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Bahreini F, Rayzan E, Rezaei N. microRNA-related single-nucleotide polymorphisms and breast cancer. J Cell Physiol 2020; 236:1593-1605. [PMID: 32716070 DOI: 10.1002/jcp.29966] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
Breast cancer, as the most common cancer in women which affects patients both mentally and physically, requires great attention in many areas and many levels as this cancer is known to be multifactorial. Single-stranded molecules called microRNAs with near 22 nucleotides are seen to act in central dogma of molecular biology by inhibiting the translation process; it is demonstrated that any alteration in their sequence especially single-nucleotide polymorphisms (SNPs) may lead into increasing the breast cancer risk. miR-SNPs are considered to be the potential biomarkers for early detection of breast cancer. As a result, this review documents the well-known miR-SNPs that are known to be associated with breast cancer. In this regard, two principals were discussed: (a) SNPs in the target genes of microRNAs and the alteration in gene expression due to this phenomenon; (b) changes based on the SNPs in the microRNA coding region and the impact on their interaction with target messenger RNA.
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Affiliation(s)
- Farbod Bahreini
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elham Rayzan
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- International Hematology/Oncology of Pediatrics Experts, Universal Scientific Education and Research Network, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity, Universal Scientific Education and Research Network, Tehran, Iran
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2
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Faryal R, Ishfaq M, Hayat T, Mahjabeen I, Kayani M. Novel SYK gene variations and changes in binding sites of miRs in breast cancer patients. Cancer Biomark 2016; 16:319-26. [DOI: 10.3233/cbm-160569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- R. Faryal
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - M. Ishfaq
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - T. Hayat
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - I. Mahjabeen
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - M.A. Kayani
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
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Zutter MM, Bloom KJ, Cheng L, Hagemann IS, Kaufman JH, Krasinskas AM, Lazar AJ, Leonard DGB, Lindeman NI, Moyer AM, Nikiforova MN, Nowak JA, Pfeifer JD, Sepulveda AR, Willis JE, Yohe SL. The Cancer Genomics Resource List 2014. Arch Pathol Lab Med 2015; 139:989-1008. [PMID: 25436904 DOI: 10.5858/arpa.2014-0330-cp] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CONTEXT Genomic sequencing for cancer is offered by commercial for-profit laboratories, independent laboratory networks, and laboratories in academic medical centers and integrated health networks. The variability among the tests has created a complex, confusing environment. OBJECTIVE To address the complexity, the Personalized Health Care (PHC) Committee of the College of American Pathologists proposed the development of a cancer genomics resource list (CGRL). The goal of this resource was to assist the laboratory pathology and clinical oncology communities. DESIGN The PHC Committee established a working group in 2012 to address this goal. The group consisted of site-specific experts in cancer genetic sequencing. The group identified current next-generation sequencing (NGS)-based cancer tests and compiled them into a usable resource. The genes were annotated by the working group. The annotation process drew on published knowledge, including public databases and the medical literature. RESULTS The compiled list includes NGS panels offered by 19 laboratories or vendors, accompanied by annotations. The list has 611 different genes for which NGS-based mutation testing is offered. Surprisingly, of these 611 genes, 0 genes were listed in every panel, 43 genes were listed in 4 panels, and 54 genes were listed in 3 panels. In addition, tests for 393 genes were offered by only 1 or 2 institutions. Table 1 provides an example of gene mutations offered for breast cancer genomic testing with the annotation as it appears in the CGRL 2014. CONCLUSIONS The final product, referred to as the Cancer Genomics Resource List 2014, is available as supplemental digital content.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sophia L Yohe
- From the Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee (Dr Zutter); the Department of Pathology, Clarient Diagnostic Services, Aliso Viejo, California (Dr Bloom); the Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis (Dr Cheng); the Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri (Drs Hagemann and Pfeifer); Surveys, College of American Pathologists, Northfield, Illinois (Dr Kaufman); the Department of Pathology, Emory University, Atlanta, Georgia (Dr Krasinskas); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology and Laboratory Medicine, Fletcher Allen Health Care, Burlington, Vermont (Dr Leonard); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Lindeman); the Department of Pathology, Mayo Clinic, Rochester, Minnesota (Dr Moyer); Molecular and Genomic Pathology Laboratory, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Dr Nikiforova); the Department of Pathology, NorthShore University Health System, Evanston, Illinois (Dr Nowak); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Sepulveda); the Department of Pathology, Case Medical Center/Case Western Reserve University, Cleveland, Ohio (Dr Willis); and the Department of Molecular Pathology and Hematopathology, University of Minnesota, Minneapolis (Dr Yohe)
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Blancato J, Graves A, Rashidi B, Moroni M, Tchobe L, Ozdemirli M, Kallakury B, Makambi KH, Marian C, Mueller SC. SYK Allelic Loss and the Role of Syk-Regulated Genes in Breast Cancer Survival. PLoS One 2014; 9:e87610. [PMID: 24523870 PMCID: PMC3921124 DOI: 10.1371/journal.pone.0087610] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/20/2013] [Indexed: 11/26/2022] Open
Abstract
Heterozygotic loss of SYK, a non-receptor tyrosine kinase, gives rise to mouse mammary tumor formation where Syk protein levels are reduced by about half; loss of SYK mRNA is correlated with invasive cell behavior in in vitro models; and SYK loss has been correlated with distant metastases in patients. Here, allelic loss of the SYK gene was explored in breast ductal carcinoma in situ (DCIS) using fluorescence in situ hybridization and pyrosequencing, respectively, and in infiltrating ductal carcinoma (IDC) using genomic data from The Cancer Genome Atlas (TCGA). Allelic loss was present in a subset of DCIS cases where adjacent IDC was present. SYK copy number loss was found in about 26% of 1002 total breast cancer cases and 30% of IDC cases. Quantitative immunofluorescence revealed Syk protein to be six-fold higher in infiltrating immune cells compared with epithelial cells. This difference distorted tumor cell mRNA and protein levels in extracts. 20% of 1002 IDC cases contained elevated immune cell infiltration as estimated by elevated immune-specific mRNAs. In cases without immune cell infiltration, loss of SYK copy number was associated with a significant reduction of SYK mRNA. Here we define a 55 Gene Set consisting of Syk interacting, motility- and invasion-related genes. We found that overall survival was significantly reduced in IDC and Luminal A+B cases where copy number and mutations of these 55 genes were affected (Kaplan-Meier, Logrank test p-value 0.007141 and Logrank test p-value 0.001198, respectively). We conclude that reduction in Syk expression and contributions of genomic instability to copy number and mutations in the 55 Syk interacting genes significantly contribute to poorer overall patient survival. A closer examination of the role of Syk interacting motility and invasion genes and their prognostic and/or causative association with metastatic disease and patient outcome is warranted.
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Affiliation(s)
- Jan Blancato
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D. C., United States of America
| | - Ashley Graves
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D. C., United States of America
| | - Banafsheh Rashidi
- Department of Pathology, Georgetown University Medical Center, Washington, D. C., United States of America
| | - Maria Moroni
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Leopold Tchobe
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D. C., United States of America
- University of the District of Columbia/Lombardi Comprehensive Cancer Center Partnership, Washington, D. C., United States of America
| | - Metin Ozdemirli
- Department of Pathology, Georgetown University Medical Center, Washington, D. C., United States of America
| | - Bhaskar Kallakury
- Department of Pathology, Georgetown University Medical Center, Washington, D. C., United States of America
| | - Kepher H. Makambi
- Department of Biostatistics and Bioinformatics, Georgetown University Medical Center, Washington, D. C., United States of America
| | - Catalin Marian
- Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- Biochemistry Department, University of Medicine and Pharmacy, “Victor Babes”, Timisoara, Romania
| | - Susette C. Mueller
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D. C., United States of America
- * E-mail:
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He M, Fan J, Jiang R, Tang WX, Wang ZW. Expression of DNMTs and genomic DNA methylation in gastric signet ring cell carcinoma. Mol Med Rep 2013; 8:942-8. [PMID: 23820855 DOI: 10.3892/mmr.2013.1566] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/24/2013] [Indexed: 12/22/2022] Open
Abstract
The aim of the present study was to investigate the protein expression of DNA methyltransferases (DNMTs) and genomic DNA methylation status of genomes in gastric signet ring cell carcinoma (SRC). Immunohistochemistry was performed to analyze DNMT expression and methylated DNA immunoprecipitation microarray (MeDIP‑chip) and MeDIP quantitative real‑time PCR (MeDIP‑qPCR) were performed to analyze the genomic DNA methylation status in gastric SRC tissue. An increase in DNMT1 and decrease in DNMT3A expression in SRC tissue was observed compared with matched non‑cancerous tissue. However, expression of other DNMTs, DNMT2, DNMT3B and DNMT3L, was not found to differ significantly between carcinoma and control. The MeDIP‑chip assay revealed that methylation of gene promoters and CpG islands in SRC was higher than those in matched control tissue. However, MeDIP‑qPCR analysis demonstrated that specific tumor‑related genes, including ABL2, FGF18, TRAF2, EGFL7 and RAB33A were aberrantly hypomethylated in SRC tissue. Results of the current study indicate that gastric SRC may produce complex patterns of aberrant DNA methylation and DNMT expression.
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Affiliation(s)
- Miao He
- Department of General Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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Shakeel S, Mahjabeen I, Kayani MA, Faryal R. Association of SYK Genetic Variations with Breast Cancer Pathogenesis. Asian Pac J Cancer Prev 2013; 14:3309-14. [DOI: 10.7314/apjcp.2013.14.5.3309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Cho P, Gelinas L, Corbett NP, Tebbutt SJ, Turvey SE, Fortuno ES, Kollmann TR. Association of common single-nucleotide polymorphisms in innate immune genes with differences in TLR-induced cytokine production in neonates. Genes Immun 2013; 14:199-211. [DOI: 10.1038/gene.2013.5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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