Non-random distribution of gastric cancer susceptible loci on human chromosomes

Enrichment analysis and chromosomal distribution of gout susceptible loci identified by genome-wide association studies

Gout is an inherited and common inflammatory arthritic disease. Many researchers will identify polymorphic loci of gout susceptibility by conducting genome-wide association studies (GWAS). In the present study, the enrichment analysis and chromosomal distribution were performed using predicted polymorphic loci associated with gout risk. The polymorphic loci associated to gout were obtained from the GWAS database. Overall, this database contains 64,806 gout patients and 2,856,174 controls. Gene ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by using the Enrichr online server. A total of 110 common polymorphic protein-coding loci associated with gout risk were identified and included in the analysis. The results of the KEGG analysis showed that the gout-associated loci were mainly related to ABC transporters, endocrine and other factor-regulated calcium reabsorption, and gastric acid secretion pathways. The gene ontology analysis showed that the biological processes of the gout-associated loci were vascular transport, transport across the blood-brain barrier, positive regulation of transporter activity, and positive regulation of transcription by RNA polymerase II. The top cellular component was the external side of the apical plasma membrane. Statistical analysis revealed that the human chromosome segments 1q22, 4p16.1, 6p21.1-p21.2, 11q13.1-q13.2, 12q13.11-q13.3, and 12q24.1 had significantly bearing higher numbers of gout susceptibility loci.

Chromosomal Distribution of Ankylosing Spondylitis Susceptibility Loci

Objectives

Previous studies have been indicated that susceptible loci of several multifactorial diseases were non-randomly distributed on human genome. There is no published data on chromosomal distribution of genes associated with risk of ankylosing spondylitis. Therefore, the present study was carried out.

Methods

Published meta-analyses indexed in the PubMed database were used in the present study. Non-randomness chromosomal distribution of these loci was evaluated by the statistical method of Tai et al.

Results

A total of 88 articles were obtained. There was 32 ankylosing spondylitis associated genes. The present study revealed that the human chromosome segments 6p11.2-p21.33, 19q13.2-q13.42, and 2q11.2-q14.1 were ankylosing spondylitis associated-rich regions by bearing 7, 6 and 4 susceptible loci, respectively.

Conclusion

Ankylosing spondylitis associated-genes non-randomly have been distributed non-randomly on human chromosomes.

The genetic polymorphisms at the promoter region of HLA-DQB1 gene, creating responsive elements for NF1/CTF and converting the TFII-D binding site to GR-alpha

Human leukocyte antigen-DQB1 (HLA-DQB1, OMIM: 604305) is the human major histocompatibility complex (MHC) system. HLA genes are classified into three classes (I, II, and III). The HLA-DQB1 belongs to class II, is mainly involved in the actions of the human immune system and plays a fundamental role in donor-recipient matching in transplantation and can be associated with most autoimmune diseases. In this study, the potential influence(s) of the G-71C (rs71542466) and T-80C (rs9274529) genetic polymorphisms were investigated. These polymorphisms, located in the HLA-DQB1 promoter region, have a significant frequency in the world population. The online software ALGGEN-PROMO.v8.3 was used in this work. The results indicate that the C allele at the -71 position actually creates a new potential binding site for NF1/CTF and the C allele at the -80 position changes the TFII-D binding site into a GR-alpha response element. The NF1/CTF plays the role of activator and the GR-alpha is the inhibitor; thus, according to the roles of these transcription factors, it is suggested that the above-mentioned polymorphisms alter the expression levels of HLA-DQB1. Therefore, this genetic variation is associated with autoimmune diseases; however, this cannot be generalized because this is the first report and more studies are needed in the future.