used to test for associations between the GSV and overall survival (OS) in these tumors. RESULTS The median follow-up time for OS was 9.21 years (GWAS cohort) and 2.37 years (replication cohort). In both cohorts, CACNA2D1:rs2299187, ESRRG:rs946465 and ESRRG:rs1416612 were each individually significantly associated with survival. In silico analysis of ESRRG:rs946465 identifies that it produces a splice variant in ESRRG. Variant alleles of CACNA2D1:rs2299187 and ESRRG:rs946465 were associated with higher expression of the corresponding protein. CONCLUSIONS Putatively functional polymorphisms in the MAP-Kinase and estrogen pathways, identified through GWAS and replicated in an independent dataset were associated with the survival of HNC patients.
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Affiliation(s)
- Abul Kalam Azad
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Isabelle Bairati
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Xin Qiu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Hala Girgis
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lu Cheng
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daryl Waggott
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Dangxiao Cheng
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maryam Mirshams
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - James Ho
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - André Fortin
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Eric Vigneault
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Shao-Hui Huang
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Brian O'Sullivan
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - John Waldron
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada,; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada,; Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada
| | - David Goldstein
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Francois Meyer
- Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Wei Xu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Geoffrey Liu
- Ontario Cancer Institute and Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada,; Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA.
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Warburton A, Breen G, Rujescu D, Bubb VJ, Quinn JP. Characterization of a REST-Regulated Internal Promoter in the Schizophrenia Genome-Wide Associated Gene MIR137. Schizophr Bull 2015; 41:698-707. [PMID: 25154622 PMCID: PMC4393679 DOI: 10.1093/schbul/sbu117] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MIR137 has been identified as a candidate gene for schizophrenia from genome-wide association studies via association with an intronic single nucleotide polymorphism (SNP), rs1625579. The location of the SNP suggests one mechanism in which transcriptional or posttranscriptional regulation of miR-137 expression could underlie schizophrenia. We identified and validated a novel promoter of the MIR137 gene adjacent to miR-137 itself which can direct the expression of distinct mRNA isoforms encoding miR-137. Analysis of both endogenous gene expression and reporter gene assays determined that this internal promoter is regulated by repressor element-1 silencing transcription factor (REST), which has previously been associated with pathways linked to schizophrenia. Distinct isoforms of REST mediate differential expression at this locus, suggesting the relative levels of these isoforms are important for miR-137 expression profiles. The internal promoter contains a variable number tandem repeat (VNTR) domain adjacent to the pre-miR-137 sequence. The reporter gene activity directed by this promoter was modified by the genotype of the VNTR. Differential expression was also observed in response to cocaine, which is known to regulate the REST pathway in SH-SY5Y cells. Our data support the hypothesis that a "gene × environment" interaction could modify the level of miR-137 expression via this internal promoter and that the genotype of the VNTR could modulate transcriptional responses. We demonstrate that this promoter region is not in disequilibrium with rs1625579 and therefore would supply a distinct pathway to potentially alter miR-137 levels in response to environmental cues.
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Affiliation(s)
- Alix Warburton
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK;
| | - Gerome Breen
- King’s College London, MRC Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, London, UK; ,National Institute for Health Research (NIHR), Biomedical Research Centre for Mental Health, South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King’s College London SE5 8DF, UK;
| | - Dan Rujescu
- Department of Psychiatry, University of Halle-Wittenberg, Halle, Germany
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK;
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK; ,*To whom correspondence should be addressed; Department of Molecular and Clinical Pharmacology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK; tel: +44-151-794-5498, fax: +44-151-794-5517, e-mail:
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Roshan-Moniri M, Hsing M, Butler MS, Cherkasov A, Rennie PS. Orphan nuclear receptors as drug targets for the treatment of prostate and breast cancers. Cancer Treat Rev 2015; 40:1137-52. [PMID: 25455729 DOI: 10.1016/j.ctrv.2014.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 02/06/2023]
Abstract
Nuclear receptors (NRs), a family of 48 transcriptional factors, have been studied intensively for their roles in cancer development and progression. The presence of distinctive ligand binding sites capable of interacting with small molecules has made NRs attractive targets for developing cancer therapeutics. In particular, a number of drugs have been developed over the years to target human androgen- and estrogen receptors for the treatment of prostate cancer and breast cancer. In contrast, orphan nuclear receptors (ONRs), which in many cases lack known biological functions or ligands, are still largely under investigated. This review is a summary on ONRs that have been implicated in prostate and breast cancers, specifically retinoic acid-receptor-related orphan receptors (RORs), liver X receptors (LXRs), chicken ovalbumin upstream promoter transcription factors (COUP-TFs), estrogen related receptors (ERRs), nerve growth factor 1B-like receptors, and ‘‘dosage-sensitive sex reversal, adrenal hypoplasia critical region, on chromosome X, gene 1’’ (DAX1). Discovery and development of small molecules that can bind at various functional sites on these ONRs will help determine their biological functions. In addition, these molecules have the potential to act as prototypes for future drug development. Ultimately, the therapeutic value of targeting the ONRs may go well beyond prostate and breast cancers.
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Misawa A, Inoue S. Estrogen-Related Receptors in Breast Cancer and Prostate Cancer. Front Endocrinol (Lausanne) 2015; 6:83. [PMID: 26074877 PMCID: PMC4443769 DOI: 10.3389/fendo.2015.00083] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/05/2015] [Indexed: 01/23/2023] Open
Abstract
Estrogen-signaling pathways are implicated in the development of breast cancer and prostate cancer. Various studies have focused on additional signaling pathways, mediated by estrogen-related receptors (ERRs). ERRs are constitutively active receptors that share a high degree of homology with the classical estrogen receptors (ERs). However, they do not bind to estrogen, while ERs do. ERRs are involved in the development of alternative pathways that lead to the development of cancer and are regarded as potential therapeutic targets for the treatment of breast cancer and prostate cancer that do not respond to conventional therapies. In this review, we first present general structural features of ERRs. Then, we focus on breast cancer and prostate cancer, which are primarily hormone-dependent cancers, and summarizes recent progress in elucidating the involvement of each ERR in these two types of malignancies.
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Affiliation(s)
- Aya Misawa
- Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Inoue
- Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
- *Correspondence: Satoshi Inoue, Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8655, Japan,
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Quinn JP, Warburton A, Myers P, Savage AL, Bubb VJ. Polymorphic variation as a driver of differential neuropeptide gene expression. Neuropeptides 2013; 47:395-400. [PMID: 24210140 DOI: 10.1016/j.npep.2013.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 11/15/2022]
Abstract
The regulation of neuropeptide gene expression and their receptors in a tissue specific and stimulus inducible manner will determine in part behaviour and physiology. This can be a dynamic process resulting from short term changes in response to the environment or long term modulation imposed by epigenetically determined mechanisms established during life experiences. The latter underpins what is termed 'nature and nurture, or 'gene×environment interactions'. Dynamic gene expression of neuropeptides or their receptors is a key component of signalling in the CNS and their inappropriate regulation is therefore a predicted target underpinning psychiatric disorders and neuropathological processes. Finding the regulatory domains within our genome which have the potential to direct gene expression is a difficult challenge as 98% of our genome is non-coding and, with the exception of proximal promoter regions, such elements can be quite distant from the gene that they regulate. This review will deal with how we can find such domains by addressing both the most conserved non-exonic regions in the genome using comparative genomics and the most recent or constantly evolving DNA such as repetitive DNA or retrotransposons. We shall also explore how polymorphic changes in such domains can be associated with CNS disorders by altering the appropriate gene expression patterns which maintain normal physiology.
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Affiliation(s)
- John P Quinn
- Neurogenetics in Wellbeing and Disease Section, Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Sherrington Building, Ashton Street, Liverpool L69 3GE, UK.
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Karimi P, Hematti S, Safari F, Tavassoli M. Polymorphic AAAG repeat length in estrogen-related receptor gamma (ERRγ) and risk of breast cancer in Iranian women. Cancer Invest 2013; 31:600-3. [PMID: 24125170 DOI: 10.3109/07357907.2013.845672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Estrogen-related receptors (ERRs) alpha, beta, and gamma are orphan nuclear receptors that modulate the estrogen signaling pathway and play roles in the regulation of breast cancer cell growth. To determine the association between breast cancer risk and alleles of the tetranucleotide repeat (AAAG)n in the intron of ERRγ gene, a case-control study of 200 breast cancer patients and 200 controls was performed in Iranian women. Our results demonstrate that women with short AAAG repeat are at higher risk of breast cancer (OR 7). This result suggests a possible involvement of polymorphic AAAG repeat of ERRγ gene in regulating its expression.
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Affiliation(s)
- Padideh Karimi
- Department of Biology, Faculty of Sciences, University of Isfahan, Hezar-Jarib, Isfahan, Iran,1
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McIver LJ, McCormick JF, Martin A, Fondon JW, Garner HR. Population-scale analysis of human microsatellites reveals novel sources of exonic variation. Gene 2012; 516:328-34. [PMID: 23274653 DOI: 10.1016/j.gene.2012.12.068] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 12/15/2012] [Indexed: 11/29/2022]
Abstract
Using our microsatellite specific genotyping method, we analyzed tandem repeats, which are known to be highly variable with some recognized as biomarkers causative of disease, in over 500 individuals who were exon sequenced in a 1000 Genomes Project pilot study. We were able to genotype over 97% of the microsatellite loci in the targeted regions. A total of 25,115 variations were observed, including repeat length and single nucleotide polymorphisms, corresponding to an average of 45.6 variations per individual and a density of 1.1 variations per kilobase. Standard variant detection did not report 94.2% of the exonic repeat length variations in part because the alignment techniques are not ideal for repetitive regions. Additionally some standard variation detection tools rely on a database of known variations, making them less likely to call repeat length variations as only a small percent of these loci (~6000) have been accurately characterized. A subset of the hundreds of non-synonymous variations we identified was experimentally validated, indicating an accuracy of 96.5% for our microsatellite-based genotyping method, with some novel variants identified in genes associated with cancer. We propose that microsatellite-based genotyping be used as a part of large scale sequencing studies to identify novel variants.
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Affiliation(s)
- L J McIver
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
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Campregher C, Schmid G, Ferk F, Knasmüller S, Khare V, Kortüm B, Dammann K, Lang M, Scharl T, Spittler A, Roig AI, Shay JW, Gerner C, Gasche C. MSH3-deficiency initiates EMAST without oncogenic transformation of human colon epithelial cells. PLoS One 2012; 7:e50541. [PMID: 23209772 PMCID: PMC3507781 DOI: 10.1371/journal.pone.0050541] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 10/25/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND/AIM Elevated microsatellite instability at selected tetranucleotide repeats (EMAST) is a genetic signature in certain cases of sporadic colorectal cancer and has been linked to MSH3-deficiency. It is currently controversial whether EMAST is associated with oncogenic properties in humans, specifically as cancer development in Msh3-deficient mice is not enhanced. However, a mutator phenotype is different between species as the genetic positions of repetitive sequences are not conserved. Here we studied the molecular effects of human MSH3-deficiency. METHODS HCT116 and HCT116+chr3 (both MSH3-deficient) and primary human colon epithelial cells (HCEC, MSH3-wildtype) were stably transfected with an EGFP-based reporter plasmid for the detection of frameshift mutations within an [AAAG]17 repeat. MSH3 was silenced by shRNA and changes in protein expression were analyzed by shotgun proteomics. Colony forming assay was used to determine oncogenic transformation and double strand breaks (DSBs) were assessed by Comet assay. RESULTS Despite differential MLH1 expression, both HCT116 and HCT116+chr3 cells displayed comparable high mutation rates (about 4×10(-4)) at [AAAG]17 repeats. Silencing of MSH3 in HCECs leads to a remarkable increased frameshift mutations in [AAAG]17 repeats whereas [CA]13 repeats were less affected. Upon MSH3-silencing, significant changes in the expression of 202 proteins were detected. Pathway analysis revealed overexpression of proteins involved in double strand break repair (MRE11 and RAD50), apoptosis, L1 recycling, and repression of proteins involved in metabolism, tRNA aminoacylation, and gene expression. MSH3-silencing did not induce oncogenic transformation and DSBs increased 2-fold. CONCLUSIONS MSH3-deficiency in human colon epithelial cells results in EMAST, formation of DSBs and significant changes of the proteome but lacks oncogenic transformation. Thus, MSH3-deficiency alone is unlikely to drive human colon carcinogenesis.
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Affiliation(s)
- Christoph Campregher
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Gerald Schmid
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Franziska Ferk
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Siegfried Knasmüller
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Vineeta Khare
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Benedikt Kortüm
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Kyle Dammann
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Michaela Lang
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Theresa Scharl
- ACIB GmbH, c/o Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Statistics and Probability Theory, University of Technology, Vienna, Austria
| | - Andreas Spittler
- Department of Surgery, Research Laboratories & Core Facility Flow Cytometry, Medical University of Vienna, Vienna, Austria
| | - Andres I. Roig
- Department of Cell Biology, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jerry W. Shay
- Department of Cell Biology, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Christopher Gerner
- Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christoph Gasche
- Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria
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Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 2011; 32:1075-99. [PMID: 21853507 PMCID: PMC3177966 DOI: 10.1002/humu.21557] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/17/2011] [Indexed: 12/21/2022]
Abstract
Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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