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Szczepanek J, Skorupa M, Jarkiewicz-Tretyn J, Cybulski C, Tretyn A. Harnessing Epigenetics for Breast Cancer Therapy: The Role of DNA Methylation, Histone Modifications, and MicroRNA. Int J Mol Sci 2023; 24:ijms24087235. [PMID: 37108398 PMCID: PMC10138995 DOI: 10.3390/ijms24087235] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/24/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Breast cancer exhibits various epigenetic abnormalities that regulate gene expression and contribute to tumor characteristics. Epigenetic alterations play a significant role in cancer development and progression, and epigenetic-targeting drugs such as DNA methyltransferase inhibitors, histone-modifying enzymes, and mRNA regulators (such as miRNA mimics and antagomiRs) can reverse these alterations. Therefore, these epigenetic-targeting drugs are promising candidates for cancer treatment. However, there is currently no effective epi-drug monotherapy for breast cancer. Combining epigenetic drugs with conventional therapies has yielded positive outcomes and may be a promising strategy for breast cancer therapy. DNA methyltransferase inhibitors, such as azacitidine, and histone deacetylase inhibitors, such as vorinostat, have been used in combination with chemotherapy to treat breast cancer. miRNA regulators, such as miRNA mimics and antagomiRs, can alter the expression of specific genes involved in cancer development. miRNA mimics, such as miR-34, have been used to inhibit tumor growth, while antagomiRs, such as anti-miR-10b, have been used to inhibit metastasis. The development of epi-drugs that target specific epigenetic changes may lead to more effective monotherapy options in the future.
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Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Monika Skorupa
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
| | | | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-204 Szczecin, Poland
| | - Andrzej Tretyn
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
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2
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Chhichholiya Y, Suryan AK, Suman P, Munshi A, Singh S. SNPs in miRNAs and Target Sequences: Role in Cancer and Diabetes. Front Genet 2021; 12:793523. [PMID: 34925466 PMCID: PMC8673831 DOI: 10.3389/fgene.2021.793523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/28/2021] [Indexed: 12/27/2022] Open
Abstract
miRNAs are fascinating molecular players for gene regulation as individual miRNA can control multiple targets and a single target can be regulated by multiple miRNAs. Loss of miRNA regulated gene expression is often reported to be implicated in various human diseases like diabetes and cancer. Recently, geneticists across the world started reporting single nucleotide polymorphism (SNPs) in seed sequences of miRNAs. Similarly, SNPs are also reported in various target sequences of these miRNAs. Both the scenarios lead to dysregulated gene expression which may result in the progression of diseases. In the present paper, we explore SNPs in various miRNAs and their target sequences reported in various human cancers as well as diabetes. Similarly, we also present evidence of these mutations in various other human diseases.
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Affiliation(s)
- Yogita Chhichholiya
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Aman Kumar Suryan
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Prabhat Suman
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Sandeep Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
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3
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Sánchez-Chaparro MM, Garza-Veloz I, Zayas-Villanueva OA, Martinez-Fierro ML, Delgado-Enciso I, Gomez-Govea MA, Martínez-de-Villarreal LE, Reséndez-Pérez D, Rodríguez-Sánchez IP. Genetic Variants in the 3'UTR of BRCA1 and BRCA2 Genes and their Putative Effects on the microRNA Mechanism in Hereditary Breast and Ovarian Cancer. Diagnostics (Basel) 2020; 10:diagnostics10050298. [PMID: 32414209 PMCID: PMC7277914 DOI: 10.3390/diagnostics10050298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/01/2020] [Accepted: 04/10/2020] [Indexed: 12/31/2022] Open
Abstract
Hereditary breast and ovarian cancer (HBOC) syndrome is mainly caused by mutations in the BRCA1 and BRCA2 genes. The 3’UTR region allows for the binding of microRNAs, which are involved in genetic tune regulation. We aimed to identify allelic variants on 3’UTR miRNA-binding sites in the BRCA1 and BRCA2 genes in HBOC patients. Blood samples were obtained from 50 patients with HBOC and from 50 controls. The 3’UTR regions of BRCA1 and BRCA2 were amplified by PCR and sequenced to identify genetic variants using bioinformatics tools. We detected nine polymorphisms in 3’UTR, namely: four in BRCA1 (rs3092995 (C/G), rs8176318 (C/T), rs111791349 (G/A), and rs12516 (C/T)) and five in BRCA2 (rs15869 (A/C), rs7334543 (A/G), rs1157836 (A/G), and rs75353978 (TT/del TT)). A new variant in position c.*457 (A/C) on 3’UTR of BRCA2 was also identified. The following three variants increased the risk of HBOC in the study population: rs111791349-A, rs15869-C, and c.*457-C (odds ratio (OR) range 3.7–15.4; p < 0.05). Genetic variants into the 3’UTR of BRCA1 and BRCA2 increased the risk of HBOC between 3.7–15.4 times in the study population. The presence/absence of these polymorphisms may influence the loss/creation of miRNA binding sites, such as hsa-miR-1248 in BRCA1 3′UTR or the hsa-miR-548 family binding site in BRCA2. Our results add new evidence of miRNA participation in the pathogenesis of HBOC.
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Affiliation(s)
- María Marisela Sánchez-Chaparro
- Laboratory of Immunology and Virology, Collage of Biological Sciences, Universidad Autónoma de Nuevo Leon, San Nicolas de los Garza, Nuevo Leon 66451, Mexico; (M.M.S.-C.); (D.R.-P.)
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Human Medicine and HS Academic Unit, Universidad Autonoma de Zacatecas, Zacatecas, Zacatecas 98160, Mexico;
| | - Omar Alejandro Zayas-Villanueva
- University Center Against Cancer (CUCC), Hospital Universitario “Dr. José E. González”, Collage of Medicine, Universidad Autónoma de Nuevo Leon, Monterrey, Nuevo Leon 64460, Mexico;
| | - Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Human Medicine and HS Academic Unit, Universidad Autonoma de Zacatecas, Zacatecas, Zacatecas 98160, Mexico;
- Correspondence: (M.L.M.-F.); (I.P.R.-S.); Tel.: +52-492-925-6690 (M.L.M.-F.); +52-818-329-4217 (I.P.R.-S.)
| | - Iván Delgado-Enciso
- Faculty of Medicine, Universidad de Colima, Colima, Colima 28040, Mexico;
- Colima State Cancer Institute, Universidad de Colima, Colima, Colima 28040, Mexico
| | - Mayra Alejandra Gomez-Govea
- Laboratory of Molecular and Structural Physiology, Collage of Biological Sciences, Universidad Autonoma de Nuevo Leon, San Nicolas de los Garza, Nuevo Leon 66451, Mexico;
| | | | - Diana Reséndez-Pérez
- Laboratory of Immunology and Virology, Collage of Biological Sciences, Universidad Autónoma de Nuevo Leon, San Nicolas de los Garza, Nuevo Leon 66451, Mexico; (M.M.S.-C.); (D.R.-P.)
| | - Iram Pablo Rodríguez-Sánchez
- Laboratory of Molecular and Structural Physiology, Collage of Biological Sciences, Universidad Autonoma de Nuevo Leon, San Nicolas de los Garza, Nuevo Leon 66451, Mexico;
- Correspondence: (M.L.M.-F.); (I.P.R.-S.); Tel.: +52-492-925-6690 (M.L.M.-F.); +52-818-329-4217 (I.P.R.-S.)
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4
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Malhotra P, Read GH, Weidhaas JB. Breast Cancer and miR-SNPs: The Importance of miR Germ-Line Genetics. Noncoding RNA 2019; 5:ncrna5010027. [PMID: 30897768 PMCID: PMC6468861 DOI: 10.3390/ncrna5010027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/08/2019] [Accepted: 03/15/2019] [Indexed: 12/11/2022] Open
Abstract
Recent studies in cancer diagnostics have identified microRNAs (miRNAs) as promising cancer biomarkers. Single nucleotide polymorphisms (SNPs) in miRNA binding sites, seed regions, and coding sequences can help predict breast cancer risk, aggressiveness, response to stimuli, and prognosis. This review also documents significant known miR-SNPs in miRNA biogenesis genes and their effects on gene regulation in breast cancer, taking into account the genetic background and ethnicity of the sampled populations. When applicable, miR-SNPs are evaluated in the context of other patient factors, including mutations, hormonal status, and demographics. Given the power of miR-SNPs to predict patient cancer risk, prognosis, and outcomes, further study of miR-SNPs is warranted to improve efforts towards personalized medicine.
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Affiliation(s)
- Poonam Malhotra
- Department of Radiation Oncology, David Geffen School of Medicine, University of California, Los Angeles, CA 90001, USA.
| | - Graham H Read
- Department of Radiation Oncology, David Geffen School of Medicine, University of California, Los Angeles, CA 90001, USA.
| | - Joanne B Weidhaas
- Department of Radiation Oncology, David Geffen School of Medicine, University of California, Los Angeles, CA 90001, USA.
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Sirisena ND, Adeyemo A, Kuruppu AI, Samaranayake N, Dissanayake VHW. Genetic Variants Associated with Clinicopathological Profiles in Sporadic Breast Cancer in Sri Lankan Women. J Breast Cancer 2018; 21:165-172. [PMID: 29963112 PMCID: PMC6015979 DOI: 10.4048/jbc.2018.21.2.165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/27/2018] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Several single nucleotide polymorphisms (SNPs) have been reported to be associated with clinicopathological profiles in sporadic breast cancer based on studies conducted on major population groups. The knowledge of the effects of these common genetic variants in South Asian populations remains limited. The present study aimed to investigate the association between a selected set of SNPs and the clinicopathological profiles in sporadic breast cancer in Sri Lankan women. METHODS A total of 350 postmenopausal women with histologically confirmed invasive breast cancer were genotyped for 58 SNPs located in 36 breast cancer related genes. The clinicopathological factors that were investigated included age of onset, tumor histologic grade, and lymph node involvement, as well as estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2 (HER2) status. Association testing was performed using logistic regression models adjusted for confounding factors. RESULTS Seven SNPs showed significant associations with clinicopathological profiles in breast cancer. The G allele of BRCA1:rs799917 (p=0.047; β [standard error; SE]=-1.069 [0.537]) and the G allele of NQO2:rs17136117 (p=0.040, β [SE]=1.901 [0.923]) were found to be associated with age of onset between 50 and 59 years. The C allele of CDH1:rs13689 (odds ratio [OR], 2.121; p=0.033) was found to be associated with ER-positive breast cancer. The A allele of AKT1:rs1130214 (OR, 2.095; p=0.011) and the C allele of NQO2:rs2071002 (OR, 1.632; p=0.045) were associated with HER2-positive breast cancer. The C allele of BRCA2:rs15869 (OR, 1.600; p=0.041) and the C allele of CCND1:rs7177 (OR, 1.555; p=0.041) were associated with high tumor histologic grade. CONCLUSION The common genetic variants identified in the AKT1, BRCA1, BRCA2, CCND1, CDH1, and NQO2 genes could serve as potential clinical and prognostic biomarkers in sporadic breast cancer patients. Further studies are required to validate our current findings in other populations.
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Affiliation(s)
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, USA
| | | | - Nilakshi Samaranayake
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
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6
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Zhu L, Sturgis EM, Zhang H, Lu Z, Tao Y, Wei Q, Li G. Genetic variants in microRNA-binding sites of DNA repair genes as predictors of recurrence in patients with squamous cell carcinoma of the oropharynx. Int J Cancer 2017. [PMID: 28646528 DOI: 10.1002/ijc.30849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The incidence of squamous cell carcinoma of the oropharynx (SCCOP) continues to rise because of increasing rates of human papillomavirus (HPV) infection. Inherited polymorphisms in DNA repair pathways may influence the risk of SCCOP development and the prognosis of SCCOP. We sought to determine whether polymorphisms in microRNA (miRNA)-binding sites within 3'-untranslated regions (3'UTRs) of genes in DNA repair pathways modulate the risk of SCCOP recurrence. We evaluated the associations between nine such polymorphisms and SCCOP recurrence in 1,008 patients with incident SCCOP using the log-rank test and multivariable Cox models. In an analysis of all the patients, patients with variant genotypes of BRCA1 rs12516 and RAD51 rs7180135 had better disease-free survival (log-rank, p = 0.0002 and p = 0.0003, respectively) and lower risk of SCCOP recurrence (hazard ratio [HR], 0.5, 95% confidence interval [CI], 0.2-0.8, and HR, 0.5, 95% CI, 0.3-0.9, respectively) than patients with common homozygous genotypes of the two polymorphisms after multivariable adjustment. Moreover, in tumor HPV16-positive patients, patients with variant genotypes of the same two polymorphisms also had better disease-free survival (log-rank, p = 0.004 and p = 0.003, respectively) and lower recurrence risk (HR, 0.2, 95% CI, 0.1-0.6, and HR, 0.2, 95% CI, 0.0-0.7, respectively) than patients with common homozygous genotypes of the two polymorphisms. No such significant associations were found for other polymorphisms. These findings support significant roles of BRCA1 rs12516 and RAD51 rs7180135 in modifying the risk of recurrence of SCCOP, particularly HPV16-positive SCCOP. However, these results must be validated in larger studies.
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Affiliation(s)
- Lijun Zhu
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Oral and Maxillofacial Surgery, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Erich M Sturgis
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hua Zhang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Otorhinolaryngology-Head and Neck Surgery, Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Zhongming Lu
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Otolaryngology-Head and Neck Surgery, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China
| | - Ye Tao
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Otolaryngology & head and neck Surgery, 2nd affiliated hospital of Anhui Medical University, Hefei, China
| | - Qingyi Wei
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX.,Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
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7
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Li W, Li G, Fan Z, Liu T. Tumor-suppressive microRNA-452 inhibits migration and invasion of breast cancer cells by directly targeting RAB11A. Oncol Lett 2017; 14:2559-2565. [PMID: 28781694 DOI: 10.3892/ol.2017.6426] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/03/2017] [Indexed: 01/04/2023] Open
Abstract
Breast cancer is the most common type of malignant tumor in females, and metastasis is the most common cause of breast cancer-associated mortality. Previous studies have identified that abnormal expression of microRNAs is commonly observed in human cancer and may be crucial for cancer metastasis. In the present study, microRNA-452 (miR-452) was investigated for its ability to act as a tumor suppressor in breast cancer. miR-452 expression was quantified in breast cancer tissue samples and cell lines with reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Transwell migration and invasion assays were used to investigate the effect of miR-452 on the migration and invasion capabilities of breast cancer cells. Potential target genes of miR-452 were identified with miRanda and TargetScan. A luciferase reporter assay was performed to validate RAB11A as a putative target of miR-452, and was corroborated by RT-qPCR and western blot analyses. Finally, small interfering RNA (siRNA) was used to knockdown RAB11A expression and confirm whether miR-452 inhibited breast cancer cell migration and invasion via the negative regulation of RAB11A. The results revealed that miR-452 was downregulated in breast cancer tissues and cell lines, and that its downregulation may be associated with breast cancer metastasis, as miR-452 expression inhibited the migration and invasion capacities of breast cancer cells. RT-qPCR and western blot analyses indicated that miR-452 negatively regulated the expression of RAB11A mRNA and protein. The luciferase reporter assay revealed that miR-452 specifically bound to the 3'-untranslated region of RAB11A. Furthermore, inhibition of RAB11A with siRNA inhibited breast cancer cell migration and invasion. In conclusion, the present study has demonstrated that miR-452 may act as a tumor suppressor gene via inhibition of cell migration and invasion by targeting RAB11A in breast cancer.
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Affiliation(s)
- Wanjun Li
- Department of Pathology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, Shaanxi 723000, P.R. China
| | - Guoyin Li
- Department of Pathology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, Shaanxi 723000, P.R. China
| | - Zhigang Fan
- Department of Medical Oncology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, Shaanxi 723000, P.R. China
| | - Tao Liu
- Department of Pathology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, Shaanxi 723000, P.R. China
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8
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Cao J, Luo C, Yan R, Peng R, Wang K, Wang P, Ye H, Song C. rs15869 at miRNA binding site in BRCA2 is associated with breast cancer susceptibility. Med Oncol 2016; 33:135. [DOI: 10.1007/s12032-016-0849-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/27/2016] [Indexed: 12/13/2022]
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9
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Association of PALB2 sequence variants with the risk of early-onset breast cancer in patients from Turkey. Mol Biol Rep 2016; 43:1273-1284. [DOI: 10.1007/s11033-016-4061-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/16/2016] [Indexed: 02/05/2023]
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10
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Garcia AI, Buisson M, Damiola F, Tessereau C, Barjhoux L, Verny-Pierre C, Sornin V, Dondon MG, Eon-Marchais S, Caron O, Gautier-Villars M, Coupier I, Buecher B, Vennin P, Belotti M, Lortholary A, Gesta P, Dugast C, Noguès C, Fricker JP, Faivre L, Stoppa-Lyonnet D, Andrieu N, Sinilnikova OM, Mazoyer S. Mutation screening of MIR146A/B and BRCA1/2 3'-UTRs in the GENESIS study. Eur J Hum Genet 2016; 24:1324-9. [PMID: 26785832 DOI: 10.1038/ejhg.2015.284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/11/2015] [Accepted: 12/16/2015] [Indexed: 01/08/2023] Open
Abstract
Although a wide number of breast cancer susceptibility alleles associated with various levels of risk have been identified to date, about 50% of the heritability is still missing. Although the major BRCA1 and BRCA2 genes are being extensively screened for truncating and missense variants in breast and/or ovarian cancer families, potential regulatory variants affecting their expression remain largely unexplored. In an attempt to identify such variants, we focused our attention on gene regulation mediated by microRNAs (miRs). We screened two genes, MIR146A and MIR146B, producing miR-146a and miR-146b-5p, respectively, that regulate BRCA1, and the 3'- untranslated regions (3'-UTRs) of BRCA1 and BRCA2 in the GENESIS French national case/control study (BRCA1- and BRCA2-negative breast cancer cases with at least one sister with breast cancer and matched controls). We identified one rare variant in MIR146A, four in MIR146B, five in BRCA1 3'-UTR and one in BRCA2 3'-UTR in 716 index cases and 619 controls. Among these 11 rare variants, 7 were identified each in 1 index case. None of the three relevant MIR146A/MIR146B variants affected the pre-miR sequences. The potential causality of the four relevant BRCA1/BRCA2 3'-UTRs variants was evaluated with luciferase reporter assays and co-segregation studies, as well as with bioinformatics analyses to predict miRs-binding sites, RNA secondary structures and RNA accessibility. This is the first study to report the screening of miR genes and of BRCA2 3'-UTR in a large series of familial breast cancer cases. None of the variant identified in this study gave convincing evidence of potential pathogenicity.
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Affiliation(s)
- Amandine I Garcia
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Monique Buisson
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Francesca Damiola
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Chloé Tessereau
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Laure Barjhoux
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Carole Verny-Pierre
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Valérie Sornin
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Marie-Gabrielle Dondon
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France
| | - Séverine Eon-Marchais
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France
| | | | - Olivier Caron
- Département de Médecine Oncologique, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | | | - Isabelle Coupier
- Hôpital Arnaud de Villeneuve, CHU Montpellier, Service de Génétique médicale et Oncogénétique, Montpellier, France.,ICM Val d'Aurel, Unité d'Oncogénétique, Montpellier, France
| | | | | | | | - Alain Lortholary
- Centre Catherine de Sienne, Service d'Oncologie Médicale, Nantes, France
| | - Paul Gesta
- CH Georges Renon, Service Oncogénétique pour la consultation oncogénétique régionale Poitou-Charentes, Niort, France
| | | | | | | | - Laurence Faivre
- Hôpital d'Enfants, Service de Génétique Médicale, Dijon, France.,Centre Georges François Leclerc, Oncogénétique, Dijon, France
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Service de Génétique, Paris, France.,Inserm, U830, Université Paris-Descartes, Paris, France
| | - Nadine Andrieu
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France
| | - Olga M Sinilnikova
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France.,Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Sylvie Mazoyer
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
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11
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Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M. LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. Nucleic Acids Res 2015; 43:8123-34. [PMID: 26304545 PMCID: PMC4787796 DOI: 10.1093/nar/gkv803] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 07/28/2015] [Indexed: 01/22/2023] Open
Abstract
In cancer research, background models for mutation rates have been extensively calibrated in coding regions, leading to the identification of many driver genes, recurrently mutated more than expected. Noncoding regions are also associated with disease; however, background models for them have not been investigated in as much detail. This is partially due to limited noncoding functional annotation. Also, great mutation heterogeneity and potential correlations between neighboring sites give rise to substantial overdispersion in mutation count, resulting in problematic background rate estimation. Here, we address these issues with a new computational framework called LARVA. It integrates variants with a comprehensive set of noncoding functional elements, modeling the mutation counts of the elements with a β-binomial distribution to handle overdispersion. LARVA, moreover, uses regional genomic features such as replication timing to better estimate local mutation rates and mutational hotspots. We demonstrate LARVA's effectiveness on 760 whole-genome tumor sequences, showing that it identifies well-known noncoding drivers, such as mutations in the TERT promoter. Furthermore, LARVA highlights several novel highly mutated regulatory sites that could potentially be noncoding drivers. We make LARVA available as a software tool and release our highly mutated annotations as an online resource (larva.gersteinlab.org).
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Affiliation(s)
- Lucas Lochovsky
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Jing Zhang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Yao Fu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Ekta Khurana
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA Department of Computer Science, Yale University, New Haven, CT 06520, USA
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