Functional Consequences Of Single Nucleotide Polymorphisms Research Articles

Angular limb deformity associated with TSPAN18, NRG3 and NOVA2 in Rambouillet rams

Angular limb deformity (ALD) affects many species of livestock and companion animals. The mechanisms of ALD development are not well understood, but previous research suggests the involvement of genetic risk factors. A case-control genome-wide association study (GWAS) was conducted with 40 ALD-affected and 302 unaffected Rambouillet rams and 40,945 single nucleotide polymorphisms (SNPs). Forelimbs of 6 ALD-affected rams were examined and diagnosed with osteochondrosis. Genome-wide or chromosome-wide significant SNPs were positioned exonic, intronic or within the 3′UTR of genes TSPAN18, NRG3 and NOVA2, respectively. These genes have previously described roles related to angiogenesis and osteoblast, osteoclast and chondrocyte proliferation and differentiation, which suggests the possibility for their involvement in the pathogenesis of osteochondrosis. Functional consequences of SNPs were evaluated through transcription factor binding site analysis, which predicted binding sites for transcription factors of known importance to bone growth, including SOX6, SOX9 and RUNX2. The identification of genetic risk factors for ALD may help to improve animal welfare and production in Rambouillet, a breed known to be at risk for ALD development. This study proposes genes TSPAN18, NRG3 and NOVA2 as targets for further research towards understanding the etiology of ALD in Rambouillet sheep.

A bioinformatics approach to investigating the structural and functional consequences of SNPs in TMPRSS2 for COVID‐19 infection

SARS‐CoV‐2 is a highly infectious virus that is responsible for the COVID‐19 global pandemic that swept the world in 2020. Disease outcomes range from asymptomatic to fatal. The virus initiates entry into host cells by the binding of its spike protein to the ACE2 receptor. Entry is finalized by the activation of spike glycoprotein by proteases including transmembrane protease, serine 2 (TMPRSS2) and FURIN which cleave the spike protein of the virus. Single nucleotide polymorphisms (SNPs) in TMPRSS2 may lead to functional changes which could underlie differences in disease severity. TMPRSS2 is also known to activate different respiratory illnesses including coronaviruses and influenza A (Shen et al., 2020). Previous studies have shown that knockout TMPRSS2 mice appeared healthy, experienced a decrease in viral spread within the respiratory system, and had a less severe immune response when infected with SARS‐CoV and MERS‐CoV (Baughn et al., 2020). Thus, we asked whether genetic variations in TMPRSS2 in humans lead to differences in infection rates or severity of disease symptoms of SARS‐CoV‐2. We examined the NCBI dbSNP database to identify SNPs in the TMPRSS2 gene. As of 10 December 2020, we found there were 11,023 intron variants, 393 missense variants, 186 synonymous variants, 3 in‐frame insertion variants, 2 in‐frame deletion variants, and 1 initiator codon variant reported. To narrow these down to 23 SNPs of interest, we first searched the ClinVar database to identify SNPs with general clinical significance, followed by searching the literature to determine SNPs specifically related to SARS‐CoV‐2 severity. One missense variant, rs12329760, results in an amino acid substitution, V160M, which has been predicted to alter TMPRSS2 function. A subset of these SNPs show differences in frequency in world populations, and we wondered if these SNPs had structural and functional consequences for the protein. A crystal structure of TMPRSS2 is not currently available. To visualize the structural consequences of amino acid substitutions, we performed homology modeling on TMPRSS2 (UniProt O15393) using the structure prediction software HHPred, RaptorX, and SwissModel based on the ~30% similarity to hepsin. The predicted structures of TMPRSS2 with various amino acid substitutions were then docked to the SARS‐CoV‐2 spike protein using I‐TASSER and Haddock 2.4 to observe differences in binding interactions and therefore determine which sequence changes are predicted to alter binding interactions, potentially contributing to the wide variation of symptoms caused by COVID‐19.Baughn, L. B., Sharma, N., Elhaik, E., Sekulic, A., Bryce, A. H., & Fonseca, R. (2020). Targeting TMPRSS2 in SARS‐CoV‐2 Infection. Mayo Clinic proceedings, 95(9), 1989–1999. https://doi.org/10.1016/j.mayocp.2020.06.018Shen, L.W.; Mao, H.J.;, Wu, Y.L.; Tanaka,Y.; Zhang,W. (2017) TMPRSS2: A potential target for treatment of influenza virus and coronavirus infections, Biochimie, 142, 1‐10. https://doi.org/10.1016/j.biochi.2017.07.016

Identification and prediction of the consequences of nonsynonymous SNPs in glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of zebrafish Danio rerio

The recent progress in DNA sequencing and computational algorithms dramatically heightened the value of single nucleotide polymorphism (SNP) databases. The experimental studies of mutation for the particular gene of interest are laborious and time-consuming. In this study, we used several computational algorithms to investigate the structural and functional consequences of SNPs on the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of zebrafish (Danio rerio). The GAPDH gene is involved in multiple cellular activities, in addition to its association with classical glycolytic pathway. It has most commonly been used as the housekeeping gene for differential gene expression profiling, including western blots. The computational analysis, which used sequence-based tools such as SIFT, PANTHER, PROVEAN, and I-Mutant2.0, predicted deleterious nonsynonymous SNPs (nsSNPs) at p.W194R in the GAPDH gene. The SWISS Model tool generated a homology-modeled 3D structure of GAPDH by applying homologous protein structures retrieved from the RCSB PDB databank (PDB ID: 1U8F_O, 1ZNQ_O, 1J0X_O, 3GPD_R, and 1SZJ_G). The sequence identities of the above selected models were 86%, 86%, 86%, 83%, and 75%, respectively. The Procheck quality assessment in the Ramachandran plot showed that the incorporated mutation (p.W194R) led to a shifting of amino acid residues from the most favored regions towards the disallowed region, as compared to the native counterpart. The lowered ERRAT and PROSA Z scores in the mutant confirmed the overall deteriorating quality of mutant GAPDH. We also predicted an effect of mutation on increased H-bonding patterns due to mutant residue. The molecular docking analysis, while binding GAPDH to its ligand (NAD+), also revealed elevated global energy in the mutant. Altogether, this study demonstrated the impact of nsSNPs on the protein structure and function. The results of work provide an insight/roadmap for future investigations with regard to the pathological consequences of nsSNPs using in vivo methods.

English

The MLH1 gene responsible for colon cancer has been examined to identify functional consequences of single-nucleotide polymorphisms (SNPs). 16 SNPs have been identified in the MLH1 gene in which all are found to be nonsynonymous. Non synymous SNPs are relevant in many of the human inherited diseases since they change the aminoacid sequence of the protein. 56% of the identified nsSNPs have been reported as damaging. In the analysis of SNPs using SIFT, UTRscan, FastSNP and PolyPhen-2, it was recognized that rs41295284 and rs35001569 were responsible for the alteration in levels of expression. It has been concluded that among all SNPs of MLH1 gene, the mutation in rs41295284 and rs35001569 have the most significant effect on functional variation.   Key words: Single nucleotide polymorphism, non-synonymous, colon cancer.

The ApoE gene of Alzheimer's disease (AD)

The ApoE gene responsible for the Alzheimer's disease has been examined to identify functional consequences of single-nucleotide polymorphisms (SNPs). Eighty-eight SNPs have been identified in the ApoE gene in which 31 are found to be nonsynonymous, 8 of them are coding synonymous, 33 are found to be in intron, and 3 are in untranslated region. The SNPs found in the untranslated region consisted of two SNPs from 5' and one SNP from the 3'. Twenty-nine percent of the identified nsSNPs have been reported as damaging. In the analysis of SNPs in the UTR regions, it has been recognized that rs72654467 from 5' and rs71673244 from 5' and 3' are responsible for the alteration in levels of expression. Both native and mutant protein structures were analyzed along with the stabilization residues. It has been concluded that among all SNPs of ApoE, the mutation in rs11542041 (R132S) has the most significant effect on functional variation.