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Merabet N, Ramoz N, Boulmaiz A, Bourefis A, Benabdelkrim M, Djeffal O, Moyse E, Tolle V, Berredjem H. SNPs-Panel Polymorphism Variations in GHRL and GHSR Genes Are Not Associated with Prostate Cancer. Biomedicines 2023; 11:3276. [PMID: 38137497 PMCID: PMC10741232 DOI: 10.3390/biomedicines11123276] [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: 11/02/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Prostate cancer (PCa) is a major public health problem worldwide. Recent studies have suggested that ghrelin and its receptor could be involved in the susceptibility to several cancers such as PCa, leading to their use as an important predictive way for the clinical progression and prognosis of cancer. However, conflicting results of single nucleotide polymorphisms (SNPs) with ghrelin (GHRL) and its receptor (GHSR) genes were demonstrated in different studies. Thus, the present case-control study was undertaken to investigate the association of GHRL and GHSR polymorphisms with the susceptibility to sporadic PCa. A cohort of 120 PCa patients and 95 healthy subjects were enrolled in this study. Genotyping of six SNPs was performed: three tag SNPs in GHRL (rs696217, rs4684677, rs3491141) and three tag SNPs in the GHSR (rs2922126, rs572169, rs2948694) using TaqMan. The allele and genotype distribution, as well as haplotypes frequencies and linked disequilibrium (LD), were established. Multifactor dimensionality reduction (MDR) analysis was used to study gene-gene interactions between the six SNPs. Our results showed no significant association of the target polymorphisms with PCa (p > 0.05). Nevertheless, SNPs are often just markers that help identify or delimit specific genomic regions that may harbour functional variants rather than the variants causing the disease. Furthermore, we found that one GHSR rs2922126, namely the TT genotype, was significantly more frequent in PCa patients than in controls (p = 0.040). These data suggest that this genotype could be a PCa susceptibility genotype. MDR analyses revealed that the rs2922126 and rs572169 combination was the best model, with 81.08% accuracy (p = 0.0001) for predicting susceptibility to PCa. The results also showed a precision of 98.1% (p < 0.0001) and a PR-AUC of 1.00. Our findings provide new insights into the influence of GHRL and GHSR polymorphisms and significant evidence for gene-gene interactions in PCa susceptibility, and they may guide clinical decision-making to prevent overtreatment and enhance patients' quality of life.
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Affiliation(s)
- Nesrine Merabet
- Laboratory of Applied Biochemistry and Microbiology, Department of Biochemistry, Faculty of Sciences, Badji Mokhtar University, Annaba 23000, Algeria; (A.B.); (A.B.); (M.B.)
- Unit 85 PRC (Physiology of Reproduction and Behavior), Centre INRAe of Tours, University of Tours, 37380 Nouzilly, France;
| | - Nicolas Ramoz
- University Paris Cité, INSERM U1266, Institute of Psychiatry and Neuroscience of Paris (IPNP), 75014 Paris, France; (N.R.); (V.T.)
| | - Amel Boulmaiz
- Laboratory of Applied Biochemistry and Microbiology, Department of Biochemistry, Faculty of Sciences, Badji Mokhtar University, Annaba 23000, Algeria; (A.B.); (A.B.); (M.B.)
| | - Asma Bourefis
- Laboratory of Applied Biochemistry and Microbiology, Department of Biochemistry, Faculty of Sciences, Badji Mokhtar University, Annaba 23000, Algeria; (A.B.); (A.B.); (M.B.)
| | - Maroua Benabdelkrim
- Laboratory of Applied Biochemistry and Microbiology, Department of Biochemistry, Faculty of Sciences, Badji Mokhtar University, Annaba 23000, Algeria; (A.B.); (A.B.); (M.B.)
| | - Omar Djeffal
- Private Medical Uro-Chirurgical Cabinet, Cité SafSaf, BatR02 n°S01, Annaba 23000, Algeria;
| | - Emmanuel Moyse
- Unit 85 PRC (Physiology of Reproduction and Behavior), Centre INRAe of Tours, University of Tours, 37380 Nouzilly, France;
| | - Virginie Tolle
- University Paris Cité, INSERM U1266, Institute of Psychiatry and Neuroscience of Paris (IPNP), 75014 Paris, France; (N.R.); (V.T.)
| | - Hajira Berredjem
- Laboratory of Applied Biochemistry and Microbiology, Department of Biochemistry, Faculty of Sciences, Badji Mokhtar University, Annaba 23000, Algeria; (A.B.); (A.B.); (M.B.)
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CircRNA_0058063 functions as a ceRNA in bladder cancer progression via targeting miR-486-3p/FOXP4 axis. Biosci Rep 2021; 40:222397. [PMID: 32181485 PMCID: PMC7103589 DOI: 10.1042/bsr20193484] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022] Open
Abstract
Emerging evidence has uncovered critical regulatory roles of circular RNAs (circRNAs) function as dynamic scaffolding molecules in tumorigenesis and progression. However, the aberrant expression and clinical significance of hsa_circ_0058063 (circRNA_0058063) in bladder cancer (BC) remain poorly understood. circRNA expression was analyzed via a microarray in cancerous tissue and non-carcinoma tissues. Luciferase reporter assays and RNA immunoprecipitation (RIP) were both conducted to uncover the function of circRNA_0058063 in BC. circRNA_0058063 was overexpressed in BC tissues compared with adjacent normal tissues. Knockdown of circRNA_0058063 dramatically decreased cell proliferation and invasion, and promoted apoptosis in 5637 and BIU-87 cell lines. Furthermore, mechanistic investigations showed that circRNA_0058063 and FOXP4 could directly bind to miR-486-3p, demonstrating that circRNA_0058063 regulated FOXP4 expression by competitively binding to miR-486-3p. Taken together, circRNA_0058063 functions by sponging miR-486-3p in BC progression, which could act as a new biomarker and further developed to be a therapeutic target in BC.
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Elucidation of the Genomic-Epigenomic Interaction Landscape of Aggressive Prostate Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6641429. [PMID: 33511206 PMCID: PMC7825361 DOI: 10.1155/2021/6641429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022]
Abstract
Background Majority of prostate cancer (PCa) deaths are attributed to localized high-grade aggressive tumours which progress rapidly to metastatic disease. A critical unmet need in clinical management of PCa is discovery and characterization of the molecular drivers of aggressive tumours. The development and progression of aggressive PCa involve genetic and epigenetic alterations occurring in the germline, somatic (tumour), and epigenomes. To date, interactions between genes containing germline, somatic, and epigenetic mutations in aggressive PCa have not been characterized. The objective of this investigation was to elucidate the genomic-epigenomic interaction landscape in aggressive PCa to identify potential drivers aggressive PCa and the pathways they control. We hypothesized that aggressive PCa originates from a complex interplay between genomic (both germline and somatic mutations) and epigenomic alterations. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect gene expression, molecular networks, and signaling pathways which in turn drive aggressive PCa. Methods We addressed these hypotheses by performing integrative data analysis combining information on germline mutations from genome-wide association studies with somatic and epigenetic mutations from The Cancer Genome Atlas using gene expression as the intermediate phenotype. Results The investigation revealed signatures of genes containing germline, somatic, and epigenetic mutations associated with aggressive PCa. Aberrant DNA methylation had effect on gene expression. In addition, the investigation revealed molecular networks and signalling pathways enriched for germline, somatic, and epigenetic mutations including the STAT3, PTEN, PCa, ATM, AR, and P53 signalling pathways implicated in aggressive PCa. Conclusions The study demonstrated that integrative analysis combining diverse omics data is a powerful approach for the discovery of potential clinically actionable biomarkers, therapeutic targets, and elucidation of oncogenic interactions between genomic and epigenomic alterations in aggressive PCa.
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Mamidi TKK, Wu J, Hicks C. Mapping the Germline and Somatic Mutation Interaction Landscape in Indolent and Aggressive Prostate Cancers. JOURNAL OF ONCOLOGY 2019; 2019:4168784. [PMID: 31814827 PMCID: PMC6878815 DOI: 10.1155/2019/4168784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/19/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND A majority of prostate cancers (PCas) are indolent and cause no harm even without treatment. However, a significant proportion of patients with PCa have aggressive tumors that progress rapidly to metastatic disease and are often lethal. PCa develops through somatic mutagenesis, but emerging evidence suggests that germline genetic variation can markedly contribute to tumorigenesis. However, the causal association between genetic susceptibility and tumorigenesis has not been well characterized. The objective of this study was to map the germline and somatic mutation interaction landscape in indolent and aggressive tumors and to discover signatures of mutated genes associated with each type and distinguishing the two types of PCa. MATERIALS AND METHODS We integrated germline mutation information from genome-wide association studies (GWAS) with somatic mutation information from The Cancer Genome Atlas (TCGA) using gene expression data from TCGA on indolent and aggressive PCas as the intermediate phenotypes. Germline and somatic mutated genes associated with each type of PCa were functionally characterized using network and pathway analysis. RESULTS We discovered gene signatures containing germline and somatic mutations associated with each type and distinguishing the two types of PCa. We discovered multiple gene regulatory networks and signaling pathways enriched with germline and somatic mutations including axon guidance, RAR, WINT, MSP-RON, STAT3, PI3K, TR/RxR, and molecular mechanisms of cancer, NF-kB, prostate cancer, GP6, androgen, and VEGF signaling pathways for indolent PCa and MSP-RON, axon guidance, RAR, adipogenesis, and molecular mechanisms of cancer and NF-kB signaling pathways for aggressive PCa. CONCLUSION The investigation revealed germline and somatic mutated genes associated with indolent and aggressive PCas and distinguishing the two types of PCa. The study revealed multiple gene regulatory networks and signaling pathways dysregulated by germline and somatic alterations. Integrative analysis combining germline and somatic mutations is a powerful approach to mapping germline and somatic mutation interaction landscape.
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Affiliation(s)
- Tarun Karthik Kumar Mamidi
- Informatics Institute, University of Alabama at Birmingham, School of Medicine, 1720 2nd Avenue South, Birmingham, AL 35294-3412, USA
| | - Jiande Wu
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA-70112, USA
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA-70112, USA
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Interactions between Germline and Somatic Mutated Genes in Aggressive Prostate Cancer. Prostate Cancer 2019; 2019:4047680. [PMID: 31007957 PMCID: PMC6441536 DOI: 10.1155/2019/4047680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/29/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the USA. Advances in high-throughput genotyping and next generation sequencing technologies have enabled discovery of germline genetic susceptibility variants and somatic mutations acquired during tumor formation. Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the possible oncogenic interactions and cooperation between germline and somatic variation and their role in aggressive PCa remain largely unexplored. Here we investigated the possible oncogenic interactions and cooperation between genes containing germline variation from genome-wide association studies (GWAS) and genes containing somatic mutations from tumor genomes of 305 men with aggressive tumors and 52 control samples from The Cancer Genome Atlas (TCGA). Network and pathway analysis were performed to identify molecular networks and biological pathways enriched for germline and somatic mutations. The analysis revealed 90 functionally related genes containing both germline and somatic mutations. Transcriptome analysis revealed a 61-gene signature containing both germline and somatic mutations. Network analysis revealed molecular networks of functionally related genes and biological pathways including P53, STAT3, NKX3-1, KLK3, and Androgen receptor signaling pathways enriched for germline and somatic mutations. The results show that integrative analysis is a powerful approach to uncovering the possible oncogenic interactions and cooperation between germline and somatic mutations and understanding the broader biological context in which they operate in aggressive PCa.
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Mamidi TKK, Wu J, Hicks C. Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer. BMC Cancer 2019; 19:229. [PMID: 30871495 PMCID: PMC6417124 DOI: 10.1186/s12885-019-5440-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 03/06/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the United States. High-throughput genotyping has enabled discovery of germline genetic susceptibility variants (herein referred to as germline mutations) associated with an increased risk of developing PCa. However, germline mutation information has not been leveraged and integrated with information on acquired somatic mutations to link genetic susceptibility to tumorigenesis. The objective of this exploratory study was to address this knowledge gap. METHODS Germline mutations and associated gene information were derived from genome-wide association studies (GWAS) reports. Somatic mutation and gene expression data were derived from 495 tumors and 52 normal control samples obtained from The Cancer Genome Atlas (TCGA). We integrated germline and somatic mutation information using gene expression data. We performed enrichment analysis to discover molecular networks and biological pathways enriched for germline and somatic mutations. RESULTS We discovered a signature of 124 genes containing both germline and somatic mutations. Enrichment analysis revealed molecular networks and biological pathways enriched for germline and somatic mutations, including, the PDGF, P53, MYC, IGF-1, PTEN and Androgen receptor signaling pathways. CONCLUSION Integrative genomic analysis links genetic susceptibility to tumorigenesis in PCa and establishes putative functional bridges between the germline and somatic variation, and the biological pathways they control.
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Affiliation(s)
- Tarun Karthik Kumar Mamidi
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA, 70112, USA
| | - Jiande Wu
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA, 70112, USA
| | - Chindo Hicks
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar, New Orleans, LA, 70112, USA.
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Vijayakumar S, Henegan JC, Zhang X, Wang W, Day WA, Vijayakumar V, Moreno CS, Gomez CR. Enriching gene expression profiles will help personalize prostate cancer management for African-Americans: A perspective. Urol Oncol 2017; 35:315-321. [DOI: 10.1016/j.urolonc.2017.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/20/2017] [Accepted: 04/04/2017] [Indexed: 12/25/2022]
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Hicks C, Ramani R, Sartor O, Bhalla R, Miele L, Dlamini Z, Gumede N. An Integrative Genomics Approach for Associating Genome-Wide Association Studies Information With Localized and Metastatic Prostate Cancer Phenotypes. Biomark Insights 2017; 12:1177271917695810. [PMID: 28469398 PMCID: PMC5391982 DOI: 10.1177/1177271917695810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/05/2017] [Indexed: 01/01/2023] Open
Abstract
High-throughput genotyping has enabled discovery of genetic variants associated with an increased risk of developing prostate cancer using genome-wide association studies (GWAS). The goal of this study was to associate GWAS information of patients with primary organ–confined and metastatic prostate cancer using gene expression data and to identify molecular networks and biological pathways enriched for genetic susceptibility variants involved in the 2 disease states. The analysis revealed gene signatures for the 2 disease states and a gene signature distinguishing the 2 patient groups. In addition, the analysis revealed molecular networks and biological pathways enriched for genetic susceptibility variants. The discovered pathways include the androgen, apoptosis, and insulinlike growth factor signaling pathways. This analysis established putative functional bridges between GWAS discoveries and the biological pathways involved in primary organ–confined and metastatic prostate cancer.
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Affiliation(s)
- Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, USA
| | - Ritika Ramani
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Oliver Sartor
- Department of Medicine, Tulane University, New Orleans, LA, USA
| | - Ritu Bhalla
- Department of Pathology, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, USA
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA, USA
| | - Zodwa Dlamini
- Department of Biology, Mangosuthu University of Technology, Durban, South Africa
| | - Njabulo Gumede
- Department of Biology, Mangosuthu University of Technology, Durban, South Africa
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Hicks C, Koganti T, Giri S, Tekere M, Ramani R, Sitthi-Amorn J, Vijayakumar S. Integrative genomic analysis for the discovery of biomarkers in prostate cancer. Biomark Insights 2014; 9:39-51. [PMID: 25057237 PMCID: PMC4085106 DOI: 10.4137/bmi.s13729] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 04/03/2014] [Accepted: 04/06/2014] [Indexed: 12/18/2022] Open
Abstract
Genome-wide association studies (GWAS) have achieved great success in identifying single nucleotide polymorphisms (SNPs, herein called genetic variants) and genes associated with risk of developing prostate cancer. However, GWAS do not typically link the genetic variants to the disease state or inform the broader context in which the genetic variants operate. Here, we present a novel integrative genomics approach that combines GWAS information with gene expression data to infer the causal association between gene expression and the disease and to identify the network states and biological pathways enriched for genetic variants. We identified gene regulatory networks and biological pathways enriched for genetic variants, including the prostate cancer, IGF-1, JAK2, androgen, and prolactin signaling pathways. The integration of GWAS information with gene expression data provides insights about the broader context in which genetic variants associated with an increased risk of developing prostate cancer operate.
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Affiliation(s)
- Chindo Hicks
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA. ; Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA. ; Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS, USA. ; Department of Public Health Sciences, University of Lusaka, Lusaka, Zambia
| | - Tejaswi Koganti
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Shankar Giri
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Memory Tekere
- Department of Environmental Sciences, University of South Africa, UNISA Florida Campus, Florida, South Africa
| | - Ritika Ramani
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Srinivasan Vijayakumar
- Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS, USA
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