Towards Post-Meiotic Sperm Production: Genetic Insight into Human Infertility from Mouse Models.

Declined quality and quantity of sperm is currently the major cause of patients suffering from infertility. Male germ cell development is spatiotemporally regulated throughout the whole developmental process. While it has been known that exogenous factors, such as environmental exposure, diet and lifestyle, et al, play causative roles in male infertility, recent progress has revealed abundant genetic mutations tightly associated with defective male germline development. In mammals, male germ cells undergo dramatic morphological change (i.e., nuclear condensation) and chromatin remodeling during post-meiotic haploid germline development, a process termed spermiogenesis; However, the molecular machinery players and functional mechanisms have yet to be identified. To date, accumulated evidence suggests that disruption in any step of haploid germline development is likely manifested as fertility issues with low sperm count, poor sperm motility, aberrant sperm morphology or combined. With the continually declined cost of next-generation sequencing and recent progress of CRISPR/Cas9 technology, growing studies have revealed a vast number of disease-causing genetic variants associated with spermiogenic defects in both mice and humans, along with mechanistic insights partially attained and validated through genetically engineered mouse models (GEMMs). In this review, we mainly summarize genes that are functional at post-meiotic stage. Identification and characterization of deleterious genetic variants should aid in our understanding of germline development, and thereby further improve the diagnosis and treatment of male infertility.

Major histocompatibility complex class II polymorphic variants are associated with asthma predisposition in the Punjabi population of Lahore, Pakistan.

INTRODUCTION: Various genome wide association studies have manifested that Major Histocompatibility Complex (MHC) region on chromosome 6p21 houses many potential candidate genes for asthma. OBJECTIVE: This Case-Control association study was planned to determine the association of 10 Single Nucleotide Polymorphisms (SNPs), residing within and around MHC genes' region on chromosome 6p21, with Asthma in Punjabi population of Lahore, Pakistan. METHODS: A total of 161 subjects, 61 physician-diagnosed asthma patients and 100 age-matched healthy controls, were recruited from Lahore, a city in Punjab. Ten single nucleotide polymorphisms (SNPs) (rs9378249, rs2070600, rs404860, rs6689, rs1049124, rs1063355, rs1049225, rs1049219, rs7773955 and rs928976) located within or near AGER, NOTCH and HLA genes in MHC region, were genotyped in both patients and controls using single base extension reaction and capillary electrophoresis-based genetic analyser. Statistical models were applied using SHEsis Plus. Results were adjusted for various cofactors (age, gender and environment) and by applying multiple corrections. Haplotype and linkage disequilibrium analyses were performed on Haploview software v4.1. RESULTS: Three of the studied SNPs rs1049124, rs1049219 and rs7773955 show independent significant association with asthma under allelic and genotypic models. Two of the haplotypes, H7 and H13, "CTAATTT" and "CCACTAT", respectively, for rs2070600, rs404860, rs6689, rs1049124, rs1063355, rs1049219 and rs7773955, are found to be significantly associated with the disease. CONCLUSION: This study reports association of SNP variants residing on HLA-DQB1 and HLA-DQA2 genes and haplotypes H7 and H13 on genomic region 6p21 with Asthma in the Punjabi population of Lahore, Pakistan.

Novel association of genetic variants in non-coding regulatory regions with HIV-1 infection.

Host genetic variability interplays with the environment and variegating viral factors to determine the outcome in HIV-1/AIDS. Several GWAS studies have reported that genetic heterogeneity of individuals leads to differential HIV susceptibility. Proxy SNPs that are in Linkage Disequilibrium to the GWAS SNPs could be important targets in HIV pathogenesis and need to be analyzed further for their potential regulatory role. Current study thus aimed to identify novel proxy SNPs that may play a critical role in HIV susceptibility and disease progression. 372 SNPs, associated with HIV-1/AIDS pathogenesis, were retrieved via GWAS catalogue. 1854 proxy SNPs, in Linkage Disequilibrium (r2 = 0.8) to the GWAS reported SNPs, were identified using the SNAP web tool. Regulatory functions of aforementioned 1854 polymorphic sites (GWAS SNPs and their proxy SNPs) were acquired from RegulomeDB. 178 of the proxy SNPs showed evidence of strong regulatory potential returning a score of ≤3. Among these regulatory SNPs, 22 had already been reported for their association with HIV/AIDS while 156 SNPs showed novel association. Three of these novel SNPs (g.rs6457282T>C, g.rs17064977C>T and g.rs3130350G>T) were validated using sequence specific PCR (SSP-PCR) on HIV-infected patients. For g.rs6457282T>C and rs17064977C>T, CT genotype was determined to be significantly associated with increased risk of HIV-1 infection (rs6457282T>C: OR = 9.5, 95% CI = 3.0792-29.3099, p = 0.0001; rs17064977C>T: OR = 8.1077, 95% CI = 3.1125-21.119, p = 0.0001). Moreover, the association of interacting protein partners of affected genes with HIV-1 elucidates the significance of corresponding SNPs in HIV disease outcome that further needs to be functionally deciphered.

Scoping Review of Crimean-Congo Hemorrhagic Fever (CCHF) Literature and Implications of Future Research.

Crimean-Congo hemorrhagic fever (CCHF) is one of the severe forms of high-fatality hemorrhagic fever transmitted by bite of infected ticks or body fluids of infected individuals. Lack of sufficient research and endemic potential of the disease is posing serious threats to public health. The aim of this review was to explore the current status of Crimean-Congo hemorrhagic fever virus (CCHFV) related research and to identify knowledge gaps and the areas that are yet to be explored. An interpretative scoping review methodology was followed to systematically characterize the most recent literature. Literature survey was conducted using electronic databases: PubMed, Scopus, ScienceDirect and Google Scholar. This comprehensive research yielded more than 300 records, but we excluded 100 articles based on our inclusion criteria and duplicates removal. All articles (n=85) that have been published currently were discussed in this scoping review. From a total of 303 documents retrieved, 85 met the criteria. All the documents (case studies, review articles, systematic reviews, meta-analysis, case control studies, cohort studies, randomised control trials, and longitudinal studies) were included in the study. The articles mainly cover different areas such as epidemiology, prevalence, diagnosis, pathogenesis, clinical outcomes, molecular basis, phylogenetics, transmission and treatment of CCHF. Treatment and prevention related knowledge is limited; therefore, future research should focus the development of therapeutics to mitigate the increasing risk of CCHF. Priority future goal should be studies on the molecular basis and treatment of CCHFV infection because several knowledge gaps have been identified in these areas.

Increasing Prevalence of Untypable and Mixed Genotypes of Hepatitis C Virus in Pakistan: Latest Trends in 2018.

Hepatitis C virus (HCV) genotyping is a critical parameter that acts as predictor of treatment response. According to previously reported findings, about 11 million population of Pakistan are HCV infected. Accumulating data suggest that genotype is the most prevalent genotype and mixed and untypable genotypes are the least prevalent genotypes of HCV. We observed that overall prevalence of mixed genotype (5.03%) and untypable genotype (3.3%) of HCV is on constant rise. This study highlights that the emergence of novel quasispecies could be reason of treatment failure in patients receiving direct-acting antiviral drugs.

rs12603332 is associated with male asthma patients specifically in urban areas of Lahore, Pakistan.

OBJECTIVE: rs12603332, an important regulatory site variant, is known to alter the regulatory motif E2A that is involved in the maturation of B-lymphocytes. The study was designed to check whether different environmental exposures alter its risk allele association with asthma or not. METHODS: 200 Physician-diagnosed asthma patients and 108 healthy individuals were enrolled from hospitals of Lahore. After quantitation of DNA extracted from peripheral blood, amplification of genomic region with rs12603332, followed by single base extension (SBE), was performed. Allele and genotype frequencies were calculated by SHEsis and Haploview software packages. Statistical analyses on PLINK were also performed, taking different factors as covariates. HaploReg analysis was done to predict the effect of risk allele on different regulatory motifs. RESULTS: Risk allele for rs12603332 i.e., "C" allele was found to be significantly associated with male patients residing in urban localities. CONCLUSION: The finding suggests that on exposure with urban environment, risk allele carriers tend to develop asthma symptoms via epigenetic regulation of motif associated with maturation of B-lymphocytes.