Identification of genetic associations of SP110/MYBBP1A/RELA with pulmonary tuberculosis in the Chinese Han population

Deng, Shaoli; Li, Liang; Hui, Pei; Zhou, Jia; Wang, Meiyan; Yue, Jun; Wan, Chunling; He, Guang; He, Lin

doi:10.1007/s00439-012-1244-5

Cited by 37 publications

(48 citation statements)

References 32 publications

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“…The human SP110 gene is postulated to play roles in the development of clinical TB [4]. And current meta-analysis result supports that the SP110 rs9061 T allele may confer significant risk of PTB in East Asian populations [5]. However, SP110's effects on progression to lung cavitation are unknown yet.…”

Section: Introductionmentioning

confidence: 91%

“…A total of 424 blood donors matched with cases were recruited as healthy controls described in the previous study [5], among whom, 284 were men and 140 women; the mean age (±SD) was 41.17 ± 17.68 years. There were no significant differences between PTB patients and healthy controls with regard to gender or age (p = 0.266 and 0.329, respectively).…”

Section: Subjectsmentioning

confidence: 99%

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The effects of SP110’s associated genes on fresh cavitary pulmonary tuberculosis in Han Chinese population

Jiang

Yue

et al. 2015

Clin Exp Med

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SP110 is a promising anti-Mycobacterium tuberculosis (MTB) gene. To investigate the effects of SP110 and its associated genes, i.e., MYBBP1A and RELA, on pathological progression of MTB infection, an association study with 424 patients of fresh pulmonary tuberculosis (PTB) and 424 healthy controls was performed. Moreover, classification and regression tree and multifactor dimensionality reduction were employed to explore the effects of gene-gene interactions on cavitary PTB. The results indicated that both the heterozygous genotype GC and homozygous genotype CC in rs3809849 had significant effects on the risk of PTB (OR 1.42, 95 % CI 1.06-1.92, p 0.019; OR 1.55, 95 % CI 1.04-2.33, p = 0.033, respectively), and heterozygous genotype CT in rs9061 also had similar effects (OR 1.43, 95 % CI 1.07-1.90, p = 0.014). The rs3809849 and rs9905742 in MYBBP1A were also significantly associated with cavitary PTB (p = 0.00046 and 0.039, respectively), while rs9061 in SP110 had no such association (p = 0.06931) except its significant association with non-cavitary PTB (p = 0.0093). The interaction of MYBBP1A and RELA had significant effect on cavitary PTB (OR 4.24, 95 % CI 1.44-12.49, p = 0.005). These suggest that MYBBP1A instead of SP110 may be a genetic risk factor for cavitary PTB and play important effects on its whole progress.

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Section: Introductionmentioning

confidence: 91%

Section: Subjectsmentioning

confidence: 99%

The effects of SP110’s associated genes on fresh cavitary pulmonary tuberculosis in Han Chinese population

Jiang

Yue

et al. 2015

Clin Exp Med

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“…Odds ratios (OR), 95% confidence Interval (CI) and other statistical analyses were implemented using the R software version 3.1.2. The THESIAS program was used to perform the haplotype analysis (Tregouet et al 2004;Cai et al 2013). The global test for the association of the combined SNPs in TNF-α with PCOS was the (n−1) df test; here, n refers to the number of haplotypes.…”

Section: Discussionmentioning

confidence: 99%

“…A total of 2 ml anti-coagulated blood was drawn from each subject to extract genomic DNA using the previous methods (Cai et al 2013;Jiang et al 2016). The DNA was stored at −20℃ until it was used.…”

Section: Genotyping Analysismentioning

confidence: 99%

A Missense Variant rs4645843 in TNF-α Gene Is a Risk Factor of Polycystic Ovary Syndrome in the Uygur Population

Zhao

Wan

2017

Tohoku J. Exp. Med.

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Polycystic ovary syndrome (PCOS) is a complex endocrine syndrome, resulting from the interaction of gene variants and environmental factors. PCOS is viewed as a proinflammatory state and is characterized by hyperandrogenism, hyperinsulinemia, and over-weight. In China, the incidence of PCOS is higher in the Uygur population than that in the Chinese Han population. The association of the tumor necrosis factor α (TNF-α ) gene with PCOS remains to be clarified. Here, we investigated the association of TNF-α polymorphisms with PCOS in the Uygur population (393 patients with PCOS and 381 healthy subjects). Two single-nucleotide polymorphisms in TNF-α were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method: rs1800629 (-308G/A polymorphism), a commonly tested variant and rs4645843 (6213C/T polymorphism) that causes a Pro-to-Leu substitution at position 84, the most damaging variant of TNF-α based on in silico analysis. We thus found that both the genotypic and allelic distributions of rs4645843 were significantly different between PCOS and control groups (p = 0.03 and 0.024, respectively), whereas those of rs1800629 were similar between the groups. Furthermore, rs4645843 was significantly associated with serum testosterone levels and the score of Homeostatic Model Assessment for Insulin Resistance (HOMA-IR), but no such association was found with rs1800629. Importantly, both rs4645843 and rs1800629 were significantly associated with higher body mass index (p < 0.05). This is the first study that shows the association of TNF-α gene with PCOS in the Uygur population. The TNF-α gene may influence the pathogenesis of PCOS through regulating testosterone level, obesity and HOMA-IR.

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“…Genomic deoxyribonucleic acid (DNA) was isolated according to the widely-used standard protocols (Cai et al 2013;Hao et al 2014;Jiang et al 2016). The genomic DNA libraries were constructed based on Illumina protocols.…”

Section: Whole-exome Sequencing (Wes)mentioning

confidence: 99%

A SLC24A2 Gene Variant Uncovered in Pancreatic Ductal Adenocarcinoma by Whole Exome Sequencing

Wang

Shao

Chen

et al. 2017

Tohoku J. Exp. Med.

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Pancreatic ductal adenocarcinoma (PDAC) presents as an aggressive malignancy caused by environmental and genetic factors. In order to identify causal genes for PDAC, we performed whole exome sequencing (WES) to detect gene mutations in seven pairs of PDAC tissue and adjacent non-tumor tissue samples. Finally, we found a new nonsynonymous single nucleotide variant (nsSNV) in solute carrier 24 family member 2 (SLC24A2) gene resulting in the substitution of native glutamic acid (E) into aspartic acid (D) at position of 287 amino acid (E287D) in SLC24A2 protein, and confirmed this variant by Sanger gene sequencing. SLC24A2 is a potassium-dependent sodium-calcium exchanger and can transport metal ion across cell membrane. Multiple in silico variants' effects analyses methods including SIFT, PolyPhen, PROVEAN, and PANTHER demonstrated this variant had probably damaging effects, which was consistent with the results obtained from Mutation Taster software analysis with a probability of 0.99999997 to be "disease causing." The three dimension (3D) structure analysis results suggested this variant had little effects on the solubility and hydrophobicity of the protein; but it could decrease the protein stability by increasing the total protein structure energy (−8874.33 kJ/mol for the mutant and −8963.54 kJ/mol for the native) and by causing the mutant protein decreasing three stabilizing residues. Less stability of the mutant 287D protein than the native E287 protein was also supported by I-Mutant and Western-blotting analysis results. Overall, a new mutation in SLC24A2 gene was identified to decrease the stability of SLC24A2, which may have potential clinical usages.

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Identification of genetic associations of SP110/MYBBP1A/RELA with pulmonary tuberculosis in the Chinese Han population

Cited by 37 publications

References 32 publications

The effects of SP110’s associated genes on fresh cavitary pulmonary tuberculosis in Han Chinese population

The effects of SP110’s associated genes on fresh cavitary pulmonary tuberculosis in Han Chinese population

A Missense Variant rs4645843 in <i>TNF-</i><i>α</i> Gene Is a Risk Factor of Polycystic Ovary Syndrome in the Uygur Population

A <i>SLC24A2</i> Gene Variant Uncovered in Pancreatic Ductal Adenocarcinoma by Whole Exome Sequencing

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