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Aloufi A, Aubee J, Vargas KM, Apprey V, Thompson K, Copeland R, Kanaan Y, Ricks-Santi L, Brim H, Abbas M. Vitamin D receptor polymorphisms and associated miRNAs in the development of breast cancer in African American women. Gene 2024; 927:148695. [PMID: 38945313 DOI: 10.1016/j.gene.2024.148695] [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: 01/08/2024] [Revised: 05/31/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024]
Abstract
Breast cancer (BCa) is a prevalent form of cancer in women, exhibiting varying rates and distribution across different ethnic groups. Among these groups, African American (AA) women have the highest incidence of BCa and the lowest levels of Vitamin D (VD). Numerous studies have explored the connection between variations in the VDR gene and BCa risk, particularly in different populations, but research on the AA population remains limited. Epigenetic modifications, including specific microRNAs (miRNAs), can influence gene expression without altering the genetic code and have been implicated in cancer initiation and progression. Our hypothesis suggests that VDR gene variations may increase BCa risk in AA women and that changes in miRNA expression profiles could contribute to BCa development. Using data from the 1000 Genome Project, we identified five VDR gene variants with significant frequency differences between AA and European-American (EA) populations. We genotyped 404 African American BCa cases and controls for five variants using TaqMan® assays. SNPstats assessed their association with BCa risk. The rs1544410 variant's recessive model (A/A) showed a decreased BCa risk in AA (odds ratio 0.33, 95% CI: 0.15-0.73, p-value 0.0041). Conversely, the rs2853563 variant's recessive model (A/A) was linked to an increased BCa risk (odds ratio 4.04, 95% CI: 1.49-10.95, p-value 0.0022). We investigated miRNA expression influenced by VD in HCC1806 Triple-Negative Breast Cancer (TNBC) cell lines with the A/A allele for rs2853563. nCounter® Nanostring technology assessed miRNA profiles after calcitriol treatment. Our results indicated that calcitriol treatment led to reduced expression of six miRNAs, four of which are associated with tumor suppression in the presence of the AA genotype in TNBC cell lines. These findings suggest that specific VDR genotypes could have a potential effect on the miRNAs expression which could potentially serve as markers for cell proliferation in TNBC.
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Affiliation(s)
- Abrar Aloufi
- Howard University, Department of Microbiology, Washington, DC, USA
| | - Joseph Aubee
- Howard University, Department of Microbiology, Washington, DC, USA
| | - Kevin Monsalve Vargas
- MedStar Georgetown University Hospital, Pre/Postoperative Services, Washington, DC, USA
| | - Victor Apprey
- The National Human Genome Center, Howard University, Washington, DC, USA
| | - Karl Thompson
- Howard University, Department of Microbiology, Washington, DC, USA
| | - Robert Copeland
- Howard University, Department of Microbiology, Washington, DC, USA
| | - Yasmine Kanaan
- Howard University, Department of Microbiology, Washington, DC, USA
| | | | - Hassan Brim
- Howard University, Department of Pathology, Washington, DC, USA.
| | - Muneer Abbas
- Howard University, Department of Microbiology, Washington, DC, USA; The National Human Genome Center, Howard University, Washington, DC, USA.
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Fan Z, Peng W, Wang Z, Zhang L, Liu K. Identification of biomarkers associated with metabolic cardiovascular disease using mRNA-SNP-miRNA regulatory network analysis. BMC Cardiovasc Disord 2021; 21:351. [PMID: 34301176 PMCID: PMC8305867 DOI: 10.1186/s12872-021-02166-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/14/2021] [Indexed: 12/28/2022] Open
Abstract
Background CVD is the leading cause of death in T2DM patients. However, few biomarkers have been identified to detect and diagnose CVD in the early stage of T2DM. The aim of our study was to identify the important mRNAs, micro (mi)RNAs and SNPs (single nucleotide polymorphisms) that are associated with metabolic cardiovascular disease. Materials and methods Expression profiles and GWAS data were obtained from Gene Expression Omnibus (GEO) database. MiRNA-sequencing was conducted by Illumina HiSeq 2000 platform in T2DM patients and T2DM with CVD patients. EQTL analysis and gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. MRNA-miRNA co-expression network and mRNA-SNP-miRNA interaction network were established and visualized by Cytoscape 3.7.2. Results In our study, we identified 56 genes and 16 miRNAs that were significantly differentially expressed. KEGG analyses results indicated that B cell receptor signaling pathway and hematopoietic cell lineage were included in the biological functions of differentially expressed genes. MRNA-miRNA co-expression network and mRNA-SNP-miRNA interaction network illustrated that let-7i-5p, RASGRP3, KRT1 and CEP41 may be potential biomarkers for the early detection and diagnosis of CVD in T2DM patients. Conclusion Our results suggested that downregulated let-7i-5p, and upregulated RASGRP3, KRT1 and CEP41 may play crucial roles in molecular mechanisms underlying the initiation and development of CVD in T2DM patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-021-02166-4.
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Affiliation(s)
- Zhiyuan Fan
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Wenjuan Peng
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Zhiwen Wang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ling Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China
| | - Kuo Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing, China.
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Functional Analysis of Haplotypes in Bovine PSAP Gene and Their Relationship with Beef Cattle Production Traits. Animals (Basel) 2020; 11:ani11010049. [PMID: 33383762 PMCID: PMC7824473 DOI: 10.3390/ani11010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 11/19/2022] Open
Abstract
Simple Summary With the rapid development of information technology and molecular biotechnology, animal molecular breeding technology is playing an increasingly important role in beef cattle breeding. Prosaposin (PSAP) is involved in regulating the growth and development of animals, and it is reported that PSAP is an important marker-assisted selection (MAS) in cattle herd. The purpose of this study was to explore the novel variants in 3’ UTR of cattle PSAP and evaluate their effects on the morphological traits of four Chinese cattle breeds. In this study, 13 variants were identified in the PSAP 3’ UTR from 501 individuals belonging to four cattle breeds. In Nanyang cattle, the distribution of haplotypes was different from the other three breeds. Two groups of haplotypes had association with morphological traits by changing the secondary structures of PSAP 3’ UTR rather than the miR-184 target sites. This study not only expands the genetic variation spectrum of cattle PSAP but also contributes to MAS genetics and breeding of Chinese cattle breeds. Abstract The purpose of this study was to explore functional variants in the prosaposin (PSAP) three prime untranslated region (3’ UTR) and clarify the relationship between the variants and morphological traits. Through Sanger sequencing, 13 variations were identified in bovine PSAP in four Chinese cattle breeds, with six of them being loci in 3’ UTR. In particular, Nanyang (NY) cattle had a special genotype and haplotype distribution compared to the other three breeds. NY cattle with ACATG and GCGTG haplotypes had higher morphological traits than GTACA and GTACG haplotypes. The results of dual-luciferase reporter assay showed that ACATG and GCGTG haplotypes affected the morphological traits of NY cattle by altering the secondary structure of PSAP 3’ UTR rather than the miR-184 target sites. The findings of this study could be an evidence of a complex and varying mechanism between variants and animal morphological traits and could be used to complement candidate genes for molecular breeding.
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Wu C, Han R, Yang S, Jiang Y, Shu Z, Liu J, Ji S, Yan W, Liu B. A case–control study of microRNA polymorphisms in gastric cancer screening by SNP chip combined with time of flight mass spectrometry. Biomark Med 2020; 14:1563-1572. [DOI: 10.2217/bmm-2020-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aims: To explore new SNP sites of miRNAs associated with gastric cancer, thereby providing valuable biomarkers to diagnose and screen gastric cancer. Materials & methods: A 1:1 case–control study was carried out. Microarrays were used to screen the SNP loci of miRNAs in the genomes of matched pairs of patients, 96 with gastric cancer and 96 healthy controls. For validation, mass spectrometry was used to classify miRNA SNP loci in 622 pairs of subjects. Results: rs7143252 was linked to a higher occurrence of gastric cancer. Conclusion: These results suggest that rs7143252 could be used as a specific biomarker to diagnose and screen gastric cancer.
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Affiliation(s)
- Chuancheng Wu
- School of Public Health, Fujian Medical University, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
- Fujian Provincial Key Laboratory of Environment Factors & Cancer, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
| | - Renjie Han
- School of Public Health, Fujian Medical University, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
- Fujian Provincial Key Laboratory of Environment Factors & Cancer, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
- Department of Occupational Health, Fuzhou Center for Disease Control & Prevention, Fuzhou, Fujian, 350004, China
| | - Shuangfeng Yang
- School of Public Health, Fujian Medical University, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
- Fujian Provincial Key Laboratory of Environment Factors & Cancer, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
| | - Yu Jiang
- School of Public Health, Fujian Medical University, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
- Fujian Provincial Key Laboratory of Environment Factors & Cancer, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
| | - Zhixiong Shu
- School of Public Health, Fujian Medical University, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
- Fujian Provincial Key Laboratory of Environment Factors & Cancer, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
| | - Jin Liu
- School of Public Health, Fujian Medical University, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
| | - Shumi Ji
- School of Public Health, Fujian Medical University, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
- Fujian Provincial Key Laboratory of Environment Factors & Cancer, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
| | - Wei Yan
- Department of Science and Education, Hospital of Xianyou County, No. 910, 825 Main Street, Licheng Town, Putian, 351200, China
| | - Baoying Liu
- School of Public Health, Fujian Medical University, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
- Fujian Provincial Key Laboratory of Environment Factors & Cancer, 1 Xueyuan Road, Minhou Fuzhou, 350122, China
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Müller S, Wallner S, Schmitz G, Loew T, Stempfl T, Möhle C, Strack C, Sag S, Baessler A, Fischer M. SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss. Gene 2020; 753:144787. [PMID: 32439373 DOI: 10.1016/j.gene.2020.144787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Diet induced weight loss represents an intervention for obesity to prevent associated diseases. However there is considerable inter-individual variation. Single nucleotide polymorphisms (SNPs) and plasma miRNA might be contributing factors. We therefore hypothesized that changes in the miRNA pattern during weight loss depend on the SNP genotype. METHODS Plasma miRNA profiles from 12 patients were determined before and after a three month weight loss intervention by Illumina sequencing. 46 further patients were analyzed by qPCR. SNP genotypes were determined on the Sequenom iPLEX platform. RESULTS Samples before and after weight loss were analyzed by miRNA-seq and delta miRNA levels ranked according to p-value. Levels of miRNAs 25, 93 and 106 that are expressed from a common genomic cluster were reduced after weight loss. Those results were substantiated in a qPCR analysis of 46 additional patients. This is in accordance with mouse data showing a functional involvement of this cluster in obesity. Correlation of the changes in miRNA abundance with SNP genotypes revealed a statistical association of all three miRNAs with known obesity susceptibility SNPs. CONCLUSION Diet induced weight loss leads to SNP dependent modulation of miRNAs from the miR 25/93/106 gene cluster in humans.
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Affiliation(s)
- Stephanie Müller
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany; Clinic for Internal Medicine 2, Regensburg University Hospital, Regensburg, Germany
| | - Stefan Wallner
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany.
| | - Gerd Schmitz
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Thomas Loew
- Department of Psychosomatics, Regensburg University Hospital, Regensburg, Germany
| | - Thomas Stempfl
- Center of Excellence for Fluorescent Bioanalytics (KFB), University of Regensburg, Regensburg, Germany
| | - Christoph Möhle
- Center of Excellence for Fluorescent Bioanalytics (KFB), University of Regensburg, Regensburg, Germany
| | - Christina Strack
- Clinic for Internal Medicine 2, Regensburg University Hospital, Regensburg, Germany
| | - Sabine Sag
- Clinic for Internal Medicine 2, Regensburg University Hospital, Regensburg, Germany
| | - Andrea Baessler
- Clinic for Internal Medicine 2, Regensburg University Hospital, Regensburg, Germany
| | - Marcus Fischer
- Clinic for Internal Medicine 2, Regensburg University Hospital, Regensburg, Germany
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