Candidate genes for age at menarche are associated with endometriosis

Ponomarenko, Irina; Reshetnikov, Evgeny; Полоников, А. В.; Verzilina, I.N.; Сорокина, И. Н.; Elgaeva, Elizaveta E.; Tsepilov, Yakov A.; Yermachenko, Anna; Dvornyk, Volodymyr; Чурносов, М. И.

doi:10.1016/j.rbmo.2020.04.016

Cited by 44 publications

(48 citation statements)

References 56 publications

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“…Ten SNPs of the MMP genes (rs1799750 MMP1 , rs243865 MMP2 , rs679620 MMP3 , rs1940475 MMP8 , rs3918242, rs3918249, rs3787268, rs17576, rs17577, and rs2250889 MMP9 ) were selected for this study according to the criteria [ 27 , 28 ]: previously reported associations with digestive diseases (gastric and duodenal ulcer, gastric cancer, etc. ), regulatory potential, and MAF > 0.05.…”

Section: Methodsmentioning

confidence: 99%

Association of the functionally significant polymorphisms of the MMP9 gene with H. pylori-positive gastric ulcer in the Caucasian population of Central Russia

et al. 2021

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Background and purpose The study analyzed the association of functionally significant polymorphisms of matrix metalloproteinases (MMPs) genes with the development of gastric ulcer (GU) in Caucasians from Central Russia. Methods The 781 participants, including 434 patients with GU (196 Helicobacter pylori (H. pylori)-positive and 238 H. pylori-negative) and 347 controls (all H. pylori-negative) were recruited for the study. Ten SNPs of the MMP1 (rs1799750), MMP2 (rs243865), MMP3 (rs679620), MMP8 (rs1940475), and MMP9 (rs3918242, rs3918249, rs3787268, rs17576, rs17577, and rs2250889) genes were considered for association with GU using multiple logistic regression. The SNPs associated with GU and loci linked (r2≥0.8) to them were analyzed in silico for their functional assignments. Results The SNPs of the MMP9 gene were associated with H. pylori-positive GU: alleles C of rs3918249 (OR = 2.02, pperm = 0.008) and A of rs3787268 (OR = 1.60–1.82, pperm ≤ 0.016), and eight haplotypes of all studied MMP9 gene SNPs (OR = 1.85–2.04, pperm ≤ 0.016) increased risk for H. pylori-positive GU. None of the analyzed SNPs was independently associated with GU and H. pylori-negative GU. Two haplotypes of the MMP9 gene (contributed by rs3918242, rs3918249, rs17576, and rs3787268) increased risk for GU (OR = 1.62–1.65, pperm ≤ 0.006). Six loci of the MMP9 gene, which are associated with H. pylori-positive GU, and 65 SNPs linked to them manifest significant epigenetic effects, have pronounced eQTL (17 genes) and sQTL (6 genes) values. Conclusion SNPs of the MMP9 were associated with H. pylori-positive GU but not with H. pylori-negative GU in Caucasians of Central Russia.

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Section: Methodsmentioning

confidence: 99%

Association of the functionally significant polymorphisms of the MMP9 gene with H. pylori-positive gastric ulcer in the Caucasian population of Central Russia

et al. 2021

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“…The SNPs associated with EH and those strongly linked to them were evaluated for their functional significance (non-synonymous SNPs 49 , regulatory potential 50 , 51 , and eQTLs 52 ). The loci in linkage disequilibrium (LD) (r 2 ≥ 0.8) with the EH-associated ones were determined using HaploReg (v4.1) ( http://archive.broadinstitute.org/mammals/haploreg/haploreg.php ) and the data of the European population from the 1000 Genomes Project Phase 1 42 , 50 , 53 , 54 .…”

Section: Methodsmentioning

confidence: 99%

“…The effect of the candidate SNPs for EH on gene expression in various tissues and organs was estimated using the GTExportal data ( http://www.gtexportal.org/ ) as of 10.12.2019 (Release V8 updated on 26/08/2019) (dbGaP Accession phs000424.v8.p2) 52 . The False Discovery Rate (FDR) ≤ 0.05 was applied as statistical significance threshold 55 .…”

Section: Methodsmentioning

confidence: 99%

Polymorphisms of the matrix metalloproteinase genes are associated with essential hypertension in a Caucasian population of Central Russia

Moskalenko

Ponomarenko

Reshetnikov

et al. 2021

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This study aimed to determine possible association of eight polymorphisms of seven MMP genes with essential hypertension (EH) in a Caucasian population of Central Russia. Eight SNPs of the MMP1, MMP2, MMP3, MMP7, MMP8, MMP9, and MMP12 genes and their gene–gene (epistatic) interactions were analyzed for association with EH in a cohort of 939 patients and 466 controls using logistic regression and assuming additive, recessive, and dominant genetic models. The functional significance of the polymorphisms associated with EH and 114 variants linked to them (r2 ≥ 0.8) was analyzed in silico. Allele G of rs11568818 MMP7 was associated with EH according to all three genetic models (OR = 0.58–0.70, pperm = 0.01–0.03). The above eight SNPs were associated with the disorder within 12 most significant epistatic models (OR = 1.49–1.93, pperm < 0.02). Loci rs1320632 MMP8 and rs11568818 MMP7 contributed to the largest number of the models (12 and 10, respectively). The EH-associated loci and 114 SNPs linked to them had non-synonymous, regulatory, and eQTL significance for 15 genes, which contributed to the pathways related to metalloendopeptidase activity, collagen degradation, and extracellular matrix disassembly. In summary, eight studied SNPs of MMPs genes were associated with EH in the Caucasian population of Central Russia.

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“…A blood sample (4–5 ml) was collected by venipuncture from all study participants in EDTA-coated tubes (Vacutainer®). Genomic DNA was isolated from the buffy coat using a standard phenol/chloroform procedure (as described earlier 37 ).…”

Section: Methodsmentioning

confidence: 99%

Functionally significant polymorphisms of the MMP-9 gene are associated with peptic ulcer disease in the Caucasian population of Central Russia

Minyaylo

Ponomarenko

Reshetnikov

et al. 2021

Sci Rep

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This study analyzed the association of functionally significant SNPs of matrix metalloproteinase (MMP) genes in the development of peptic ulcer disease (PUD) in Caucasians from Central Russia. Ten SNPs of the MMP-1, MMP-2, MMP-3, MMP-8, and MMP-9 genes were analyzed for association with PUD in a cohort of 798 patients with PUD (including 404 H. pylori-positive and 394 H. pylori-negative) and 347 H. pylori-negative controls using logistic regression and assuming the additive, recessive, and dominant genetic models. The variants of MMP-1, MMP-2, MMP-3, and MMP-8 did not manifest any significant associations with the diseases. Five SNPs of the MMP-9 gene demonstrated such association. Allele G of the rs17576 MMP-9 locus conferred a higher risk for PUD (ORadj = 1.31, pperm = 0.016), haplotype AACG of loci rs17576-rs3787268-rs2250889-rs17577 of the MMP-9 gene decreased risk for PUD (ORadj = 0.17, pperm = 0.003). Also, allele C of rs3918249, allele G of rs17576 and haplotype CG of rs3918249-rs17576 of the MMP-9 gene increased risk for H. pylori-positive PUD (ORadj = 1.82, pperm = 0.002; ORadj = 1.53–1.95 pperm = 0.001–0.013 and ORadj = 1.49 pperm = 0.009 respectively). The above loci and 50 linked to them possess significant regulatory effects and may affect the alternative splicing of four genes and the expression of 17 genes in various organs and tissues related to the PUD pathogenesis.

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Candidate genes for age at menarche are associated with endometriosis

Cited by 44 publications

References 56 publications

Association of the functionally significant polymorphisms of the MMP9 gene with H. pylori-positive gastric ulcer in the Caucasian population of Central Russia

Association of the functionally significant polymorphisms of the MMP9 gene with H. pylori-positive gastric ulcer in the Caucasian population of Central Russia

Polymorphisms of the matrix metalloproteinase genes are associated with essential hypertension in a Caucasian population of Central Russia

Functionally significant polymorphisms of the MMP-9 gene are associated with peptic ulcer disease in the Caucasian population of Central Russia

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