Relationship Between Genetic Polymorphisms of the TNF Gene and Hallux Valgus Susceptibility

Identification of copy number variants contributing to hallux valgus

Hallux valgus is a common form of foot deformity, and genetic factors contribute substantially to the pathogenesis of hallux valgus deformity. We conducted a genetic study on the structural variants underlying familial hallux valgus using whole exome sequencing approach. Twenty individuals from five hallux valgus families and two sporadic cases were included in this study. A total of 372 copy number variations were found and passed quality control filtering. Among them, 43 were only present in cases but not in controls or healthy individuals in the database of genomic variants. The genes covered by these copy number variations were enriched in gene sets related to immune signaling pathway, and cytochrome P450 metabolism. The hereditary CNVs demonstrate a dominant inheritance pattern. Two candidate pathogenic CNVs were further validated by quantitative-PCR. This study suggests that hallux valgus is a degenerative joint disease involving the dysregulation of immune and metabolism signaling pathways.

New insights into hallux valgus by whole exome sequencing study

The traditional view is that the occurrence and development of hallux valgus (HV) are mainly due to environmental factors. Recent studies have suggested the large contribution of genetic heritability to HV, but it remains elusive about the genetic variants underlying the development of HV. To gain knowledge about the molecular mechanisms of HV pathogenesis by genetic approach, whole exome sequencing studies were performed in 10 individuals (7 affected by HV and 3 unaffected) from three independent families. Specific mutations were found to be related to the pathogenesis of HV and conform to the laws of inheritance. A total of 36 genes with functional candidate single nucleotide variants were identified. Genetic predisposition plays an important role in the development of HV. Interestingly, some of these genes are related to chronic arthritis, such as the complement encoding gene C7, or are related to long toe or long fingers, such as TTN, COL6A3, LARS, FIG4, and CBS. This study identified rare potentially pathogenic mutations represented by genes related to digital anomalies and chronic arthritis underlying the familial types of HV, which acquired new insights into the genetic and physiological foundations of HV, thereby might improve accurate prevention and drug development for HV.

Correlation of SNPs in Myeloid differentiation-2 (MD-2) gene with the susceptibility to clinical mastitis in Chinese Holstein dairy cows

Myeloid differentiation-2 (MD-2), as an essential component of the CD14-TLR4/MD-2 receptor complex, is critical in identifying bacterial Lipopolysaccharide (LPS) and activating innate immune responses. To evaluate the relationship between MD-2 polymorphisms (including 5′ end and exon regions) and clinical mastitis, population genetic analysis was performed via PCR single strand conformation polymorphism (PCR-SSCP) and direct sequencing in Chinese Holstein dairy cows. Eleven pairs of primer PCR products for SSCP analysis: six pairs of primers (P1-P6) for the 5′-end, four (P7–P10) for the exon regions, and one (P11) for 3′-untranslational region. There were six SSCP bands (named: EE, EF, FF, EQ, EM and EN genotype) in the PCR amplification products of primer P1, two bands in P4 (CD and DD) and three bands in P5 (AA, AB, and BB). Total of five (g.-2173 C/G, g.-2148 C/T, g.-2089 G/T, g.-555 G/A and g.-121 C/A) single nucleotides polymorphism sites (SNPs) were identified in 5′-end of the MD-2 gene. Data showed that SNPs g.-555 (G/A) had significant differences (P<0.01). However, only Gram-negative bacteria (e.g. E. coli) were screened in the milk of the clinical mastitis cows, indicating that this SNPs g.-555 (G/A) in MD-2 gene may play an important role in susceptibility to clinical mastitis infected with Gram-negative bacteria in Chinese Holstein dairy cows.

Apolipoprotein E (APOE) genotype-associated disease risks: a phenome-wide, registry-based, case-control study utilising the UK Biobank

BACKGROUND

The three main alleles of the APOE gene (ε4, ε3 and ε2) carry differential risks for conditions including Alzheimer's disease (AD) and cardiovascular disease. Due to their clinical significance, we explored disease associations of the APOE genotypes using a hypothesis-free, data-driven, phenome-wide association study (PheWAS) approach.

METHODS

We used data from the UK Biobank to screen for associations between APOE genotypes and over 950 disease outcomes using genotype ε3ε3 as a reference. Data was restricted to 337,484 white British participants (aged 37-73 years).

FINDINGS

After correction for multiple testing, PheWAS analyses identified associations with 37 outcomes, representing 18 distinct diseases. As expected, ε3ε4 and ε4ε4 genotypes associated with increased odds of AD (p ≤ 7.6 × 10^-46), hypercholesterolaemia (p ≤ 7.1 × 10^-17) and ischaemic heart disease (p ≤ 2.3 × 10^-4), while ε2ε3 provided protection for the latter two conditions (p ≤ 3.7 × 10^-10) compared to ε3ε3. In contrast, ε4-associated disease protection was seen against obesity, chronic airway obstruction, type 2 diabetes, gallbladder disease, and liver disease (all p ≤ 5.2 × 10^-4) while ε2ε2 homozygosity increased risks of peripheral vascular disease, thromboembolism, arterial aneurysm, peptic ulcer, cervical disorders, and hallux valgus (all p ≤ 6.1 × 10^-4). Sensitivity analyses using brain neuroimaging, blood biochemistry, anthropometric, and spirometric biomarkers supported the PheWAS findings on APOE associations with respective disease outcomes.

INTERPRETATION

PheWAS confirms strong associations between APOE and AD, hypercholesterolaemia, and ischaemic heart disease, and suggests potential ε4-associated disease protection and harmful effects of the ε2ε2 genotype, for several conditions.

FUNDING

National Health and Medical Research Council of Australia.

Association of single nucleotide polymorphisms in TNF-α (-308G/A and -238G/A) to dengue: Case-control and meta-analysis study

Dengue is an acute viral disease whose clinical condition is related to the interaction of factors related to the Dengue virus (DENV), environment and the host, with the immunity of the human host contributing a substantial role in the pathogenesis of DENV infection. Studies have demonstrated that single nucleotide polymorphisms (SNPs) in the promoter regions of cytokine genes such as tumor necrosis factor (TNF-α) affect transcription and/or expression; and therefore, may influence the pathogenesis of infectious diseases, such as dengue. Consequently, the objective of this study was to assess through a case-control study whether there was an association between the presence of SNPs -308G/A and -238G/A in the TNF-α gene and 158 patients with dengue and 123 controls. No association was found between the SNPs and the dengue cases in the study population. We then performed a meta-analysis, retrieving data from case-control studies in the literature for the same polymorphisms. For SNP-308G/A, the GG genotype was associated with dengue fever (DF) risk (OR = 1.24, 1.00-1.53; p = 0.05; I² = 0%), while the GA genotype (OR = 0.75, 0.60-0.93; p = 0.01; I² = 0%) and allele A (OR = 0.75, 0.60-0.93; p = 0.01; I² = 0%) were associated with protection. The genotype GG population in the Asian continent (OR = 1.81 [1.06, 3.09], p = 0.03, I² = 0%) and American (OR = 1.29 [1.00, 1.65], p = 0.05, I² = 0%) was also associated with protection in the comparison between the cases versus the control group. In each comparison, the dominant model AA + GA (p < 0.00001) conferred protection. For SNP-238G/A the GA genotype was associated with risk for dengue hemorrhagic fever (DHF; OR = 2.17, 1.28-3.67; p = 0.004; I² = 0%)), and the dominant AA + GA model (p < 0.00001) was associated with protection in each comparison. In summary, our results did not associate SNPs in the TNF-α gene to dengue in the Brazilian northeast population. However, combined literature data suggested the effect of the GG and GA genotypes of the SNP-308G/A on risk and protection, respectively, in Asian and American populations.