1
|
Elwafa RAHA, Bordiny ME, Salama M, Fawzy A, Omar OM. Cyclin D2 gene variance and expression level in pediatric acute lymphoblastic leukemia. Pediatr Blood Cancer 2023; 70:e30678. [PMID: 37731174 DOI: 10.1002/pbc.30678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND Cyclin D2 (CCND2) is a crucial player in cell cycle regulation. CCND2 polymorphisms contribute to cancer predisposition. OBJECTIVES To evaluate the association of CCND2 rs3217927 single nucleotide polymorphisms (SNP) and its expression levels with acute lymphoblastic leukemia (ALL) susceptibility in Egyptian children and its potential prognostic role. METHODS The 5' nuclease allelic discrimination assay was used to evaluate the frequency of CCND2 rs3217927 SNP in 80 newly diagnosed children with ALL and 80 age- and sex-matched controls. CCND2 relative expression levels were determined by real-time quantitative polymerase chain reaction. RESULTS The genotype analysis revealed that the GG genotype and G allele were significantly more prevalent among ALL patients than controls (p ˂ .001). Regression analysis demonstrated that Egyptian children carrying only one G allele had about 31-fold increased risk to develop ALL compared to A allele carriers. CCND2 was overexpressed in ALL patients compared to controls (p < .001). The CCND2 overexpression was associated with the GG genotype and G allele (p < .001). Furthermore, G allele was an independent negative prognostic marker for central nervous system (CNS) involvement (odds ratio [OR] = 4.676; 95% confidence interval [CI]: 1.2-18.6), risk stratification (OR = 38; 95% CI: 7.7-188.2), and chemoresistance (OR = 9.864; 95% CI: 5.6-70.3) in ALL patients. CONCLUSIONS G allele of CCND2 rs3217927 SNP might be associated with increased risk for ALL in Egyptian children besides being an independent negative prognostic marker for their risk stratification and therapeutic outcome. CCND2 rs3217927 SNP genotyping might be used to demarcate ALL patients with aggressive disease phenotypes who may be candidate for alternative targeted therapeutic strategies.
Collapse
Affiliation(s)
| | - Magdy El Bordiny
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Mostafa Salama
- Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Amira Fawzy
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Omneya Magdy Omar
- Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| |
Collapse
|
2
|
Sanchez A, Lhuillier J, Grosjean G, Ayadi L, Maenner S. The Long Non-Coding RNA ANRIL in Cancers. Cancers (Basel) 2023; 15:4160. [PMID: 37627188 PMCID: PMC10453084 DOI: 10.3390/cancers15164160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
ANRIL (Antisense Noncoding RNA in the INK4 Locus), a long non-coding RNA encoded in the human chromosome 9p21 region, is a critical factor for regulating gene expression by interacting with multiple proteins and miRNAs. It has been found to play important roles in various cellular processes, including cell cycle control and proliferation. Dysregulation of ANRIL has been associated with several diseases like cancers and cardiovascular diseases, for instance. Understanding the oncogenic role of ANRIL and its potential as a diagnostic and prognostic biomarker in cancer is crucial. This review provides insights into the regulatory mechanisms and oncogenic significance of the 9p21 locus and ANRIL in cancer.
Collapse
Affiliation(s)
| | | | | | - Lilia Ayadi
- CNRS, Université de Lorraine, IMoPA, F-54000 Nancy, France
| | | |
Collapse
|
3
|
Chen Y, He L, Zhou H, Li W, Qiu C. Transcriptional profiling of exosomes derived from plasma of canine with mammary tumor by RNA-seq analysis. Genomics 2023; 115:110660. [PMID: 37257521 DOI: 10.1016/j.ygeno.2023.110660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/16/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
Canine mammary tumor (CMT) are the second most common tumor in dogs. Exosomes can act as biomarkers for the early diagnosis of tumors, and also be involved in the pathogenesis and metastasis mechanism of tumors. The expression profile of exosomal RNA revealed that there were a total of 5547 differentially expressed mRNAs, and 196 differentially expressed lncRNAs. GO and KEGG enrichment analysis found that the differentially expressed mRNAs and lncRNA target genes were associated with metabolic processes, DNA replication, cell proliferation, cell junction, and cell adhesion. In conclusion, this study revealed lncRNA and mRNA expression profiles in exosomes derived from plasma of CMT and further annotated their potential functions. The data obtained in this study will also provide valuable resources for understanding lncRNA information in plasma exosomes of dogs with CMT, and contribute to the study of early diagnostic markers and pathogenesis of CMT.
Collapse
Affiliation(s)
- Yu Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Lixin He
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Han Zhou
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Wenxuan Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Changwei Qiu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| |
Collapse
|
4
|
Zhu Q, Zhu Z, Renaud SJ, Hu L, Guo Y. The Oncogenic Role of Cyclin-Dependent Kinase Inhibitor 2C in Lower-Grade Glioma. J Mol Neurosci 2023; 73:327-344. [PMID: 37223854 DOI: 10.1007/s12031-023-02120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
Lower-grade gliomas (LGGs) are slow-growing, indolent tumors that usually affect younger patients and present a therapeutic challenge due to the heterogeneity of their clinical presentation. Dysregulation of cell cycle regulatory factors is implicated in the progression of many tumors, and drugs that target cell cycle machinery have shown efficacy as promising therapeutic approaches. To date, however, no comprehensive study has examined how cell cycle-related genes affect LGG outcomes. The cancer genome atlas (TCGA) data were used as the training set for differential analysis of gene expression and patient outcomes; the Chinese glioma genome atlas (CGGA) was used for validation. Levels of one candidate protein, cyclin-dependent kinase inhibitor 2C (CDKN2C), and its relationship to clinical prognosis were determined using a tissue microarray containing 34 LGG tumors. A nomogram was constructed to model the putative role of candidate factors in LGG. Cell type proportion analysis was performed to evaluate immune cell infiltration in LGG. Various genes encoding cell cycle regulatory factors showed increased expression in LGG and were significantly related to isocitrate dehydrogenase and chromosome arms 1p and 19q mutation status. CDKN2C expression independently predicted the outcome of LGG patients. High M2 macrophage values along with elevated CDKN2C expression were associated with poorer prognosis in LGG patients. CDKN2C plays an oncogenic role in LGG, which is associated with M2 macrophages.
Collapse
Affiliation(s)
- Qiongni Zhu
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhimin Zhu
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Shanghai, 200235, China
| | - Stephen James Renaud
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON, Canada
| | - Lei Hu
- Department of Pharmacy, Peking University People's Hospital, Beijing, 100044, China.
| | - Ying Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
| |
Collapse
|
5
|
Kleinbielen T, Olasagasti F, Azcarate D, Beristain E, Viguri-Díaz A, Guerra-Merino I, García-Orad Á, de Pancorbo MM. In silico identification and in vitro expression analysis of breast cancer-related m 6A-SNPs. Epigenetics 2022; 17:2144-2156. [PMID: 35971775 PMCID: PMC9665143 DOI: 10.1080/15592294.2022.2111137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Research on m6A-associated SNPs (m6A-SNPs) has emerged recently due to their possible critical roles in many key biological processes. In this sense, several investigations have identified m6A-SNPs in different diseases. In order to gain a more complete understanding of the role that m6A-SNPs can play in breast cancer, we performed an in silico analysis to identify the m6A-SNPs associated with breast cancer and to evaluate their possible effects. For this purpose, we downloaded SNPs related to breast cancer and a list of m6A-SNPs from public databases in order to identify which ones appear in both. Subsequently, we assessed the identified m6A-SNPs in silico by expression quantitative trait loci (eQTL) analysis and differential gene expression analysis. We genotyped the m6A-SNPs found in the in silico analysis in 35 patients with breast cancer, and we carried out a gene expression analysis experimentally on those that showed differences. Our results identified 981 m6A-SNPs related to breast cancer. Four m6A-SNPs showed an eQTL effect and only three were in genes that presented an altered gene expression. When the three m6A-SNPs were evaluated in the tissue sample of our breast cancer patients, only the m6A-SNP rs76563149 located in ZNF354A gene presented differences in allele frequencies and a low gene expression in breast cancer tissues, especially in luminal B HER2+ subtype. Future investigations of these m6A-SNPs should expand the study in different ethnic groups and increase the sample sizes to test their association with breast cancer and elucidate their molecular function.
Collapse
Affiliation(s)
- Tamara Kleinbielen
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Felix Olasagasti
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
| | - Daniel Azcarate
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Elena Beristain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Molecular Genetics Laboratory, Araba University Hospital, Osakidetza Basque Health Service. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Amparo Viguri-Díaz
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Isabel Guerra-Merino
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - África García-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- BioCruces Bizkaia Health Research Institute. Postal code: 48903. Barakaldo, Bizkaia, Spain
| | - Marian M. de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| |
Collapse
|
6
|
Híveš M, Jurečeková J, Kliment J, Grendár M, Kaplán P, Dušenka R, Evin D, Vilčková M, Holečková KH, Sivoňová MK. Role of Genetic Variations in CDK2, CCNE1 and p27KIP1 in Prostate Cancer. Cancer Genomics Proteomics 2022; 19:362-371. [PMID: 35430569 DOI: 10.21873/cgp.20326] [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: 03/02/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Our aim was to investigate possible influences of genetic variants in genes involved in the G1/S transition [cyclin-dependent kinase-2 (CDK2), cyclin E1 (CCNE1) and cyclin-dependent kinase inhibitor 1B (p27KIP1)] on the expression/activity of their corresponding proteins and to assess the functional impact of these variants on the risk of prostate cancer. MATERIALS AND METHODS We genotyped 530 cases and 562 healthy controls for two relevant single nucleotide polymorphisms (CDK2 rs2069408 and CCNE1 rs997669) by TaqMan genotyping assay. p27KIP1 rs2066827 polymorphisms were studied by polymerase chain reaction-restriction fragment length polymorphism assay. In addition, the expression of CDK2, CCNE1 and p27KIP1 was evaluated by quantitative real-time-polymerase chain reaction and western blotting in 44 prostate cancer tissues and 31 benign prostatic hyperplasia tissues. RESULTS No association was found between CDK2 rs2069408, CCNE1 rs997669 or p27KIP1 rs2066827 polymorphisms and an increased risk of prostate cancer development. Higher CDK2 expression was more prevalent in those with rs2069408 GG genotype than in AA carriers (p>0.05). We also noted reduced p27KIP1 protein expression in those with the p27KIP1 G109 allele. No difference was observed for CCNE1 expression in relation to the risky genotype (CC). A significant association was detected between CCNE1 mRNA overexpression and development of higher-grade carcinomas (Gleason score >7, p<0.05). CONCLUSION Polymorphisms CDK2 rs2069408, CCNE1 rs997669 and p27KIP1 rs2066827 have no significant impact on prostate cancer risk nor on the gene and protein expression of CDK2, CCNE1 and p27KIP1, although high CCNE1 expression was significantly associated with a higher tumour grade in patients with prostate cancer.
Collapse
Affiliation(s)
- Márk Híveš
- Department of Medical Biochemistry, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovak Republic
| | - Jana Jurečeková
- Department of Medical Biochemistry, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovak Republic
| | - Ján Kliment
- Department of Urology, Comenius University in Bratislava, Jessenius Faculty of Medicine and University Hospital Martin, Martin, Slovak Republic
| | - Marián Grendár
- Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovak Republic
| | - Peter Kaplán
- Department of Medical Biochemistry, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovak Republic
| | - Róbert Dušenka
- Department of Urology, Comenius University in Bratislava, Jessenius Faculty of Medicine and University Hospital Martin, Martin, Slovak Republic
| | - Daniel Evin
- Department of Medical Biochemistry, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovak Republic.,Department of Nuclear Medicine, Comenius University in Bratislava, Jessenius Faculty of Medicine and University Hospital Martin, Martin, Slovak Republic
| | - Marta Vilčková
- Department of Medical Biochemistry, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovak Republic
| | - Klaudia Híveš Holečková
- Department of Urology, Comenius University in Bratislava, Jessenius Faculty of Medicine and University Hospital Martin, Martin, Slovak Republic.,Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovak Republic
| | - Monika Kmeťová Sivoňová
- Department of Medical Biochemistry, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovak Republic;
| |
Collapse
|
7
|
A New Computational Approach to Evaluating Systemic Gene–Gene Interactions in a Pathway Affected by Drug LY294002. Processes (Basel) 2020. [DOI: 10.3390/pr8101230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In this study, we investigate how drugs systemically affect genes via pathways by integrating information from interactions between chemical compounds and molecular expression datasets, and from pathway information such as gene sets using mathematical models. First, we adopt drug-induced gene expression datasets; then, employ gene set enrichment analysis tools for selecting candidate enrichment pathways; and lastly, implement the inverse algorithm package for identifying gene–gene regulatory networks in a pathway. We tested LY294002-induced datasets of the MCF7 breast cancer cell lines, and found a CELL CYCLE pathway with 101 genes, ERBB signaling pathway consisting of 82 genes, and MTOR pathway consisting of 45 genes. We consider two interactions: quantity strength depending on number of interactions, and quality strength depending on weight of interaction as positive (+) and negative (−) interactions. Our methods revealed ANAPC1-CDK6 (−0.412) and ORC2L- CHEK1(0.951) for the CELL CYCLE pathway; INS-RPS6 (−3.125) and PRKAA2-PRKAA2 (+1.319) for the MTOR pathway; and CBLB-RPS6KB1 (−0.141), RPS6KB1-CBLC (+0.238) for the ERBB signaling pathway to be top quality interactions. Top quantity interactions discovered include 12; the CDC (−,+) gene family for the CELL CYCLE pathway, 20; PIK3 (−), 23; PIK3CG (+) for the MTOR pathway, 11; PAK (−), 10; PIK3 (+) for the ERBB signaling pathway.
Collapse
|
8
|
Genetic Association of rs2237572 Cyclin-Dependent Kinase 6 Gene with Breast Cancer in Iraq. Indian J Clin Biochem 2020; 36:304-311. [PMID: 34220005 DOI: 10.1007/s12291-020-00895-5] [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: 12/07/2019] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
Abstract
This case-control study is aimed to evaluate serum concentration of Cyclin-Dependent Kinase 6 (CDK6) and the genetic association between rs2237572 CDK6 gene and breast cancer (BC) in Iraq. To attain this goal, 80 patients with BC as cases and 80 healthy individuals as controls were included. Further, BC patients were sorted according to the molecular classification into four subtypes of Luminal A, Luminal B, Her2/neu enriched and TPN. Serum concentration of CDK6 enzyme, allelic and genotypic frequencies of rs2237572 CDK6, and the occurrence of BC phenotype and its subtypes in the studied population were investigated. ELISA technique was used to perform the biochemical testing, while the molecular analysis was achieved by real-time PCR, high resolution melting analysis, conventional PCR, as well as sequencing analysis. The results revealed no significant difference in serum concentration of CDK6 enzyme between patients and healthy controls (p > 0.05). Also, no significant differences were shown between BC patients subtypes (p > 0.05). The rs2237572 CDK6 genotypes were associated with the BC and affirmed that allele C was inherited as a recessive risk factor. Moreover, a highly significant difference between patients' subtypes in the genotypic frequency of rs2237572 (p < 0.01) was noted. Furthermore, the association of rs2237572 genotypes and CDK6 serum concentration in BC patients showed a considered significant difference between C/C and T/T, C/C and T/C and the CDK6 level (p < 0.05). Nevertheless, T/T and T/C did not show any significant difference with the CDK6 level. Hence, it was concluded that the rs2237572 of CDK6 gene is significantly correlated with BC.
Collapse
|
9
|
Chasseloup F, Pankratz N, Lane J, Faucz FR, Keil MF, Chittiboina P, Kay DM, Hussein Tayeb T, Stratakis CA, Mills JL, Hernández-Ramírez LC. Germline CDKN1B Loss-of-Function Variants Cause Pediatric Cushing's Disease With or Without an MEN4 Phenotype. J Clin Endocrinol Metab 2020; 105:5813889. [PMID: 32232325 PMCID: PMC7190031 DOI: 10.1210/clinem/dgaa160] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/27/2020] [Indexed: 12/13/2022]
Abstract
CONTEXT Germline loss-of-function CDKN1B gene variants cause the autosomal dominant syndrome of multiple endocrine neoplasia type 4 (MEN4). Even though pituitary neuroendocrine tumors are a well-known component of the syndrome, only 2 cases of Cushing's disease (CD) have so far been described in this setting. AIM To screen a large cohort of CD patients for CDKN1B gene defects and to determine their functional effects. PATIENTS We screened 211 CD patients (94.3% pediatric) by germline whole-exome sequencing (WES) only (n = 157), germline and tumor WES (n = 27), Sanger sequencing (n = 6), and/or germline copy number variant (CNV) analysis (n = 194). Sixty cases were previously unpublished. Variant segregation was investigated in the patients' families, and putative pathogenic variants were functionally characterized. RESULTS Five variants of interest were found in 1 patient each: 1 truncating (p.Q107Rfs*12) and 4 nontruncating variants, including 3 missense changes affecting the CDKN1B protein scatter domain (p.I119T, p.E126Q, and p.D136G) and one 5' untranslated region (UTR) deletion (c.-29_-26delAGAG). No CNVs were found. All cases presented early (10.5 ± 1.3 years) and apparently sporadically. Aside from colon adenocarcinoma in 1 carrier, no additional neoplasms were detected in the probands or their families. In vitro assays demonstrated protein instability and disruption of the scatter domain of CDKN1B for all variants tested. CONCLUSIONS Five patients with CD and germline CDKN1B variants of uncertain significance (n = 2) or pathogenic/likely pathogenic (n = 3) were identified, accounting for 2.6% of the patients screened. Our finding that germline CDKN1B loss-of-function may present as apparently sporadic, isolated pediatric CD has important implications for clinical screening and genetic counselling.
Collapse
Affiliation(s)
- Fanny Chasseloup
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
- Departmentof Endocrinology, Cochin Hospital, Assistance Publique Hôpitaux de Paris, Institut Cochin, INSERM U1016 CNRS 8104 Paris Descartes University, Paris, France
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Fabio R Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Margaret F Keil
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Prashant Chittiboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland
| | - Denise M Kay
- Newborn Screening Program, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Tara Hussein Tayeb
- College of Medicine, Sulaimani University, Sulaimani, Kurdistan, Iraq
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - James L Mills
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Laura C Hernández-Ramírez
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
- Correspondence and Reprint Requests: Laura C. Hernández-Ramírez, MD, PhD, Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, CRC, Rm 1E-3216, Bethesda, MD 20892-1862, USA. E-mail:
| |
Collapse
|
10
|
Yang C, Sun J, Yong L, Liang C, Liu T, Xu Y, Yang J, Liu X. Deficiency of PTEN and CDKN2A Tumor-Suppressor Genes in Conventional and Chondroid Chordomas: Molecular Characteristics and Clinical Relevance. Onco Targets Ther 2020; 13:4649-4663. [PMID: 32547095 PMCID: PMC7259488 DOI: 10.2147/ott.s252990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/11/2020] [Indexed: 12/03/2022] Open
Abstract
Introduction Chordoma is a malignant tumor predominantly involving the skull base and vertebral column. This study aimed to investigate the molecular characteristics of PTEN and CDKN2A in conventional and chondroid chordomas and their correlation with clinical prognosis. Materials and Methods A total of 42 patients were enrolled, including 26 patients with conventional chordoma and 16 patients with chondroid chordoma. Clinicopathological profiles and tissue specimens were collected. Gene sequencing and fluorescence in situ hybridization were performed to identify genetic alterations in the PTEN and CDKN2A genes. Immunohistochemical staining was used for semiquantitative evaluation of PTEN and CDKN2A expression. Results Gene sequencing revealed an intron SNP (c.80–96A>G) and a missense mutation (c.10G>A; p.Gly4Arg) in the PTEN gene and a missense mutation (c.442G>A; p.Ala148Thr) in the CDKN2A gene. Loss of the PTEN locus was identified in 25 (59.5%) cases, and loss of the CDKN2A locus was found in 28 (66.7%) cases. There was no significant correlation between progression-free survival (PFS)/overall survival (OS) and loss of PTEN or CDKN2A. The patients with lower PTEN expression showed significantly shorter PFS and OS than those with higher expression, while there was no significant difference in PFS or OS between patients with lower CDKN2A expression and those with higher CDKN2A expression. Conclusion Our findings delineated the genetic landscape and expression of PTEN and CDKN2A in chordomas. PTEN expression may serve as a prognostic and predictive biomarker for chordomas.
Collapse
Affiliation(s)
- Chenlong Yang
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Jianjun Sun
- Department of Neurosurgery, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Lei Yong
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Chen Liang
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Tie Liu
- Department of Neurosurgery, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, People's Republic of China
| | - Yulun Xu
- Department of Neurosurgery, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, People's Republic of China
| | - Jun Yang
- Department of Neurosurgery, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Xiaoguang Liu
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, People's Republic of China
| |
Collapse
|
11
|
Abdeahad H, Bahrami A, Saeedi N, Shabani M, Pezeshki M, Khazaei M, Shafiee M, Ghorbani E, Ferns GA, Soleimanpour S, Rahmani F, Soleimani A, Fiuji H, Ryzhikov M, Avan A, Mahdi Hassanian S. Association between genetic variants at 9p21 locus with risk of breast cancer: A systematic review and meta-analysis. Pathol Res Pract 2020; 216:152987. [PMID: 32534702 DOI: 10.1016/j.prp.2020.152987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/04/2020] [Accepted: 04/15/2020] [Indexed: 12/27/2022]
Abstract
Breast cancer (BC) is the most frequent tumor in women and genetic factors are among the main risk factors contributing to this malignancy. Chromosome 9p21 contains important regulatory non-coding RNAs and is associated with multiple malignancies including BC. The current meta-analysis aimed to investigate the association between genetic variants within the 9p21 locus and risk of breast cancer. A literature search was performed using PubMed, Web of Science, Embase, MEDLINE, Scopus and Clinical key databases. Nine studies containing 23,726 subjects were eligible for the final analysis and specific odds ratios (OR) and confidence intervals (95% CI) were evaluated to assess the strength of the associations. In the pooled analysis, there was an association between the genetic variations in 9p21 locus (CDKN2A/2B) with risk of breast cancer with a standard OR of 1.22 (95% CI: 1.04-1.45, P = 0.016; random-effects model), supporting the significance of this locus as a novel risk factor for breast cancer patients. In conclusion, our results showed that 9p21 region is positively associated with risk of BC and its polymorphisms may be a candidate marker for BC susceptibility.
Collapse
Affiliation(s)
- Hossein Abdeahad
- Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of nutrition and integrative physiology, University of Utah, Salt lake city, Utah, USA
| | - Afsane Bahrami
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Nikoo Saeedi
- Student Research Committee, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Mohammad Shabani
- Department of Medical Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Milad Pezeshki
- Molecular Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | - Majid Khazaei
- Department of Medical Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Shafiee
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7N 4Z2, Canada
| | - Elnaz Ghorbani
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex, BN1 9PH, UK
| | - Saman Soleimanpour
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Atena Soleimani
- Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Fiuji
- Department of Biochemistry, Payame-Noor University, Mashhad, Iran
| | - Mikhail Ryzhikov
- Division of Pulmonary and Critical Care Medicine, Washington University, School of Medicine, Saint Louis, MO, USA
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
12
|
Seifi S, Pouya F, Rahmani M, Mehramiz M, Rastgar-Moghadam A, Gharib M, Rahmani F, Shahidsales S, Hassanian SM, Khazaei M, Dadjoo P, Parvin SS, Yazdinezhad Y, Parizadeh SMR, Ferns GA, Fathi M, Avan A. Association of cyclin-dependent kinase inhibitor 2A/B with increased risk of developing breast cancer. J Cell Physiol 2019; 235:5141-5145. [PMID: 31721206 DOI: 10.1002/jcp.29388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 09/03/2019] [Indexed: 11/10/2022]
Abstract
There is a growing body of data reporting the association of genetic alterations in chromosome 9P21 with the risk of developing cancer. In the current study, we studied the association of a genetic variant in CDKN2A/B, rs1333049, with the risk of developing breast cancer. A total of 339 participants with and without breast cancer entered to the study. Genotyping was done by the TaqMan real-time polymerase chain reaction (RT-PCR) method and gene expression analysis was ran by RT-PCR. Our data showed that the minor allele homozygote in the total population was 10%, whereas for heterozygote was 38%. The dominant genetic model demonstrated that individuals with breast cancer had advanced TNM classification. Moreover, the logistic regression revealed that individuals who had CC/CG genotypes might have an enhanced risk of developing breast cancer when compared to the holders of GG genotype (e.g., OR = 2.8; 95% CI,1.4-5.4; p = .001), after regulated for confounders; age and body mass index. Furthermore, our analysis showed that the CDKN2A/B gene was downregulated in patients (p < .001). We showed a meaningful relationship of CDKN2A/B with the risk of breast cancer, cancer, showing the importance of studies in great sample size and several centers for studying the value of the marker as a risk classification in the management of patients with breast cancer.
Collapse
Affiliation(s)
- Sima Seifi
- Department of Medical Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzaneh Pouya
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Rahmani
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrane Mehramiz
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Azam Rastgar-Moghadam
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masoumeh Gharib
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzad Rahmani
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Seyed Mahdi Hassanian
- Department of Medical Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parisa Dadjoo
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyede Sara Parvin
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Yeganeh Yazdinezhad
- Orology Department, Emam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Reza Parizadeh
- Department of Medical Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Division of Medical Education, Brighton & Sussex Medical School, Brighton, United Kingdom
| | - Mehdi Fathi
- Department of Anesthesia, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
13
|
Iterative integrated imputation for missing data and pathway models with applications to breast cancer subtypes. COMMUNICATIONS FOR STATISTICAL APPLICATIONS AND METHODS 2019. [DOI: 10.29220/csam.2019.26.4.411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
14
|
Akhter N, Alzahrani FA, Dar SA, Wahid M, Sattar RSA, Hussain S, Haque S, Ansari SA, Jawed A, Mandal RK, Almalki S, Alharbi RA, Husain SA. AA genotype of cyclin D1 G870A polymorphism increases breast cancer risk: Findings of a case-control study and meta-analysis. J Cell Biochem 2019; 120:16452-16466. [PMID: 31243808 DOI: 10.1002/jcb.28800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Cyclin D1 (CCND1) polymorphisms, a regulator of the cell cycle progress from G1 to the S phase, may lead to uncontrolled cell proliferation and lack of apoptosis. G870A, a common single-nucleotide polymorphism in CCND1 influences breast cancer risk. However, the association between G870A polymorphism and breast cancer risk is ambiguous so far. MATERIALS AND METHODS In this case-control study, we analyzed the role of G870A polymorphism with breast cancer risk in Indian women. A meta-analysis of 18 studies was also performed to elucidate this association by increasing statistical power. RESULTS In our case-control study, significant risk association of the CCND1 G870A AA genotype with breast cancer in total cohort (odds ratio [OR], 2.98; 95% confidence interval [CI], 1.64-5.42; P value, 4.96e-04) and premenopausal women (OR, 3.31; 95% CI, 1.54-7.08; P value, .003) was found. The results of the meta-analysis showed that AA genotype of the CCND1 G870A polymorphism significantly increases breast cancer risk in total pooled data (AA vs GG+GA: OR = 1.20; 95% CI = 1.03 to 1.39; P value, 0.016*) and Caucasian (AA vs GG+GA: OR = 1.22; 95% CI = 0.99 to 1.51; P value, .056*) but not in Asian population. Further, a significant protective association with breast cancer was also found in the GA vs AA comparison model in pooled data (OR = 0.73; 95% CI = 0.58 to 0.92; P value, .007*) as well as in Caucasian subgroup (OR = 0.62; 95% CI = 0.49 to 0.94; P value, .022*). CONCLUSION CCND1 G870A AA genotype was found associated with breast cancer risk. Future association studies considering the environmental impact on gene expression are required to validate/explore this association.
Collapse
Affiliation(s)
- Naseem Akhter
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India.,Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia
| | - Faisal Abdulrahman Alzahrani
- Department of Biological Sciences, Rabigh College of Science and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Sajad Ahmad Dar
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohd Wahid
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India.,Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | | | - Showket Hussain
- Division of Molecular OncologyAnchor, AnchorNational Institute of Cancer Prevention and Research (ICMR), Noida, India
| | - Shafiul Haque
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India.,Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shakeel Ahmed Ansari
- AnchorAnchorCenter of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shaia Almalki
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia
| | - Raed A Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia
| | - Syed Akhtar Husain
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
15
|
Suszynska M, Klonowska K, Jasinska AJ, Kozlowski P. Large-scale meta-analysis of mutations identified in panels of breast/ovarian cancer-related genes - Providing evidence of cancer predisposition genes. Gynecol Oncol 2019; 153:452-462. [PMID: 30733081 DOI: 10.1016/j.ygyno.2019.01.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Germline mutations occurring in the highly penetrant genes BRCA1 and BRCA2 are responsible for only certain cases of familial breast cancer (BC) and ovarian cancer (OC). Thus, the use of NGS multi-gene panel (MGP) testing has recently become very popular. METHODS To estimate a reliable BC and OC risk associated with pathogenic variants in the selected candidate BC/OC predisposition genes, a comprehensive meta-analysis of 48 MGP-based studies analyzing BC/OC patients was conducted. The role of 37 genes was evaluated, comparing, in total, the mutation frequency in ~120,000 BC/OC cases and ~120,000 controls, which guaranteed strong statistical support with high confidence for most analyzed genes. RESULTS We characterized the strategies of MGP analyses and the types and localizations of the identified mutations and showed that 13 and 11 of the analyzed genes were significantly associated with an increased BC and OC risk, respectively. The risk attributed to some of these genes (e.g., CDKN2A and PALB2 for BC) was similar to that observed for BRCA2. The analysis also showed a substantial difference in the profile of genes contributing to either BC or OC risk, including genes specifically associated with a high risk of OC but not BC (e.g., RAD51C, and RAD51D). CONCLUSIONS Our study provides strong statistical proof, defines the risk for many genes often considered candidates for BC/OC predisposition and excludes the role of other genes frequently analyzed in the MGPs. In the context of clinical diagnostics, the results support the knowledge-based interpretation of identified mutations.
Collapse
Affiliation(s)
- Malwina Suszynska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Klonowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna J Jasinska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| |
Collapse
|
16
|
Hesari A, Maleksabet A, Tirkani AN, Ghazizadeh H, Iranifar E, Mohagheg F, Anoshrvani AA, Ghasemi F. Evaluation of the two polymorphisms rs1801133 in MTHFR and rs10811661 in CDKN2A/B in breast cancer. J Cell Biochem 2019; 120:2090-2097. [PMID: 30362613 DOI: 10.1002/jcb.27517] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/27/2018] [Indexed: 01/24/2023]
Abstract
The 5,10-Methylenetetrahydrofolate reductase (MTHFR) was the rate-limiting enzyme in the methyl cycle, which was encoded by the MTHFR gene. MTHFR played a key role in homocysteine plasma level and was associated with the risk of breast cancer. The cyclin-dependent kinase (CDK) inhibitor (CDKN2A/B) was the tumor suppressor in the cell cycle regulation. The single-nucleotide polymorphism was thought to be associated with the predisposition of breast cancer and in subsequent immune response in different populations. The current study was conducted on a peripheral blood sample of 100 Iranian women with breast carcinoma and 142 cancer-free healthy female volunteers. The TaqMan real-time polymerase chain reaction technique was applied for genotyping of participants. The correlation of both variants and demographic data were investigated with the risk of breast cancer. Our data showed that the MTHFR allele T and TT genotype had the higher prevalence in patients (P < 0.0001) than the control group. The frequency of risk C allele into the CDKN2A/B rs10811661 was 72%. The correlations of menarche and underlying hormonal disorder with the risk of breast cancer were investigated; also our results showed that the menopause status was statistically significant between patients and controls (P = 0.036). Our investigations demonstrated that the MTHFR rs180113 and CDKN2A/B rs10811661 had a significant correlation with the elevated risk of breast cancer and they might be potentially valuable to apply as a prognostic factor for individual health care.
Collapse
Affiliation(s)
- Amirreza Hesari
- Department of Biotechnology, Molecular and Medicine Research Center, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Nosrati Tirkani
- Department of Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamideh Ghazizadeh
- Molecular Medicine Group, Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elmira Iranifar
- Torbat Heydariyeh University of Medical Sciences, Torbat-e Heydarieh, Iran
| | - Fatoalah Mohagheg
- Department of Internal Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Ali Arash Anoshrvani
- Department of Internal Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Faezeh Ghasemi
- Department of Biotechnology, Molecular and Medicine Research Center, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran.,Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| |
Collapse
|
17
|
Saito M, Okumura K, Isogai E, Araki K, Tanikawa C, Matsuda K, Kamijo T, Kominami R, Wakabayashi Y. A Polymorphic Variant in p19 Arf Confers Resistance to Chemically Induced Skin Tumors by Activating the p53 Pathway. J Invest Dermatol 2019; 139:1459-1469. [PMID: 30684556 DOI: 10.1016/j.jid.2018.12.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
Identification of the specific genetic variants responsible for the increased susceptibility to familial or sporadic cancers is important. Using a forward genetics approach to map such loci in a mouse skin cancer model, we previously identified a strong genetic locus, Stmm3, conferring resistance to chemically induced skin papillomas on chromosome 4. Here, we report the cyclin-dependent kinase inhibitor gene Cdkn2a/p19Arf as a major responsible gene for the Stmm3 locus. We provide evidence that the function of Stmm3 is dependent on p53 and that p19ArfMSM confers stronger resistance to papillomas than p16Ink4aMSMin vivo. In addition, we found that genetic polymorphism in p19Arf between a resistant strain, MSM/Ms (Val), and a susceptible strain, FVB/N (Leu), alters the susceptibility to papilloma development, malignant conversion, and the epithelial-mesenchymal transition. Moreover, we demonstrated that the p19ArfMSM allele more efficiently activates the p53 pathway than the p19ArfFVB allele in vitro and in vivo. Furthermore, we found polymorphisms in CDKN2A in the vicinity of a polymorphism in mouse Cdkn2a associated with the risk of human cancers in the Japanese population. Genetic polymorphisms in Cdkn2a and CDKN2A may affect the cancer risk in both mice and humans.
Collapse
Affiliation(s)
- Megumi Saito
- Department of Carcinogenesis Research, Division of Experimental Animal Research, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Kazuhiro Okumura
- Department of Carcinogenesis Research, Division of Experimental Animal Research, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Eriko Isogai
- Department of Carcinogenesis Research, Division of Experimental Animal Research, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto, Japan
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan; Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Ryo Kominami
- Department of Molecular Physiology, Niigata University School of Medicine, Niigata, Japan
| | - Yuichi Wakabayashi
- Department of Carcinogenesis Research, Division of Experimental Animal Research, Chiba Cancer Center Research Institute, Chiba, Japan.
| |
Collapse
|
18
|
Ghobadi N, Mehramiz M, ShahidSales S, Rezaei Brojerdi A, Anvari K, Khazaei M, Rezayi M, Sadegh Khorrami M, Joudi‐Mashhad M, Ramshini H, Ahmadi‐Simab S, Moradi A, Hassanian SM, Ghayour‐Mobarhan M, Boroushaki MT, Ferns GA, Avan A. A genetic variant in
CDKN2A/2B
locus was associated with poor prognosis in patients with esophageal squamous cell carcinoma. J Cell Physiol 2018; 234:5070-5076. [PMID: 30238987 DOI: 10.1002/jcp.27310] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is among the leading causes of cancer related death. Despite of extensive efforts in identifying valid cancer prognostic biomarkers, only a very small number of markers have been identified. Several genetic variants in the 9p21 region have been identified that are associated with the risk of multiple cancers. Here, we explored the association of two genetic variants in the 9p21 region, CDKN2A/B, rs10811661, and rs1333049 for the first time in 273 subjects with, or without ESCC. We observed that the patients with ESCC had a higher frequency of a TT genotype for rs10811661 than individuals in the control group, and this polymorphism was also associated with tumor size. Moreover, a CC genotype for the rs1333049 polymorphism was associated with a reduced overall survival (OS) of patients with ESCC. In particular, patients with a CC (rs1333049) genotype had a significantly shorter OS (CC genotype: 34.5 ± 8.9 months vs. CG+GG: 47.7 ± 5.9 months; p value = 0.03). We have also shown the association of a novel genetic variant in CDKN2B gene with clinical outcome of patients with ESCC. Further investigations are warranted in a larger population to explore the value of emerging markers as a risk stratification marker in ESCC.
Collapse
Affiliation(s)
- Niloofar Ghobadi
- Department of Biochemistry Faculty of Sciences, Payam‐e Noor University of Mashhad Mashhad Iran
- Department of Biology Payam e Noor University, Branch of Sabzevar Sabzevar Iran
| | - Mehrane Mehramiz
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | | | | | - Kazem Anvari
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Majid Khazaei
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | - Majid Rezayi
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | - Mohammad Sadegh Khorrami
- Department of Modern Sciences and Technologies School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Mona Joudi‐Mashhad
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Hassan Ramshini
- Department of Biology Payam e Noor University, Branch of Sabzevar Sabzevar Iran
| | | | - Ali Moradi
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Seyed Mahdi Hassanian
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
- Department of Medical Biochemistry School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | | | - Mohammad Taher Boroushaki
- Department of Pharmacology and Pharmacological Research Center of Medicinal Plants Faculty of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Gordon A. Ferns
- Division of Medical Education Brighton & Sussex Medical School Brighton Sussex UK
| | - Amir Avan
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
- Department of Modern Sciences and Technologies School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| |
Collapse
|
19
|
p27-V109G Polymorphism Is Not Associated with the Risk of Prostate Cancer: A Case-Control Study of Han Chinese Men in Central China. DISEASE MARKERS 2018; 2018:1418609. [PMID: 29750086 PMCID: PMC5884233 DOI: 10.1155/2018/1418609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/28/2018] [Indexed: 12/16/2022]
Abstract
Objective We conducted an update meta-analysis aiming to verify the association between p27-V109G polymorphism and cancer risk, particular for prostate cancer (PCa). Then, we conducted a case-control study of Han Chinese in central China to verify the evidence-based results. Methods Relevant studies were collected from diverse databases up to March 2017. In addition, a hospital-based (H-B) case-control study enrolling 90 PCa patients and 140 healthy controls was included to verify these evidence-based findings. Genetic risk was calculated by odds ratio (OR) with its corresponding 95% confidence interval (CI). The p27-V109G polymorphism was determined by MassARRAY genotyping method. Results Finally, twenty-four published studies comprising 9627 cases and 12,102 controls were enrolled for the current meta-analysis. Overall analysis suggested that p27-V109G polymorphism decreased overall cancer risk in allelic contrast, heterozygote, and dominant models. When stratified analysis was conducted by ethnicity, data revealed that p27-V109G polymorphism was associated with a decreased cancer risk in Caucasians. Highlighted in the subgroup analysis by cancer type, we uncovered a significantly decreased risk of PCa in allelic contrast, dominant, homogeneous, and recessive models. However, in the validation case-control study, we failed to uncover a positive association between p27-V109G polymorphism and PCa risk. In addition, negative results were also identified when subgroup analyses were stratified by age, tumor grade, tumor stage, PSA levels, and other measurements. Conclusion Although evidence-based results suggest that p27-V109G polymorphism plays a protective role in overall cancer risk, particularly for PCa, our case-control study failed to validate any association between this particular polymorphism and PCa risk.
Collapse
|
20
|
Cheng XK, Wang XJ, Li XD, Ren XQ. Genetic association between the cyclin-dependent kinase inhibitor gene p27/Kip1 polymorphism (rs34330) and cancer susceptibility: a meta-analysis. Sci Rep 2017; 7:44871. [PMID: 28317869 PMCID: PMC5357887 DOI: 10.1038/srep44871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 02/15/2017] [Indexed: 12/19/2022] Open
Abstract
The p27 rs34330 (-79C/T) polymorphism has been widely studied for human cancer susceptibility. The current findings, however, still remained controversial. Therefore, we performed the meta-analysis to provide a more accurate result. Eligible studies were identified from PubMed database up to June 2015. The association of p27 rs34330 polymorphism and cancer susceptibility was estimated with odds ratios and corresponding 95% confidence intervals. The meta-analysis was performed with Stata 12. A total of ten studies with 11,214 cases and more than 8,776 controls were included in the meta-analysis (including breast, lung, thyroid, endometrial, and hepatocellular cancer). In pooled analysis, p27 gene rs34330 polymorphism significantly increased the cancer susceptibility. Subgroup analysis indicated that the elevated risk was observed under all the genetic models for Asians and under three genetic models for Caucasians. Results of sensitivity analysis were similar to the overall results. The results suggested that the p27 rs34330 polymorphism increased the cancer susceptibility, especially in Asians. Further well-designed and large sample size studies are warranted to verify the conclusion.
Collapse
Affiliation(s)
- Xiao-Ke Cheng
- Center for Evidence-Based Medicine, Huaihe Hospital of Henan University, Kaifeng, Henan, 475000, China
| | - Xue-Jun Wang
- Department of Emergency, Beijing Electric Power Hospital, Taipingxili Jia 1, Beijing, 100073, China
| | - Xiao-Dong Li
- Center for Evidence-Based Medicine, Huaihe Hospital of Henan University, Kaifeng, Henan, 475000, China.,Department of Urology, Huaihe Hospital of Henan University, Kaifeng, Henan, 475000, China
| | - Xue-Qun Ren
- Center for Evidence-Based Medicine, Huaihe Hospital of Henan University, Kaifeng, Henan, 475000, China.,Department of Urology, Huaihe Hospital of Henan University, Kaifeng, Henan, 475000, China.,Department of General Surgery, Huaihe Hospital of Henan University, Kaifeng, Henan, 475000, China
| |
Collapse
|
21
|
ShahidSales S, Mehramiz M, Ghasemi F, Aledavood A, Shamsi M, Hassanian SM, Ghayour-Mobarhan M, Avan A. A genetic variant in CDKN2A/B gene is associated with the increased risk of breast cancer. J Clin Lab Anal 2017; 32. [PMID: 28276595 DOI: 10.1002/jcla.22190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 01/27/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Breast cancer is among the leading cause of cancer-related-deaths in women, supporting the need for the identification of novel prognostic and predictive biomarkers. Recent studies have identified common genetic variants in a region on chromosome 9p21 associated with an increased risk of developing different cancers. Here, we explored the association of a genetic variant in CDKN2A/B, rs10811661, for the first time in 564 subjects with/without breast cancer. METHOD Genotyping was performed using TaqMan real time PCR method. The associations of this genetic variant with breast cancer risk and pathological information of patients were assessed. RESULTS We observed that patients with breast cancer had a higher frequency of TT genotype (P<.001) than control group, which was associated with advanced TNM classification (P=.04) and larger tumor size (P=.014), as detected by the recessive genetic inheritance model. Moreover, the logistic regression under recessive genetic model revealed that breast cancer patients with TT had higher risk of breast cancer, compared to CC/CT genotypes (eg, OR=4.9, 95% CI:1.9-12, P=.001), after adjusted for potential confounders, age, BMI, and family history. CONCLUSION We demonstrated that patients carrying the TT genotype for CDKN2A/B rs10811661 polymorphism had the increased risk of breast cancer susceptibility. However, further investigations are warranted in a larger and prospective setting to explore the value of this marker as a risk stratification marker in breast cancer.
Collapse
Affiliation(s)
- Soodabeh ShahidSales
- Cancer Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehraneh Mehramiz
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Faezeh Ghasemi
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Amir Aledavood
- Cancer Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehri Shamsi
- Cancer Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Department of Medical Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Metabolic syndrome Research center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Ghayour-Mobarhan
- Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Metabolic syndrome Research center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic syndrome Research center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
22
|
Paul MR, Levitt NP, Moore DE, Watson PM, Wilson RC, Denlinger CE, Watson DK, Anderson PE. Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. BMC Genomics 2016; 17:263. [PMID: 27029813 PMCID: PMC4815211 DOI: 10.1186/s12864-016-2542-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive modeling of disease phenotype for the prioritization of candidate biomarkers. The continuous nature of SNV allele fraction features allows the concurrent investigation of several genomic phenomena, including allele specific expression, clonal expansion and/or deletion, and copy number variation. RESULTS The proposed software pipeline and package, SNV Discriminant Analysis (SNV-DA), was applied on two RNA-Seq datasets with varying sample sizes sequenced at different depths: a dataset containing primary tumors from twenty patients with different disease outcomes in lung adenocarcinoma and a larger dataset of primary tumors representing two major breast cancer subtypes, estrogen receptor positive and triple negative. Predictive models were generated using the machine learning algorithm, sparse projections to latent structures discriminant analysis. Training sets composed of RNA-Seq SNV features limited to genomic regions of origin (e.g. exonic or intronic) and/or RNA-editing sites were shown to produce models with accurate predictive performances, were discriminant towards true label groupings, and were able to produce SNV rankings significantly different from than univariate tests. Furthermore, the utility of the proposed methodology is supported by its comparable performance to traditional models as well as the enrichment of selected SNVs located in genes previously associated with cancer and genes showing allele-specific expression. As proof of concept, we highlight the discovery of a previously unannotated intergenic locus that is associated with epigenetic regulatory marks in cancer and whose significant allele-specific expression is correlated with ER+ status; hereafter named ER+ associated hotspot (ERPAHS). CONCLUSION The use of models from RNA-Seq SNVs to identify and prioritize candidate molecular targets for biomarker discovery is supported by the ability of the proposed method to produce significantly accurate predictive models that are discriminant towards true label groupings. Importantly, the proposed methodology allows investigation of mutations outside of exonic regions and identification of interesting expressed loci not included in traditional gene annotations. An implementation of the proposed methodology is provided that allows the user to specify SNV filtering criteria and cross-validation design during model creation and evaluation.
Collapse
Affiliation(s)
- Matt R Paul
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA. .,Department of Cancer Biology, University of Pennsylvania, 421 Curie Blvd, Philadelphia, PA, USA.
| | - Nicholas P Levitt
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| | - David E Moore
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| | - Patricia M Watson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Robert C Wilson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Chadrick E Denlinger
- Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Surgery, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Dennis K Watson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| |
Collapse
|
23
|
Dai X, Zhang X, Wang B, Wang C, Jiang J, Wu C. Association Between Polymorphism rs678653 in Human Cyclin D1 Gene (CCND1) and Susceptibility to Cancer: A Meta-Analysis. Med Sci Monit 2016; 22:863-74. [PMID: 26979757 PMCID: PMC4798325 DOI: 10.12659/msm.895237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background To assess the association between polymorphism rs678653 in human Cyclin D1 gene (CCND1) and the risk of cancer. Material/Methods Multiple biomedical databases were systematically searched. Pooled odds ratios (OR) and 95% confidence intervals (95% CIs) were calculated in the appropriate model. Results In total, 17 case-control studies from 14 articles were included. When combing all available data, no significant association of rs678653 with cancer risk was observed under different genetic models. Stratification by ethnicity also indicated that rs678653 was not correlated with cancer risk in Taiwanese or Indian populations. When stratified by cancer type, no significant association was found between polymorphism rs678653 and digestive tract cancer, head and neck cancer, and gynecological cancer risk. Conclusions Our comprehensive meta-analysis suggests that the polymorphism rs678653 in CCND1 has no association with cancer risk in different population and disease contexts, indicating that CCND1 rs678653 does not serve a significant biological function in predicting cancer risk.
Collapse
Affiliation(s)
- Xichao Dai
- Department of Tumor Biological Treatment, The third Affiliated Hospital, Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Xizhi Zhang
- Department of Oncology, Subei People's Hospital of Jiangsu Province, Clinical Medical Medical College of Yangzhou University, Suzhou, Jiangsu, China (mainland)
| | - Buhai Wang
- Department of Oncology, Subei People's Hospital of Jiangsu Province, Clinical Medical Medical College of Yangzhou University, Suzhou, Jiangsu, China (mainland)
| | - Chaomin Wang
- Department of Oncology, Subei People's Hospital of Jiangsu Province, Clinical Medical Medical College of Yangzhou University, Suzhou, Jiangsu, China (mainland)
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Changping Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, Suzhou, Jiangsu, China (mainland)
| |
Collapse
|
24
|
Lu Y, Gao K, Zhang M, Zhou A, Zhou X, Guan Z, Shi X, Ge S. Genetic Association Between CDKN1B rs2066827 Polymorphism and Susceptibility to Cancer. Medicine (Baltimore) 2015; 94:e1217. [PMID: 26579796 PMCID: PMC4652805 DOI: 10.1097/md.0000000000001217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Much attention has been directed to the association between cancer risk and rs2066827 polymorphism of the CDKN1B gene. However, the results are indefinitive and inconclusive. This study was devised to evaluate the hypothesis that rs2066827 polymorphism is associated with the risk of cancer.Computer-based databases (EMBASE, PubMed, and CNKI) were used to seek all case-control studies evaluating rs2066827 polymorphism and susceptibility to cancer. The genetic risk was assessed by calculating pooled odds ratio (OR) with its corresponding 95% confidence interval (CI). Fixed-effects pooled ORs were calculated by the Mantel-Haenszel method (Ph > 0.05), and random-effects pooled ORs were estimated by the DerSimonian-Laird method (Ph < 0.05).Data on rs2066827 polymorphism and cancer risk were available for 9038 cancer cases and 11,596 controls participating in 17 studies. Carriage of a TG genotype was associated with a minor but significant decrease in the risk of cancer (pooled OR 0.92, 95% CI: 0.86-0.99; model, TG vs. TT). We observed a moderately decreased risk of ovarian cancer based on 1829 cases and 2868 controls (pooled OR 0.85, 95% CI: 0.74-0.97; model, TG vs. TT). A slightly deceased risk of cancer was also indicated in Caucasians consisting of 6707 cases and 8279 controls (pooled OR 0.91, 95% CI: 0.85-0.98; model, TG vs. TT).These data suggest that carriage of a TG genotype at rs2066827 polymorphism may be associated with decreased susceptibility to cancer, ovarian cancer in particular.
Collapse
Affiliation(s)
- Yongchao Lu
- From the Department of Traditional Chinese Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China (YL, AZ, ZG, XS); Department of Anorectal Surgery, Central Hospital of Jinan City, Jinan, China (KG); Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China (MZ); and Department of Science and Education, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China (XZ, SG)
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Huang YS, Fan QQ, Li C, Nie M, Quan HY, Wang L. Quantitative Assessment the Relationship between p21 rs1059234 Polymorphism and Cancer Risk. Asian Pac J Cancer Prev 2015; 16:4435-8. [PMID: 26028110 DOI: 10.7314/apjcp.2015.16.10.4435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
p21 is a cyclin-dependent kinase inhibitor, which can arrest cell proliferation and serve as a tumor suppressor. Though many studies were published to assess the relationship between p21 rs1059234 polymorphism and various cancer risks, there was no definite conclusion on this association. To derive a more precise quantitative assessment of the relationship, a large scale meta-analysis of 5,963 cases and 8,405 controls from 16 eligible published case-control studies was performed. Our analysis suggested that rs1059234 was not associated with the integral cancer risk for both dominant model [(T/T+C/T) vs C/C, OR=1.00, 95% CI: 0.84-1.18] and recessive model [T/T vs (C/C+C/T), OR=1.03, 95% CI: 0.93-1.15)]. However, further stratified analysis showed rs1059234 was greatly associated with the risk of squamous cell carcinoma of head and neck (SCCHN). Thus, larger scale primary studies are still required to further evaluate the interaction of p21 rs1059234 polymorphism and cancer risk in specific cancer subtypes.
Collapse
Affiliation(s)
- Yong-Sheng Huang
- Institute of Basic Medical Sciences and School of Basic Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China E-mail :
| | | | | | | | | | | |
Collapse
|
26
|
Barbieri RB, Bufalo NE, Secolin R, Assumpção LVM, Maciel RMB, Cerutti JM, Ward LS. Polymorphisms of cell cycle control genes influence the development of sporadic medullary thyroid carcinoma. Eur J Endocrinol 2014; 171:761-7. [PMID: 25565272 DOI: 10.1530/eje-14-0461] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The role of key cell cycle regulation genes such as, CDKN1B, CDKN2A, CDKN2B, and CDKN2C in sporadic medullary thyroid carcinoma (s-MTC) is still largely unknown. METHODS In order to evaluate the influence of inherited polymorphisms of these genes on the pathogenesis of s-MTC, we used TaqMan SNP genotyping to examine 45 s-MTC patients carefully matched with 98 controls. RESULTS A multivariate logistic regression analysis demonstrated that CDKN1B and CDKN2A genes were related to s-MTC susceptibility. The rs2066827*GT+GG CDKN1B genotype was more frequent in s-MTC patients (62.22%) than in controls (40.21%), increasing the susceptibility to s-MTC (OR=2.47; 95% CI=1.048-5.833; P=0.038). By contrast, the rs11515*CG+GG of CDKN2A gene was more frequent in the controls (32.65%) than in patients (15.56%), reducing the risk for s-MTC (OR=0.174; 95% CI=0.048-0.627; P=0.0075). A stepwise regression analysis indicated that two genotypes together could explain 11% of the total s-MTC risk. In addition, a relationship was found between disease progression and the presence of alterations in the CDKN1A (rs1801270), CDKN2C (rs12885), and CDKN2B (rs1063192) genes. WT rs1801270 CDKN1A patients presented extrathyroidal tumor extension more frequently (92%) than polymorphic CDKN1A rs1801270 patients (50%; P=0.0376). Patients with the WT CDKN2C gene (rs12885) presented larger tumors (2.9±1.8 cm) than polymorphic patients (1.5±0.7 cm; P=0.0324). On the other hand, patients with the polymorphic CDKN2B gene (rs1063192) presented distant metastases (36.3%; P=0.0261). CONCLUSION In summary, we demonstrated that CDKN1B and CDKN2A genes are associated with susceptibility, whereas the inherited genetic profile of CDKN1A, CDKN2B, and CDKN2C is associated with aggressive features of tumors. This study suggests that profiling cell cycle genes may help define the risk and characterize s-MTC aggressiveness.
Collapse
Affiliation(s)
- R B Barbieri
- University of Campinas (FCM - Unicamp)126, Tessalia Vieira de Camargo, Street. Cidade Universitaria Zeferino Vaz, Campinas - São Paulo, 13083-887 BrazilFederal University of Sao Paulo (Unifesp)669, Pedro Toledo Street, São Paulo-SP 04039-032, Brazil
| | - N E Bufalo
- University of Campinas (FCM - Unicamp)126, Tessalia Vieira de Camargo, Street. Cidade Universitaria Zeferino Vaz, Campinas - São Paulo, 13083-887 BrazilFederal University of Sao Paulo (Unifesp)669, Pedro Toledo Street, São Paulo-SP 04039-032, Brazil
| | - R Secolin
- University of Campinas (FCM - Unicamp)126, Tessalia Vieira de Camargo, Street. Cidade Universitaria Zeferino Vaz, Campinas - São Paulo, 13083-887 BrazilFederal University of Sao Paulo (Unifesp)669, Pedro Toledo Street, São Paulo-SP 04039-032, Brazil
| | - L V M Assumpção
- University of Campinas (FCM - Unicamp)126, Tessalia Vieira de Camargo, Street. Cidade Universitaria Zeferino Vaz, Campinas - São Paulo, 13083-887 BrazilFederal University of Sao Paulo (Unifesp)669, Pedro Toledo Street, São Paulo-SP 04039-032, Brazil
| | - R M B Maciel
- University of Campinas (FCM - Unicamp)126, Tessalia Vieira de Camargo, Street. Cidade Universitaria Zeferino Vaz, Campinas - São Paulo, 13083-887 BrazilFederal University of Sao Paulo (Unifesp)669, Pedro Toledo Street, São Paulo-SP 04039-032, Brazil
| | - J M Cerutti
- University of Campinas (FCM - Unicamp)126, Tessalia Vieira de Camargo, Street. Cidade Universitaria Zeferino Vaz, Campinas - São Paulo, 13083-887 BrazilFederal University of Sao Paulo (Unifesp)669, Pedro Toledo Street, São Paulo-SP 04039-032, Brazil
| | - L S Ward
- University of Campinas (FCM - Unicamp)126, Tessalia Vieira de Camargo, Street. Cidade Universitaria Zeferino Vaz, Campinas - São Paulo, 13083-887 BrazilFederal University of Sao Paulo (Unifesp)669, Pedro Toledo Street, São Paulo-SP 04039-032, Brazil
| |
Collapse
|
27
|
Identification of differently expressed genes with specific SNP Loci for breast cancer by the integration of SNP and gene expression profiling analyses. Pathol Oncol Res 2014; 21:469-75. [PMID: 25408372 DOI: 10.1007/s12253-014-9851-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 10/14/2014] [Indexed: 01/06/2023]
Abstract
This study aims to explore the relationship between gene polymorphism and breast cancer, and to screen DEGs (differentially expressed genes) with SNPs (single nucleotide polymorphisms) related to breast cancer. The SNPs of 17 patients and the preprocessed SNP profiling GSE 32258 (38 cases of normal breast cells) were combined to identify their correlation with breast cancer using chi-square test. The gene expression profiling batch8_9 (38 cases of patients and 8 cases of normal tissue) was preprocessed with limma package, and the DEGs were filtered out. Then fisher's method was applied to integrate DEGs and SNPs associated with breast cancer. With NetBox software, TRED (Transcriptional Regulatory Element Database) and UCSC (University of California Santa Cruz) database, genes-associated network and transcriptional regulatory network were constructed using cytoscape software. Further, GO (Gene Ontology) and KEGG analyses were performed for genes in the networks by using siggenes. In total, 332 DEGs were identified. There were 160 breast cancer-related SNPs related to 106 genes of gene expression profiling (19 were significant DEGs). Finally, 11co-correlated DEGs were selected. In genes-associated network, 9 significant DEGs were correlated to 23 LINKER genes while, in transcriptional regulatory network, E2F1 had regulatory relationships with 7 DEGs including MTUS1, CD44, CCNB1 and CCND2. KRAS with SNP locus of rs1137282 was involved in 35 KEGG pathways. The genes of MTUS1, CD44, CCNB1, CCND2 and KRAS with specific SNP loci may be used as biomarkers for diagnosis of breast cancer. Besides, E2F1 was recognized as the transcription factor of 7 DEGs including MTUS1, CD44, CCNB1 and CCND2.
Collapse
|
28
|
Genetic association between cyclin D1 polymorphism and breast cancer susceptibility. Tumour Biol 2014; 35:11959-65. [PMID: 25399071 DOI: 10.1007/s13277-014-2489-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 08/12/2014] [Indexed: 01/15/2023] Open
Abstract
Cyclin D1 polymorphism has been reported to be associated with risk of breast cancer, but the published studies have yielded controversial results. This study was undertaken to derive a precise risk estimate for the cyclin D1 polymorphism associated with breast cancer risk. We performed a search of EMBASE, PubMed, and Web of Science. In total, data from 18 publications were pooled and the association was assessed by odds ratios (ORs) with 95 % confidence intervals (CIs). This analysis showed that there was no obvious association between the cyclin D1 polymorphism and breast cancer risk in any of the analyzed genetic model. We found the same negative association in stratified analyses by ethnicity, source of controls, and sample size. Our meta-analysis provides an estimate that the presence of cyclin D1 polymorphism may not confer susceptibility to breast cancer.
Collapse
|
29
|
Hryhorowicz S, Ziemnicka K, Kaczmarek-Ryś M, Hoppe-Gołębiewska J, Pławski A, Skrzypczak-Zielińska M, Szkudlarek M, Gołąb M, Budny B, Ruchała M, Słomski R. CCND1 gene polymorphic variants in patients with differentiated thyroid carcinoma. Oncol Lett 2014; 9:442-448. [PMID: 25436006 PMCID: PMC4247015 DOI: 10.3892/ol.2014.2617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 09/11/2014] [Indexed: 01/15/2023] Open
Abstract
Alterations in the CCND1 gene affect the cell cycle and are frequently observed in a variety of cancers. While the most frequent mutations that occur in thyroid tumor tissue have been characterized, the genetic factors that predispose individuals to differentiated thyroid cancer (DTC) remain to be elucidated. The present study examined whether the CCND1 c.723G>A (rs9344; p.Pro241=) and c.669C>T (rs3862792; p.Phe223=) variants have an impact on DTC susceptibility. A cohort consisting of 652 patients diagnosed with DTC were analyzed and comapred with a reference group of 799 subjects from the general population. Pyrosequencing was used as the genotyping technique. In order to determine the statistical significance of differences observed in the genotypic and allelic frequencies between the compared groups, GraphPad Prism 4 was used. At the rs9344 locus in the DTC patients, a higher frequency of allele A [P=0.032; odds ratio (OR), 1.18; 95% confidence interval (CI), 1.014–1.361] and the AA homozygous genotype (P=0.028; OR, 1.41; 95% CI, 1.059–1.989) was observed compared with the control population group. The differences were stronger for papillary carcinomas (OR 1.45; 95% CI, 1.059–1.989), but were not significant in follicular tumors. No statistically significant differences were noted in the frequency of genotypes or alleles at the rs3862792 locus in the examined groups. The present findings indicate that the c.723A variant of the CCDN1 gene may be a susceptibility low penetrance allele in the development of papillary thyroid cancer in the population studied, however it does not impact on multifocality, metastatic ability or age at diagnosis. A cumulative effect of the analyzed CCND1 gene variants was also excluded.
Collapse
Affiliation(s)
- Szymon Hryhorowicz
- NanoBioMedical Center, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Katarzyna Ziemnicka
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, Poznań 60-355, Poland
| | - Marta Kaczmarek-Ryś
- Institute of Human Genetics, Polish Academy of Sciences, Poznań 60-479, Poland
| | | | - Andrzej Pławski
- Institute of Human Genetics, Polish Academy of Sciences, Poznań 60-479, Poland
| | | | - Małgorzata Szkudlarek
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, Poznań 60-355, Poland
| | - Monika Gołąb
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, Poznań 60-355, Poland
| | - Bartłomiej Budny
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, Poznań 60-355, Poland
| | - Marek Ruchała
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, Poznań 60-355, Poland
| | - Ryszard Słomski
- NanoBioMedical Center, Adam Mickiewicz University, Poznań 61-614, Poland ; Institute of Human Genetics, Polish Academy of Sciences, Poznań 60-479, Poland ; Department of Biochemistry and Biotechnology, University of Life Sciences, Poznań 60-632, Poland
| |
Collapse
|
30
|
Association between CCNE1 polymorphisms and the risk of breast cancer in a sample of southeast Iranian population. Med Oncol 2014; 31:189. [PMID: 25159285 DOI: 10.1007/s12032-014-0189-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 08/13/2014] [Indexed: 12/19/2022]
Abstract
Cyclin E1 (CCNE1) is a key proto-oncogene. The present study aimed to investigate the effects of single nucleotide polymorphisms in CCNE1 on the risk of breast cancer (BC) in an Iranian population in southeast of Iran. A total of 491 subjects including 266 BC patients and 225 healthy control women were participated in the study. Genotyping of CCNE1 rs3218073 and 72010703 polymorphisms was done using allele-specific polymerase chain reaction (AS-PCR) and rs1406 by PCR-RFLP method.Our findings showed that rs1406 C/A polymorphism increased the risk of BC in codominant (OR 1.60, 95% CI 1.05-2.43, p=0.032 CA vs CC; OR 2.35, 95% CI 1.23-4.49, p=0.011 AA vs CC) and dominant (OR 1.69, 95% CI 1.22-2.56, p=0.012 CA+AA vs CC) inheritance models. The rs1406 A allele increased the risk of BC (OR 1.37, 95% CI 1.06-1.76, p=0.019) in comparison with C allele. On the other hand, CCNE1 rs72010703 (4-bp I/D) and rs3218073 polymorphisms did not show any significant association with BC. This study indicates that CCNE1 rs1406 polymorphism may contribute to BC risk.
Collapse
|
31
|
Murali A, Nalinakumari KR, Thomas S, Kannan S. Association of single nucleotide polymorphisms in cell cycle regulatory genes with oral cancer susceptibility. Br J Oral Maxillofac Surg 2014; 52:652-8. [PMID: 24947332 DOI: 10.1016/j.bjoms.2014.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 05/21/2014] [Indexed: 12/13/2022]
Abstract
Alterations in the regulation of the cell cycle are strongly linked to tumorigenesis, so genetic variants in genes critical to control of the cycle are good candidates to have their association with susceptibility to oral cancer assessed. In this hospital-based, case-control study of 445 patients who had been newly-diagnosed with oral cancer and 449 unaffected controls, we used a multigenic approach to examine the associations among a panel of 10 selected polymorphisms in the pathway of the cell cycle that were possibly susceptible to oral cancer. Six of 9 single nucleotide polymorphisms in the cell cycle showed significant risks for oral cancer, the highest risk being evident for p27 (rs34329; Odds ratio 3.05, 95% CI 2.12 to 4.40). A significant risk of oral cancer was also evident for individual polymorphisms of cyclin E (rs1406), cyclin H (rs3093816), cyclin D1-1 (rs647451), cyclin D2 (rs3217901) and Rb1-2 (rs3092904). The risk of oral cancer increased significantly as the number of unfavourable genotypes in the pathway increased, and so the results point to a stronger combined effect of polymorphisms in important cell cycle regulatory genes on predisposition to oral cancer.
Collapse
Affiliation(s)
- Abitha Murali
- Laboratory of Cell Cycle Regulation & Molecular Oncology, Division of Cancer Research, Regional Cancer Centre, Thiruvananthapuram - 695 011, Kerala, India
| | - K R Nalinakumari
- Division of Dental Surgery, Regional Cancer Centre, Thiruvananthapuram - 695 011, Kerala, India
| | - Shaji Thomas
- Division of Surgical Oncology, Regional Cancer Centre, Thiruvananthapuram - 695 011, Kerala, India
| | - S Kannan
- Laboratory of Cell Cycle Regulation & Molecular Oncology, Division of Cancer Research, Regional Cancer Centre, Thiruvananthapuram - 695 011, Kerala, India.
| |
Collapse
|
32
|
Xiang H, Li H, Ge W, Wu W, Gao M, Wang W, Hong L, Jiang D, Zhang C. Association of CDKN1B gene polymorphisms with susceptibility to breast cancer: a meta-analysis. Mol Biol Rep 2014; 40:6371-7. [PMID: 24078094 DOI: 10.1007/s11033-013-2751-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 09/14/2013] [Indexed: 01/15/2023]
Abstract
A number of case–control studies have been conducted to investigate the association of CDKN1B gene polymorphisms with breast cancer. However, these studies reported conflicting results. The aim of our study was to quantitatively summarize the association of CDKN1B gene polymorphisms with breast cancer. Systemic searches of the PubMed, Excerpta Medica Database, and Chinese Biomedical Literature Database databases were performed, with the last report up to Oct 2012. Odds ratios (ORs) with 95 % confidence intervals (CIs) were used to assess the strength of the association. Seven studies including 6,822 cases and 7,186 controls were involved in this meta-analysis, which was performed for two CDKN1B gene polymorphisms (rs2066827 and rs34330). Significant association was found for rs34330 polymorphism (T versus C: OR = 1.10, 95 % CI = 1.03–1.18, P = 0.003; CT + TT versus CC: OR = 1.38, 95 % CI = 0.98–1.93, P = 0.07; TT versus CC + CT: OR = 1.06, 95 % CI = 0.93–1.21, P = 0.38; TT versus CC: OR = 1.23, 95 % CI = 1.04–1.45, P = 0.02; CT versus CC: OR = 1.42, 95 % CI = 0.97–2.09, P = 0.07), but not for rs2066827 polymorphism (G versus T: OR = 0.99, 95 % CI = 0.91–1.08, P = 0.84; TG + GG versus TT: OR = 0.98, 95 % CI = 0.89–1.08, P = 0.69; GG versus TT + TG: OR = 1.04, 95 % CI = 0.83–1.30, P = 0.75; GG versus TT: OR = 1.03, 95 % CI = 0.82–1.30, P = 0.77; TG versus TT: OR = 0.97, 95 % CI = 0.88–1.08, P = 0.58). This meta-analysis suggests that breast cancer may be associated with CDKN1B gene rs34330 polymorphism, but not rs2066827 polymorphism.
Collapse
|
33
|
Zhang H, Zhou Y, Rui Y, Wang Y, Li J, Rong L, Wang M, Tong N, Zhang Z, Chen J, Fang Y. Association between the polymorphism rs3217927 of CCND2 and the risk of childhood acute lymphoblastic leukemia in a Chinese population. PLoS One 2014; 9:e95059. [PMID: 24743557 PMCID: PMC3990598 DOI: 10.1371/journal.pone.0095059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/23/2014] [Indexed: 01/25/2023] Open
Abstract
CyclinD proteins, the ultimate recipients of mitogenic and oncogenic signals, play a crucial role in cell-cycle regulation. CyclinD2, one of the cyclinD family, is overexpressed in T-acute lymphoblastic leukemia (ALL) and B-cell chronic lymphocytic leukemia and involved in the pathogenesis of leukemias. Recent reports indicated that CCND2 polymorphisms are associated with human cancer risk, thusly we hypothesized that CCND2 gene polymorphisms may contribute to childhood ALL susceptibility. We selected the polymorphism rs3217927 located in the 3'UTR region of CCND2 to assess its associations with childhood ALL risk in a case-control study. A significant difference was found in the genotype distributions of rs3217927 polymorphism between cases and controls (P = 0.019) and homozygous GG genotype may be an increased risk factor for childhood ALL (adjusted OR = 1.84, 95% CI = 1.14 -2.99). Furthermore, this increased risk was more pronounced with GG genotype among high-risk ALL (adjusted OR = 1.95, 95% CI = 1.04-3.67), low-risk ALL (adjusted OR = 2.09, 95% CI = 1.13-3.87), B-phenotype ALL patients (adjusted OR = 1.78, 95% CI = 1.08-2.95) and T-phenotype ALL patients (adjusted OR = 2.87, 95% CI = 1.16-7.13). Our results provide evidence that CCND2 polymorphism rs3217927 may be involved in the etiology of childhood ALL, and the GG genotype of rs3217927 may modulate the genetic susceptibility to childhood ALL in the Chinese population. Further functional studies and investigations in larger populations should be conducted to validate our findings.
Collapse
Affiliation(s)
- Heng Zhang
- Department of Hematology and Oncology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yan Zhou
- Department of Hematology and Oncology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yaoyao Rui
- Department of Hematology and Oncology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yaping Wang
- Department of Hematology and Oncology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Jie Li
- Department of Hematology and Oncology, Soochow Children's Hospital Affiliated to Soochow University, Suzhou, China
| | - Liuchen Rong
- Department of Hematology and Oncology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Molecular and Genetic Toxicology, Cancer Center of Nanjing Medical University, Nanjing, China
| | - Na Tong
- Department of Molecular and Genetic Toxicology, Cancer Center of Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Molecular and Genetic Toxicology, Cancer Center of Nanjing Medical University, Nanjing, China
| | - Jing Chen
- Department of Hematology and Oncology, Shanghai Children's Medical Center Affiliated to Shanghai, Jiao Tong University, Shanghai, China
- * E-mail: (YF); (JC)
| | - Yongjun Fang
- Department of Hematology and Oncology, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing, China
- * E-mail: (YF); (JC)
| |
Collapse
|
34
|
Jia ZM, Liu Y, Cui SY. Lack of association between cyclin-dependent kinase inhibitor 1B rs2066827 polymorphism and breast cancer susceptibility. Tumour Biol 2014; 35:5527-31. [PMID: 24523023 DOI: 10.1007/s13277-014-1727-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 02/04/2014] [Indexed: 01/15/2023] Open
Abstract
In order to make a comprehensive assessment of the potential association between one genetic variant in the cyclin-dependent kinase inhibitor 1B gene, rs2066827, and breast cancer risk, we conducted a meta-analysis of six epidemiological studies, which included 3,139 breast cancer cases and 2,936 controls. The data showed that rs2066827 polymorphism was not associated with increased breast cancer risk in overall population. When stratifying by the race, no noteworthy associations were observed in Asians or Caucasians. Based on this meta-analysis, we conclude that the cyclin-dependent kinase inhibitor 1B rs2066827 polymorphism might not be a risk factor for breast cancer development. Further studies, either with larger sample size or involving other SNPs and haplotypes of the cyclin-dependent kinase inhibitor 1B gene, are necessary to clarify the contribution of cyclin-dependent kinase inhibitor 1B rs2066827 in breast carcinogenesis.
Collapse
Affiliation(s)
- Zhong-Ming Jia
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital, Huangheer Road, Binzhou, 256603, Shandong, China,
| | | | | |
Collapse
|
35
|
Jaiswal PK, Singh V, Mittal RD. Polymorphism at P21 codon 31 and dinucleotide polymorphism of P73 gene and susceptibility to bladder cancer in individuals from North India. INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:293-300. [PMID: 24339541 PMCID: PMC3841553 DOI: 10.4103/0971-6866.120815] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND AIM: p73, a novel P53 homolog and plays an important role in modulating cell cycle control, apoptosis and cell growth while P21, functions to negatively control the cell cycle. P53 up regulates p21 expression in response to deoxyribonucleic acid damage leading to cell cycle arrest at G1 checkpoint. In the present study, we are targeting p21 codon 31 and p73 gene variants of G4C14-to-A4T14 (Exon 2) polymorphism for bladder cancer (BC) risk in North Indians. MATERIALS AND METHODS: The above gene variants of P21 and P73 were assessed in the case-control study comprising of 200 BC cases and 200 healthy controls of the same age, gender and similar ethnicity. Genotyping was performed by polymerase chain reaction (PCR) restriction fragment length polymorphism method and PCR-based confronting two-pair primers (PCR with CTPP). RESULTS: The variant genotype of p73Exon 2 polymorphism showed significant risk for BC (p = 0.014). While combining with heterozygous genotype, variant genotype of p73Exon2 showed a significant association with BC risk (p = 0.010). While in case of p21 codon31 showed no significant association for BC risk at genotypic level. Significant association between p73Exon2 polymorphism and smoking was observed for BC risk. Furthermore, gene combination analysis revealed that AT/AT-Ser/Ser is associated with risk for BC. Variant genotype of P73Exon2 was associated with reduced risk of recurrence (p = 0.039) in superficial BC patients receiving Bacillus Calmette-Guerin treatment thus showing least survival (log rank = 0.029). CONCLUSION: Our study provided evidence that the p73 G4C14 > A4T14 (Exon2) polymorphisms were associated with higher risk of BC in North Indian population.
Collapse
Affiliation(s)
- Praveen Kumar Jaiswal
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | | | | |
Collapse
|
36
|
Abstract
BACKGROUND The chromosome 9p21.3 region has been implicated in the pathogenesis of multiple cancers. METHODS We systematically examined up to 203 tagging SNPs of 22 genes on 9p21.3 (19.9-32.8 Mb) in eight case-control studies: thyroid cancer, endometrial cancer (EC), renal cell carcinoma, colorectal cancer (CRC), colorectal adenoma (CA), oesophageal squamous cell carcinoma (ESCC), gastric cardia adenocarcinoma and osteosarcoma (OS). We used logistic regression to perform single SNP analyses for each study separately, adjusting for study-specific covariates. We combined SNP results across studies by fixed-effect meta-analyses and a newly developed subset-based statistical approach (ASSET). Gene-based P-values were obtained by the minP method using the Adaptive Rank Truncated Product program. We adjusted for multiple comparisons by Bonferroni correction. RESULTS Rs3731239 in cyclin-dependent kinase inhibitors 2A (CDKN2A) was significantly associated with ESCC (P=7 × 10(-6)). The CDKN2A-ESCC association was further supported by gene-based analyses (Pgene=0.0001). In the meta-analyses by ASSET, four SNPs (rs3731239 in CDKN2A, rs615552 and rs573687 in CDKN2B and rs564398 in CDKN2BAS) showed significant associations with ESCC and EC (P<2.46 × 10(-4)). One SNP in MTAP (methylthioadenosine phosphorylase) (rs7023329) that was previously associated with melanoma and nevi in multiple genome-wide association studies was associated with CRC, CA and OS by ASSET (P=0.007). CONCLUSION Our data indicate that genetic variants in CDKN2A, and possibly nearby genes, may be associated with ESCC and several other tumours, further highlighting the importance of 9p21.3 genetic variants in carcinogenesis.
Collapse
|
37
|
Han JY, Wang H, Xie YT, Li Y, Zheng LY, Ruan Y, Song AP, Tian XX, Fang WG. Association of germline variation in CCNE1 and CDK2 with breast cancer risk, progression and survival among Chinese Han women. PLoS One 2012; 7:e49296. [PMID: 23185313 PMCID: PMC3504019 DOI: 10.1371/journal.pone.0049296] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 10/04/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Somatic alterations of cyclin-dependent kinase 2 (CDK2)-cyclin E complex have been shown to contribute to breast cancer (BC) development and progression. This study aimed to explore the effects of single nucleotide polymorphisms (SNPs) in CDK2 and CCNE1 (a gene encoding G1/S specific cyclin E1 protein, formerly called cyclin E) on BC risk, progression and survival in a Chinese Han population. METHODOLOGY/PRINCIPAL FINDINGS We herein genotyped 6 haplotype-tagging SNPs (htSNPs) of CCNE1 and 2 htSNPs of CDK2 in 1207 BC cases and 1207 age-matched controls among Chinese Han women, and then reconstructed haplotype blocks according to our genotyping data and linkage disequilibrium status of these htSNPs. For CCNE1, the minor allele homozygotes of three htSNPs were associated with BC risk (rs3218035: adjusted odds ratio [aOR] = 3.35, 95% confidence interval [CI] = 1.69-6.67; rs3218038: aOR = 1.81, 95% CI = 1.22-2.70; rs3218042: aOR = 2.64, 95% CI = 1.31-5.34), and these three loci showed a dose-dependent manner in increasing BC risk (P(trend) = 0.0001). Moreover, the 5-SNP haplotype CCGTC, which carried none of minor alleles of the 3 at-risk SNPs, was associated with a favorable event-free survival (hazard ratio [HR] = 0.53, 95% CI = 0.32-0.90). Stratified analysis suggested that the minor-allele homozygote carriers of rs3218038 had a worse event-free survival among patients with aggressive tumours (in tumour size>2 cm group: HR = 2.06, 95% CI = 1.06-3.99; in positive lymph node metastasis group: HR = 2.41, 95% CI = 1.15-5.03; in stage II-IV group: HR = 2.03, 95% CI = 1.09-3.79). For CDK2, no significant association was found. CONCLUSIONS/SIGNIFICANCE This study indicates that genetic variants in CCNE1 may contribute to BC risk and survival in Chinese Han population. They may become molecular markers for individual evaluation of BC susceptibility and prognosis. Nevertheless, further validation studies are needed.
Collapse
Affiliation(s)
- Ji-Yuan Han
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Hui Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Yun-Tao Xie
- Breast Center, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, People' Republic of China
| | - Yan Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Li-Yuan Zheng
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Yuan Ruan
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Ai-Ping Song
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Xin-Xia Tian
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Wei-Gang Fang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| |
Collapse
|
38
|
Schaffer BS, Leland-Wavrin KM, Kurz SG, Colletti JA, Seiler NL, Warren CL, Shull JD. Mapping of three genetic determinants of susceptibility to estrogen-induced mammary cancer within the Emca8 locus on rat chromosome 5. Cancer Prev Res (Phila) 2012; 6:59-69. [PMID: 23151807 DOI: 10.1158/1940-6207.capr-12-0346-t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The ACI rat model of 17β-estradiol (E2)-induced mammary cancer has gained wide use in the study of breast cancer etiology, prevention, and genetics. Emca8, a QTL that determines susceptibility to E2-induced mammary cancer, was previously mapped to rat chromosome 5 (RNO5) in an intercross between resistant Brown Norway (BN) and susceptible ACI rats. In this study, a panel of congenic rat strains, each of which carries BN alleles across a defined segment of RNO5 on the ACI genetic background, was generated and used to map more precisely the Emca8 determinants of mammary cancer susceptibility. Three distinct genetic determinants were localized within Emca8, and two of these were mapped to intervals of less than 15 megabases. Emca8.1 harbors Cdkn2a, Cdkn2b, and other genes and is orthologous to the 9p21 breast cancer locus identified in genome-wide and candidate gene association studies. Emca8.2 harbors Cdkn2c and other genes and is orthologous to the 1p32 locus in humans that is frequently deleted in breast cancers. Both Emca8.1 and Emca8.2 harbor copy number variants that are orthologous to copy number variant regions in humans. Gene expression profiles were defined for mammary tissues from E2-treated ACI and ACI.BN-Emca8 rats to define the impact of Emca8 on gene expression and identify differentially expressed genes residing within Emca8.1 and Emca8.2. This study further illustrates the relevance of the ACI rat model of E2-induced mammary cancer for identifying novel genetic determinants of breast cancer susceptibility and defining the mechanisms through which estrogens contribute to breast cancer development. Cancer Prev Res; 6(1); 59-69. ©2012 AACR.
Collapse
Affiliation(s)
- Beverly S Schaffer
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | | | | | | | | |
Collapse
|
39
|
Ma H, Zhou Z, Wei S, Wei Q. Association between p21 Ser31Arg polymorphism and cancer risk: a meta-analysis. CHINESE JOURNAL OF CANCER 2012; 30:254-63. [PMID: 21439247 PMCID: PMC4013352 DOI: 10.5732/cjc.010.10587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
P21 (CDKN1A), a key cell cycle regulatory protein that governs cell cycle progression from G1 to S phase, can regulate cell proliferation, growth arrest, and apoptosis. The Ser31Arg polymorphism is located in the highly conserved region of p21 and may encode functionally distinct proteins. Although many epidemiological studies have been conducted to evaluate the association between the p21 Ser31Arg polymorphism and cancer risk, the findings remain conflicting. This meta-analysis with 33 077 cases and 45 013 controls from 44 published case-control studies showed that the variant homozygous 31Arg/Arg genotype was associated with an increased risk of numerous types of cancers in a random-effect model (homozygote comparison: OR = 1.17, 95% CI = 0.99 to 1.37, P = 0.0002 for the heterogeneity test; recessive model comparison: OR = 1.16, 95% CI = 1.01 to 1.33, P = 0.0001 for the heterogeneity test). Stratified analysis revealed that increased cancer risk associated with the 31Arg/Arg genotype remained significant in subgroups of colorectal cancer, estrogen-related cancer, Caucasians, population-based studies, studies with matching information or a larger sample size. Heterogeneity analysis showed that tumor type contributed to substantial between-study heterogeneity (recessive model comparison: Χ(2) = 21.83, df = 7, P = 0.003). The results from this large-sample sized meta-analysis suggest that the p21 31Arg/Arg genotype may serve as a potential marker for increased cancer risk.
Collapse
Affiliation(s)
- Hongxia Ma
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | | | | | | |
Collapse
|
40
|
The chromosome 9p21.3 coronary heart disease risk allele is associated with altered gene expression in normal heart and vascular tissues. PLoS One 2012; 7:e39574. [PMID: 22768093 PMCID: PMC3387158 DOI: 10.1371/journal.pone.0039574] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 05/22/2012] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies have identified a coronary artery disease (CAD) risk locus in a non-coding region at 9p21.3, the nearest genes being CDKN2A and CDKN2B. To understand the pathways by which this locus might influence CAD susceptibility, we investigated associations between the 9p21.3 risk genotype and global gene expression in heart tissue from donors with no diagnosed heart disease (n = 108, predominant cause of death, cerebral vascular accident) and in carotid plaque (n = 106), aorta (n = 104) and mammary artery (n = 88) tissues from heart valve and carotid endarterectomy patients. Genotyping was performed with Taqman assays and Illumina arrays, and gene expression profiles generated with Affymetrix microarrays. Associations were analyzed with an additive genetic model. In heart tissue, 46 genes were putatively altered in association with the 9p21.3 risk allele (70% down-regulated, fold-change >1.1 per allele, p<0.05 adjusted for age, gender, ethnicity, cause of death). These genes were enriched for biomarkers of myocardial infarction (p = 1.53×10−9), response to wounding (p = 2.65×10−10) and inflammatory processes (p<1.97×10−7). Among the top 10 most down-regulated genes, 7 genes shared a set of transcription factor binding sites within conserved promoter regions (p<1.14×10−5), suggesting they may be co-regulated. Canonical pathway modelling of the most differentially expressed transcripts across all tissues (154 genes, 60% down-regulated, fold-change >1.1 per allele, p<0.01) showed that 75% of the genes could be transcriptionally regulated through the cell cycle G1 phase progression pathway (p<1.08×10−258), in which CDKN2A and CDKN2B play a regulatory role. These data suggest that the cell cycle G1 phase progression pathway is activated in individuals with the 9p21.3 risk allele. This may contribute to a proliferative phenotype that promotes adverse cardiac hypertrophy and vascular remodeling, leading to an increased CAD risk.
Collapse
|
41
|
Ohsaka Y, Nishino H. Polymorphisms in the 5′-UTR of PTEN and other gene polymorphisms in normal Japanese individuals. CYTOL GENET+ 2012. [DOI: 10.3103/s0095452712020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
42
|
Normal Japanese individuals harbor polymorphisms in the p14 ARF /INK4 locus promoters and/or other gene introns. — Variation in nucleotide sequences in each individual. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0085-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
43
|
Cai H, Xiang YB, Qu S, Long J, Cai Q, Gao J, Zheng W, Shu XO. Association of genetic polymorphisms in cell-cycle control genes and susceptibility to endometrial cancer among Chinese women. Am J Epidemiol 2011; 173:1263-71. [PMID: 21454826 DOI: 10.1093/aje/kwr002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Although genetic variations in cell-cycle control genes have been previously linked to cancer risk, no study has specifically evaluated the role of these gene variants in endometrial carcinogenesis. Using data from the Shanghai Endometrial Cancer Study, a population-based case-control study with 1,199 cases and 1,212 age-matched controls (1997-2003), the authors carried out a systematic evaluation of the association of cell-cycle control genes with endometrial cancer risk. Sixty-five tagging or potentially functional single nucleotide polymorphisms in the CCNB1, CCND1, CCNE1, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, and CDKN2A genes were genotyped and evaluated. Three single nucleotide polymorphisms in the CDKN1B gene (rs11055027, rs3759216, and rs34330) were related to endometrial cancer risk, although only the association with rs34330 remained statistically significant after adjustment for multiple comparisons. The odds ratios for rs34330 were 1.33 (95% confidence interval (CI): 1.06, 1.66) and 1.51 (95% CI: 1.16, 1.94) for the CT and TT genotypes, respectively, compared with the CC genotype. In vitro luciferase reporter assays showed that the minor allele (A) in rs3759216, which was associated with decreased endometrial cancer risk (odds ratio = 0.73, 95% CI: 0.56, 0.94) without adjustment for multiple comparisons, significantly increased promoter activity. These findings suggest that polymorphisms of the CDKN1B gene may play a role in endometrial carcinogenesis.
Collapse
Affiliation(s)
- Hui Cai
- Vanderbilt Epidemiology Center, Vanderbilt University, 2525 West End Avenue, Nashville, TN 37203-1738, USA.
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Association study of selected genetic polymorphisms and occurrence of venous thromboembolism in patients with multiple myeloma who were treated with thalidomide. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2011; 11:414-20. [PMID: 21859556 DOI: 10.1016/j.clml.2011.03.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 03/04/2011] [Accepted: 03/07/2011] [Indexed: 11/23/2022]
Abstract
INTRODUCTION/BACKGROUND Venous thromboembolism (VTE), with the subsequent risk of pulmonary embolism, is a common adverse effect of thalidomide treatment in patients with multiple myeloma (MM). In our retrospective study, we analyzed candidate single-nucleotide polymorphisms (SNP), CINP (rs7011), CETP (rs289747), ALDH1A1 (rs610529), CDKN1A (rs3829963), GAN (rs2608555), vascular endothelial growth factor (rs699947), and ALDH1A1 (rs168351), previously identified in a large association study based on the hypothesis-driven candidate gene approach nominated by the International Myeloma Foundation "Bank On A Cure" (3404 SNPs). In that study, the researchers built a classification tree that enables prediction of individual risk of VTE in patients with MM. PATIENTS AND METHODS Genotypes of these SNPs were determined in an independent cohort of 111 patients with MM through TaqMan real-time polymerase chain reaction (PCR) allelic discrimination and were used for prediction of individual VTE risk. RESULTS The results of this study did not confirm the ability of this classification tree to predict VTE risk in patients with MM from the Czech Republic; of these patients, 21 (19%) developed high-grade VTE. However, in patients with VTE, we found higher frequency of the AC genotype in the CDKN1A gene (42.9% vs. 16.7%; odds ratio 3.64) in comparison with the CC genotype (P = .015). SNPs of other genes as well as age and sex of the patients had no statistically significant influence on the risk of VTE. CONCLUSION Further studies are needed to confirm the initial analysis that provided predictive information of genetic variations in patients with myeloma that may influence risk of VTE.
Collapse
|
45
|
Li Y, Li Y, Wedrén S, Li G, Charn TH, Desai KV, Bonnard C, Czene K, Humphreys K, Darabi H, Einarsdóttir K, Heikkinen T, Aittomäki K, Blomqvist C, Chia KS, Nevanlinna H, Hall P, Liu ET, Liu J. Genetic variation of ESR1 and its co-activator PPARGC1B is synergistic in augmenting the risk of estrogen receptor-positive breast cancer. Breast Cancer Res 2011; 13:R10. [PMID: 21269472 PMCID: PMC3109578 DOI: 10.1186/bcr2817] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 12/03/2010] [Accepted: 01/26/2011] [Indexed: 12/27/2022] Open
Abstract
Introduction Given the role of estrogen in breast carcinogenesis and the modification of estrogen receptor (ER) activity by its biochemical cofactors, we hypothesize that genetic variation within ER cofactor genes alters cellular response to estrogen exposure and consequently modifies the risk for ER-positive breast cancer. Methods We genotyped 790 tagging SNPs within 60 ER cofactor genes in 1,257 cases and 1,464 controls from Sweden and in 2,215 cases and 1,265 controls from Finland, and tested their associations with either ER-positive or ER-negative breast cancer. Results Seven SNPs showed consistent association with ER-positive breast cancer in the two independent samples, and six of them were located within PPARGC1B, encoding an ER co-activator, with the strongest association at rs741581 (odds ratio = 1.41, P = 4.84 × 10-5) that survived Bonferroni correction for multiple testing in the combined ER-positive breast cancer sample (Pcorrected = 0.03). Moreover, we also observed significant synergistic interaction (Pinteraction = 0.008) between the genetic polymorphisms within PPARGC1B and ESR1 in ER-positive breast cancer. By contrast, no consistent association was observed in ER-negative breast cancer. Furthermore, we found that administration of estrogen in the MCF-7 cell line induced PPARGC1B expression and enhanced occupancies of ER and RNA polymerase II within the region of SNP association, suggesting the upregulation of PPARGC1B expression by ESR1 activation. Conclusions Our study revealed that DNA polymorphisms of PPARGC1B, coding a bona fide ER co-activator, are associated with ER-positive breast cancer risk. The feed-forward transcriptional regulatory loop between PPARGC1B and ESR1 further augments their protein interaction, which provides a plausible mechanistic explanation for the synergistic genetic interaction between PPARGC1B and ESR1 in ER-positive breast cancer. Our study also highlights that biochemically and genomically informed candidate gene studies can enhance the discovery of interactive disease susceptibility genes.
Collapse
Affiliation(s)
- Yuqing Li
- Human Genetics, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Sergentanis TN, Economopoulos KP. Cyclin D1 G870A polymorphism and breast cancer risk: a meta-analysis comprising 9,911 cases and 11,171 controls. Mol Biol Rep 2010; 38:4955-63. [PMID: 21161398 DOI: 10.1007/s11033-010-0639-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 12/03/2010] [Indexed: 12/12/2022]
Abstract
Cyclin D1 represents a key molecule in the regulation of cell cycle. CCND1 G870A (rs603965) polymorphism has drawn considerable attention as the A allele may generate a variant splice product with possible oncogenic actions. A meta-analysis examining the association between CCND1 G870A polymorphism and breast cancer risk was performed. Separate analyses on Caucasian and Chinese populations were also implemented. Eligible articles were identified for the period up to July 2010. Pooled odds ratios (OR) were appropriately derived from fixed-effects or random-effects models. Sensitivity analysis excluding studies whose genotype frequencies in controls significantly deviated from Hardy-Weinberg Equilibrium (HWE) was performed. Nine case-control studies on Caucasians (7,304 cases and 8,149 controls) and four case-control studies on Chinese (2,607 cases and 3,022 controls) were eligible. At the overall analysis the A allele seemed to be associated with elevated breast cancer risk; the effect seemed to be confined to homozygous carriers (pooled OR = 1.091, 95% CI: 1.008-1.179, P = 0.030, fixed effects) as heterozygous carriers did not exhibit significantly elevated breast cancer risk. No statistically significant associations were demonstrated in Caucasians. On the other hand, Chinese AA carriers exhibited marginally elevated breast cancer risk (pooled OR = 1.144, 95% CI: 0.984-1.329, P = 0.080, fixed effects). Nevertheless, the controls in two out of the four Chinese studies deviated from HWE. In conclusion, this meta-analysis suggests that the A allele of the CCND1 G870A polymorphism may confer additional breast cancer risk when it comes to homozygosity and Chinese populations. The need for additional, methodologically sound studies on Chinese populations seems warranted.
Collapse
|
47
|
Sircoulomb F, Bekhouche I, Finetti P, Adélaïde J, Ben Hamida A, Bonansea J, Raynaud S, Innocenti C, Charafe-Jauffret E, Tarpin C, Ben Ayed F, Viens P, Jacquemier J, Bertucci F, Birnbaum D, Chaffanet M. Genome profiling of ERBB2-amplified breast cancers. BMC Cancer 2010; 10:539. [PMID: 20932292 PMCID: PMC2958950 DOI: 10.1186/1471-2407-10-539] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 10/08/2010] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Around 20% of breast cancers (BC) show ERBB2 gene amplification and overexpression of the ERBB2 tyrosine kinase receptor. They are associated with a poor prognosis but can benefit from targeted therapy. A better knowledge of these BCs, genomically and biologically heterogeneous, may help understand their behavior and design new therapeutic strategies. METHODS We defined the high resolution genome and gene expression profiles of 54 ERBB2-amplified BCs using 244K oligonucleotide array-comparative genomic hybridization and whole-genome DNA microarrays. Expression of ERBB2, phosphorylated ERBB2, EGFR, IGF1R and FOXA1 proteins was assessed by immunohistochemistry to evaluate the functional ERBB2 status and identify co-expressions. RESULTS First, we identified the ERBB2-C17orf37-GRB7 genomic segment as the minimal common 17q12-q21 amplicon, and CRKRS and IKZF3 as the most frequent centromeric and telomeric amplicon borders, respectively. Second, GISTIC analysis identified 17 other genome regions affected by copy number aberration (CNA) (amplifications, gains, losses). The expression of 37 genes of these regions was deregulated. Third, two types of heterogeneity were observed in ERBB2-amplified BCs. The genomic profiles of estrogen receptor-positive (ER+) and negative (ER-) ERBB2-amplified BCs were different. The WNT/β-catenin signaling pathway was involved in ER- ERBB2-amplified BCs, and PVT1 and TRPS1 were candidate oncogenes associated with ER+ ERBB2-amplified BCs. The size of the ERBB2 amplicon was different in inflammatory (IBC) and non-inflammatory BCs. ERBB2-amplified IBCs were characterized by the downregulated and upregulated mRNA expression of ten and two genes in proportion to CNA, respectively. IHC results showed (i) a linear relationship between ERBB2 gene amplification and its gene and protein expressions with a good correlation between ERBB2 expression and phosphorylation status; (ii) a potential signaling cross-talk between EGFR or IGF1R and ERBB2, which could influence response of ERBB2-positive BCs to inhibitors. FOXA1 was frequently coexpressed with ERBB2 but its expression did not impact on the outcome of patients with ERBB2-amplified tumors. CONCLUSION We have shown that ER+ and ER- ERBB2-amplified BCs are different, distinguished ERBB2 amplicons in IBC and non-IBC, and identified genomic features that may be useful in the design of alternative therapeutical strategies.
Collapse
Affiliation(s)
- Fabrice Sircoulomb
- Marseille Cancer Research Center, UMR891 Inserm, Institut Paoli-Calmettes, Department of Molecular Oncology, Marseille, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Mandal RK, Mittal RD. Are cell cycle and apoptosis genes associated with prostate cancer risk in North Indian population? Urol Oncol 2010; 30:555-61. [PMID: 20822933 DOI: 10.1016/j.urolonc.2010.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 05/11/2010] [Accepted: 05/13/2010] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Prostate cancer (CaP) is a heterogeneous, multifactorial, and multifocal disease. Therefore, the search for a combination of functional polymorphisms using cell cycle and apoptotic genes as tumor markers is fundamental for a more precise and reliable diagnosis. In the present study, we investigated the diagnostic value of 3 different genes associated with CaP carcinogenesis, encoding for cell cycle (MDM2, CCND1) and apoptotic (Fas) genes that are differentially expressed in CaP. METHODS In a hospital-based case control study of northern India, blood samples were obtained from 192 CaP patients and 224 cancer-free age matched unrelated healthy controls of similar ethnicity. They were genotyped for MDM2 G309T, CCND1 G870A, Fas A670G, and G1377A polymorphisms using polymerase chain restriction fragment length polymorphism (PCR-RFLP) method. RESULTS MDM2 309GG variant was at reduced risk for developing CaP (P = 0.041; OR, 0.59). Whereas CCND1 AA genotype demonstrated increased risk (P = 0.018; OR, 1.86). The diplotype analysis of Fas G670A and G1377A (G-A) was observed to be associated with a significant increase in CaP risk (P = 0.024; OR, 1.63). CONCLUSION Findings based on current sample size our results suggested a positive association of CCND1AA genotype and diplotype analysis of Fas G670A and G1377A (G-A) to be associated with CaP risk that could influence the pathophysiology, thereby modulating the risk of CaP.
Collapse
Affiliation(s)
- Raju Kumar Mandal
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Uttar Pradesh, India
| | | |
Collapse
|
49
|
Identification of single nucleotide polymorphisms in the p21 (CDKN1A) gene and correlations with longevity in the Italian population. Aging (Albany NY) 2010; 1:470-80. [PMID: 20126416 PMCID: PMC2814366 DOI: 10.18632/aging.100041] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Longevity in humans is determined by multiple environmental and genetic factors. We have investigated possible associations between longevity and Single Nucleotide Polymorphisms (SNPs) in the p21 (CDKN1A) gene, a stress-inducible senescence-associated cell cycle inhibitor, expression of which upregulates genes implicated in several age-related diseases. By sequencing the promoter and exons of p21 in genomic DNA of ten individuals over 90 years old, we have identified 30 SNPs, many of which had not been previously characterized. A cluster of minor alleles within the -4547/-3489 bp region did not alter the basal activity or p53 responsiveness of the p21 promoter. We then compared the frequency of 41 p21 SNPs between 184 centenarians and 184 younger subjects in the Italian population. Rare alleles of two exon-derived SNPs, rs1801270 and rs1059234, were significantly under-represented among the centenarians; no significant differences were found for 39 non-exonic SNPs. SNP rs1801270 causes Ser to Arg substitution at amino acid 31 and SNP rs1059234 leads to a nucleotide change in the 3'-untranslated region. Previous studies showed that the rare alleles of these two SNPs may play a role in cancer. These p21 alleles may be potentially detrimental to longevity and therefore are rare in centenarians.
Collapse
|
50
|
Zhang S, Lu J, Zhao X, Wu W, Wang H, Lu J, Wu Q, Chen X, Fan W, Chen H, Wang F, Hu Z, Jin L, Wei Q, Shen H, Huang W, Lu D. A variant in the CHEK2 promoter at a methylation site relieves transcriptional repression and confers reduced risk of lung cancer. Carcinogenesis 2010; 31:1251-8. [DOI: 10.1093/carcin/bgq089] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|