About: First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations

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About: First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations
Creator	Akhavan-Niaki, Haleh Hosseini, Mohammad Paniri, Alireza
Source	Medline; PMC
abstract	Current SARS-CoV-2 pandemy mortality created the hypothesis that some populations may be more susceptible to SARS-CoV-2. TMPRSS2 encodes a transmembrane serine protease which plays a crucial role in SARS-CoV-2 cell entry. Single nucleotide polymorphisms (SNPs) in TMPRSS2 might influence SARS-CoV2 entry into the cell. This study aimed to investigate the impact of SNPs on TMPRSS2 function and structure. In silico tools such as Ensembl, Gtex, ExPASY 2, GEPIA, CCLE, KEGG and GO were engaged to characterize TMPRSS2 and its expression profile. The functional effects of SNPs were analyzed by PolyPhen-2, PROVEN, SNAP2, SIFT and HSF. Also, Phyre2, GOR IV and PSIPRED were used to predict the secondary structure of TMPRSS2. Moreover, post-translational modification (PTM) and secretory properties were analyzed through Modpredand Phobius, respectively. Finally, miRNA profiles were investigated by PolymiRTS and miRSNPs. Out of 11,184 retrieved SNPs from dbSNP, 92 showed a different frequency between Asians and other populations. Only 21 SNPs affected the function and structure of TMPRSS2 by influencing the protein folding, PTM, splicing and miRNA function. Particularly, rs12329760 may create a de novo pocket protein. rs875393 can create a donor site, silencer and broken enhancer motifs. rs12627374 affects a wide spectrum of miRNAs profile. This study highlighted the role of TMPRSS2 SNPs and epigenetic mechanisms especially non-coding RNAs in appearance of different susceptibility to SARS-CoV-2 among different populations. Also, this study could pave the way to potential therapeutic implication of TMPRSS2 in designing antiviral drugs. Communicated by Ramaswamy H. Sarma
has issue date	2020-06-01(xsd:dateTime)
bibo:doi	10.1080/07391102.2020.1767690
bibo:pmid	32410502
has license	no-cc
sha1sum (hex)	19088f8de8ee5bd465cdfb838a05f39c21c18941
schema:url	https://doi.org/10.1080/07391102.2020.1767690
resource representing a document's title	First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations
has PubMed Central identifier	PMC7284145
has PubMed identifier	32410502
schema:publication	J Biomol Struct Dyn
resource representing a document's body	covid:19088f8de8ee5bd465cdfb838a05f39c21c18941#body_text
is schema:about of	named entity 'PROTEIN' named entity 'CURRENT' named entity 'KEGG' named entity 'SINGLE NUCLEOTIDE POLYMORPHISMS' named entity 'EFFECTS' named entity 'MOTIFS' named entity 'SERINE PROTEASE' named entity 'USED' named entity 'SARS-COV-2' named entity 'DONOR SITE' named entity 'dbSNP' named entity 'SARS-CoV2' named entity 'SARS-CoV-2' named entity 'transmembrane' named entity 'PTM' named entity 'miRNA' named entity 'TMPRSS2' named entity 'SARS-CoV-2' named entity 'Ensembl' named entity 'ExPASY' named entity 'epigenetic mechanisms' named entity 'TMPRSS2' named entity 'splicing' named entity 'KEGG' named entity 'GOR IV' named entity 'cell entry' named entity 'TMPRSS2' named entity 'random coil' named entity 'cell entry' named entity 'exon' named entity 'SARS-CoV-2' named entity 'TMPRSS2' named entity 'gene ontology' named entity 'polymorphisms' named entity 'TMPRSS2' named entity 'Ensembl' named entity 'SNPs' named entity 'Protein' named entity 'SARS' named entity 'isoforms' named entity 'cleavage' named entity 'prostate' named entity 'amino acid' named entity 'SAS' named entity 'SNPs' named entity 'dbSNP' named entity 'breast cancers' named entity 'TMPRSS2' named entity 'kidney renal clear cell carcinoma' named entity 'genomics' named entity '0.01' named entity 'TMPRSS2' named entity 'TMPRSS2' named entity 'prostate cancer' named entity 'polymorphisms' named entity 'AAs' named entity 'Tmprss2' named entity 'receptor' named entity 'carboxylation' named entity 'androgen receptor' named entity 'secondary structure' named entity 'ACE' named entity 'PSIPRED' named entity 'colon' named entity 'FASTA format' named entity 'beta strand' named entity 'proteolytic' named entity 'miRNA' named entity 'target sites' named entity 'TMPRSS2' named entity 'post-translational modifications' named entity 'SNPs' named entity 'intron' named entity 'Calu-3' named entity 'miRNA' named entity 'exonic splicing enhancers' named entity 'TMPRSS2' named entity 'SARS-CoV-2' named entity 'Phyre2'

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