Effect of APOB polymorphism rs562338 (G/A) on serum proteome of coronary artery disease patients: a “proteogenomic” approach

Abstract

In the current study, APOB (rs1052031) genotype-guided proteomic analysis was performed in a cohort of Pakistani population. A total of 700 study subjects, including Coronary Artery Disease (CAD) patients (n = 480) and healthy individuals (n = 220) as a control group were included in the study. Genotyping was carried out by using tetra primer-amplification refractory mutation system-based polymerase chain reaction (T-ARMS-PCR) whereas mass spectrometry (Orbitrap MS) was used for label free quantification of serum samples. Genotypic frequency of GG genotype was found to be 90.1%, while 6.4% was for GA genotype and 3.5% was for AA genotypes in CAD patients. In the control group, 87.2% healthy subjects were found to have GG genotype, 11.8% had GA genotype, and 0.9% were with AA genotypes. Significant (p = 0.007) difference was observed between genotypic frequencies in the patients and the control group. The rare allele AA was found to be strongly associated with the CAD [OR: 4 (1.9–16.7)], as compared to the control group in recessive genetic model (p = 0.04). Using label free proteomics, altered expression of 60 significant proteins was observed. Enrichment analysis of these protein showed higher number of up-regulated pathways, including phosphatidylcholine-sterol O-acyltransferase activator activity, cholesterol transfer activity, and sterol transfer activity in AA genotype of rs562338 (G>A) as compared to the wild type GG genotype. This study provides a deeper insight into CAD pathobiology with reference to proteogenomics, and proving this approach as a good platform for identifying the novel proteins and signaling pathways in relation to cardiovascular diseases.

Haplotype analysis and linkage disequilibrium of ApoB gene polymorphisms and its relationship with hyperlipidemia in patients with acne vulgaris

“…18,19 According to a study done by Zafar et al on rs562338 (G/A) ApoB gene polymorphism, individuals with AA genotypes experience altered serum lipid profiles more frequently than those with GG genotypes. 11 Similar findings were found in the Maonan and Han populations, except that they focused on the rs1042034 (G/A) ApoB gene polymorphism. They found that various rs1042034 (G/A) genotypes were linked to dyslipidemia.…”

“…The three alleles that were produced were GG (381 bp), AA (354 bp) and GA; both bands were present in addition to the 672 bp control band. The PCR amplification conditions were 95°C for 5 min, 35 cycles of amplification at 95°C for 1 min, 64.3°C for 1 min, 72°C for 30 s and final elongation at 72°C for 10 min 11 Genotype analysis of rs17240441 SNP To analyze the signal peptide of the gene 5 ApoB for insertion/deletion (I/D) polymorphisms, the oligonucleotide sequences 5CAG CTG GCG ATG GAC CCG CCGA3 as the five primers and 5CCA ATG ACA AAA TCC GTG AGG 3 as the three primers were used to create a primer combination that was intended to generate the first exon on the ApoB gene.…”

“…The PCR amplification conditions were 95 C for 5 min, 35 cycles of amplification at 95 C for 1 min, 64.3 C for 1 min, 72 C for 30 s and final elongation at 72 C for 10 min. 11…”

Assessment of the proteome profile of decellularized human amniotic membrane and its biocompatibility with umbilical cord‐derived mesenchymal stem cells

“…Finally, the samples were centrifuged (Centrifuge 5417R, Eppendorf, Germany) at 16000 rpm, 4°C for 20 min and protein concentrations were measured using Qubit™ Protein Assay kit (Invitrogen, Thermo Fisher Scientific, USA). The tryptic digestion of proteins and desalting of peptides was performed, using a previously reported method 26,27 . The peptide concentrations of samples were then quantified by the Qubit™ Protein Assay kit and dried peptides were kept at −20°C until further processing.…”

“…The tryptic digestion of proteins and desalting of peptides was performed, using a previously reported method. 26,27 The peptide concentrations of samples were then quantified by the Qubit™ Protein Assay kit and dried peptides were kept at À20 C until further processing.…”