The Relevance of SNPs at 3′UTR Region of CASP7 and miR-371b-5p Associated Diseases: A Computational Analysis

Safdar, Muhammad; Zaheer, Sana; Khailany, Rozhgar A.; Parvez, Sadaf; Naveed, Muhammad; Bhuiyan, Piplu; Özaslan, Mehmet; Moatasam, Rebaz; Al-Attar, Mustafa S.; Khan, Mueen Alam; Junejo, Yasmeen

doi:10.1007/s12013-020-00941-2

Cited by 5 publications

(4 citation statements)

References 52 publications

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“…The expression of K-RAS mRNA was measured by semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) method. The level of K-RAS mRNA expression in cancer tissue was significantly higher compared to healthy tissue (Safdar et al, 2020).…”

Section: Discussionmentioning

confidence: 81%

The Relevance of Common K-RAS Gene Mutations and K-RAS mRNA Expression with Clinicopathological Findings and Survival in Breast Cancer

Kamian

Ashoori

Vahidian

et al. 2023

Asian Pac J Cancer Prev

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Breast cancer is known as one of the most common cancers among women, Breast cancer accounts for 22.9% of all cancers in women, and in 2016, approximately 3.5 million women were living with a history of breast cancer in the United States (Bertucci et al., 2012; Marriotto et al., 2017). According to the latest statistics of the Iranian Cancer Research Center, about 8,500 new cases of breast cancer are reported every year, of which 1,400 deaths are caused by breast cancer. Also, currently about 40,000 people in the country are suffering from this disease (Tahergorabi et al., 2014).Over the years, many genes and proteins have been discovered that play different roles in carcinogenesis of breast cancer (Khan et al., 2019). One of the most commonly mutated human carcinogens are RAS proteins which remain a critical target for novel treatments (Marin-Ramos et al., 2019). Members of the RAS family are low molecular weight monomeric GTP-binding

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Section: Discussionmentioning

confidence: 81%

The Relevance of Common K-RAS Gene Mutations and K-RAS mRNA Expression with Clinicopathological Findings and Survival in Breast Cancer

Kamian

Ashoori

Vahidian

et al. 2023

Asian Pac J Cancer Prev

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“…MiRNAs are small noncoding RNAs that bind to specific mRNA molecules and cause mRNA degradation or suppression of target gene expression, and they play pivotal roles in the modulation of multiple cellular processes, such as proliferation, differentiation, inflammation and apoptosis 41 . Increasing evidence has demonstrated the important impact of specific genetic variations within the 3′-UTR on the binding of miRNAs to cause the gain or loss of regulation by certain miRNAs, ultimately resulting in susceptibility to multiple diseases 42 , 43 . According to bioinformatics analyses predicted by miRNASNP-v3 ( http://bioinfo.life.hust.edu.cn/miRNASNP/ ) and a previous study 27 , 38 , the 29940 G-to-C mutation in the 3′-UTR of NLRP3 might establish a new functional binding site for miR-146a-5p, which contributes to potential miR-146-5p recruitment and binding.…”

Section: Discussionmentioning

confidence: 99%

A gain-of-function NLRP3 3′-UTR polymorphism causes miR-146a-mediated suppression of NLRP3 expression and confers protection against sepsis progression

Chen²,

Hong

et al. 2021

Sci Rep

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Nucleotide-binding domain and leucine-rich repeat (LRR)-containing family protein 3 (NLRP3) regulated the maturation of inflammation-related cytokines by forming NLRP3 inflammasome, which plays pivotal roles in sepsis pathogenesis. In this study, we evaluated the genetic association of NLRP3 polymorphisms with sepsis (640 patients and 769 controls) and characterized the impact of NLRP3 polymorphisms on NLRP3 expression and inflammatory responses. No significant differences were observed in genotype/allelic frequencies of NLRP3 29940G>C between sepsis cases and controls. The G allele was significantly overrepresented in patients with septic shock than those in sepsis subgroup, and the GC/GG genetypes were related to the 28-day mortality of sepsis. Lipopolysaccharide challenge to peripheral blood mononuclear cells showed a significant suppression of NLRP3 mRNA expression and release of IL-1β and TNF-α in CC compared with the GC/GG genotype category. Functional experiments with luciferase reporter vectors containing the NLRP3 3′-UTR with the 29940 G-to-C variation in HUVECs and THP-1 cells showed a potential suppressive effect of miR-146a on NLRP3 transcription in the presence of the C allele. Taken together, these results demonstrated that the 29940 G-to-C mutation within the NLRP3 3′-UTR was a gain-of-function alteration that caused the suppression of NLRP3 expression and downstream inflammatory cytokine production via binding with miR-146a, which ultimately protected patients against susceptibility to sepsis progression and poor clinical outcome.

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“…Ten unique online databases including DIANA Tools, miRTarBase, Miranda, TargetScan, miRDB, miRecords, miRcode, miRO, miRWalk, and MiCosm were used for the detection of miRNA targeting the 3′UTR of the APOL1 gene, and then we followed several algorithms and calculations below methodologies provided (Ergun and Oztuzcu 2014;Safdar et al 2020). Accordingly, the scanning of all miRNA targets can be performed without missing any of them using the multiple databases below.…”

Section: Screening Of Mirna Targeting 3′utr Of Apol1 Genementioning

confidence: 99%

“…SNPs in the genes of miRNAs and miRSNPs in the 3′UTR of APOL1 were matched (Table 2). Cross-match SNPs were searched as done by Ergun and Oztuzcu (2014); Safdar et al (2020). Matched and unmatched SNPs are shown and interpreted for APOL1 activity with kidney diseases that has susceptibility to COVID-19.…”

Section: Screening Of Mirsnpsmentioning

confidence: 99%

SNPs at 3′UTR of APOL1 and miR-6741-3p target sites associated with kidney diseases more susceptible to SARS-COV-2 infection: in silco and in vitro studies

et al. 2021

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Acute Kidney Injury (AKI) is a common manifestation of COVID-19 and several cases have been reported in the setting of the high-risk APOL1 genotype (common genetic variants). This increases the likelihood that African American people with the high-risk genotype APOL1 are at increased risk for kidney disease in the COVID-19 environment. Single-nucleotide polymorphisms (SNPs) are found in various microRNAs (miRNAs) and target genes change the miRNA activity that leads to different diseases. Evidence has shown that SNPs increase/decrease the effectiveness of the interaction between miRNAs and disease-related target genes. The aim of this study is not only to identify miRSNPs on the APOL1 gene and SNPs in miRNA genes targeting 3′UTR but also to evaluate the effect of these gene variations in kidney patients and their association with SARS-COV-2 infection. In 3′UTR of the APOL1 gene, we detected 96 miRNA binding sites and 35 different SNPs with 10 different online software in the binding sites of the miRNA (in silico). Also we studied gene expression of patients and control samples by using qRT-PCR (in vitro). In silico study, the binding site of miR-6741-3p on APOL1 has two SNPs (rs1288875001, G > C; rs1452517383, A > C) on APOL1 3′UTR, and its genomic sequence is the same nucleotide as rs1288875001. Similarly, two other SNPs (rs1142591, T > A; rs376326225, G > A) were identified in the binding sites of miR-6741-3p at the first position. Here, the miRSNP (rs1288875001) in APOL1 3′UTR and SNP (rs376326225) in the miR-6741-3p genomic sequence are cross-matched in the same binding region. In vitro study, the relative expression levels were calculated by the 2 −ΔΔCt method & Mann-Whitney U test. The expression of APOL1 gene was different in chronic kidney patients along with COVID-19. By these results, APOL1 expression was found lower in patients than healthy (p < 0.05) in kidney patients along with COVID-19. In addition, miR-6741-3p targets many APOL1-related genes (TLR7,

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The Relevance of SNPs at 3′UTR Region of CASP7 and miR-371b-5p Associated Diseases: A Computational Analysis

Cited by 5 publications

References 52 publications

The Relevance of Common K-RAS Gene Mutations and K-RAS mRNA Expression with Clinicopathological Findings and Survival in Breast Cancer

The Relevance of Common K-RAS Gene Mutations and K-RAS mRNA Expression with Clinicopathological Findings and Survival in Breast Cancer

A gain-of-function NLRP3 3′-UTR polymorphism causes miR-146a-mediated suppression of NLRP3 expression and confers protection against sepsis progression

SNPs at 3′UTR of APOL1 and miR-6741-3p target sites associated with kidney diseases more susceptible to SARS-COV-2 infection: in silco and in vitro studies

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