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Safdar M, Ozaslan M, Mustafa RM, Smail SW, Khan SS, Khan MS, Akhtar MA, Ali HK, Younas U, Saeed M, Siddique F, Naveed M, Rehman S. The severity of COVID-19 in hypertensive patients is associated with mirSNPs in the 3' UTR of ACE2 that associate with miR-3658: In silico and in vitro studies. J Taibah Univ Med Sci 2023; 18:1030-1047. [PMID: 36926053 PMCID: PMC9981452 DOI: 10.1016/j.jtumed.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/16/2023] [Accepted: 02/18/2023] [Indexed: 03/06/2023] Open
Abstract
The SARS-CoV-2 virus targets the antigen converting enzyme 2 (ACE2) receptor, thus resulting in elevated morbidity and an increased risk of severe and fatal COVID-19 infection in individuals with hypertension and diabetes mellitus. Objectives This study aimed to identify the association between increased susceptibility and severity in order to evaluate their impact in hypertensive COVID-19 patients using in vitro and in silico models. Methods We identified 80 miRNA binding sites on ACE2 (for different miRNAs) as well as various 30 SNPs in the miRNA binding sites of the 3' untranslated region (3' UTR) in the ACE2 gene using different online software and tools. From August 2020 to August 2021, a total of 200 nasopharyngeal/mouth swabs samples were collected from Multan, Pakistan. In order to quantify the cDNA of ACE2 and miR-3658 genes, we used Rotor Gene qRT-PCR on hypertensive patients with COVID-19 as well as healthy controls. Results Interestingly, the binding site of miR-3658 corresponding to the 3' UTR of ACE2 featured three SNPs (rs1457913029, C>T; rs960535757, A>C, G; rs1423809569, C>T), and its genomic sequence featured a single SNP (rs1024225815, C>T) with the same nucleotide variation (rs1457913029, C>T) which potentially increases the severity of COVID-19. Similarly, three other SNPs (rs1557852115, C>G; rs770335293, A>G; rs1024225815, C>T) were also found on the first binding site positions of miR-3658. Our in vitro study found that ACE2 gene expression had an effect on miR-3658 in COVID-19 patients who also had hypertension. In both cases, our analysis demonstrated that the in silico model captured the same biological mechanisms as the in vitro system. Conclusion The identified SNPs could represent potential informative signatures owing to their position in the splicing site of the ACE2 gene.
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Affiliation(s)
- Muhammad Safdar
- Department of Breeding and Genetics, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Mehmet Ozaslan
- Department of Biology, Division of Molecular Biology and Genetics, Gaziantep University, Gaziantep, Turkey
| | - Rebaz M Mustafa
- Department of Chemistry, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region - F.R. Iraq
- Volumetric Apparatus and Instrumental Analysis, Modern Surveying Calibration & Testing Labs, Erbil, Kurdistan, Iraq
| | - Shukur W Smail
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, Iraq
- Department of Medical Microbiology, College of Science, Cihan University-Erbil, Kurdistan Region, Iraq
| | - Samiha S Khan
- University Medical and Dental College Faisalabad, Pakistan
| | | | - Muhammad Asad Akhtar
- Cardiovascular Research Group, Dept. Medical Biology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Hafiz Khawar Ali
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Umair Younas
- Department of Livestock Management, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Saeed
- Department of Poultry Science, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Faisal Siddique
- Department of Microbiology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Naveed
- Department of Clinical Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing, P.R China
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - SaifUr Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources of Guangxi University, Nanning, China
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Wu NS, Lin YF, Ma IC, Ko HJ, Hong YR. Many faces and functions of GSKIP: a temporospatial regulation view. Cell Signal 2022; 97:110391. [PMID: 35728705 DOI: 10.1016/j.cellsig.2022.110391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/06/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022]
Abstract
Glycogen synthase kinase 3 (GSK3)-β (GSK3β) interaction protein (GSKIP) is one of the smallest A-kinase anchoring proteins that possesses a binding site for GSK3β. Recently, our group identified the protein kinase A (PKA)-GSKIP-GSK3β-X axis; knowledge of this axis may help us decipher the many roles of GSKIP and perhaps help explain the evolutionary reason behind the interaction between GSK3β and PKA. In this review, we highlight the critical and multifaceted role of GSKIP in facilitating PKA kinase activity and its function as a scaffolding protein in signaling pathways. We also highlight how these pivotal PKA and GSK3 kinases can control context-specific functions and interact with multiple target proteins, such as β-catenin, Drp1, Tau, and other proteins. GSKIP is a key regulator of multiple mechanisms because of not only its location at certain subcellular compartments but also its serial changes during the developmental process. Moreover, the involvement of critical upstream regulatory signaling pathways in GSKIP signaling in various cancers, such as miRNA (microRNA) and lncRNA (long noncoding RNA), may help in the identification of therapeutic targets in the era of precision medicine and personalized therapy. Finally, we emphasize on the model of the early stage of pathogenesis of Alzheimer Disease (AD). Although the model requires validation, it can serve as a basis for diagnostic biomarkers development and drug discovery for early-stage AD.
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Affiliation(s)
- Nian-Siou Wu
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Yi-Fan Lin
- School of Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
| | - I Chu Ma
- China Medical University Hospital, Taichung 404, Taiwan.
| | - Huey-Jiun Ko
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Yi-Ren Hong
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan,; Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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Lu F, Chen H, Hong Y, Lin Y, Liu L, Wei N, Wu Q, Liao S, Yang S, He J, Shao Y. A gain-of-function NLRP3 3'-UTR polymorphism causes miR-146a-mediated suppression of NLRP3 expression and confers protection against sepsis progression. Sci Rep 2021; 11:13300. [PMID: 34172780 PMCID: PMC8233413 DOI: 10.1038/s41598-021-92547-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023] Open
Abstract
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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Affiliation(s)
- Furong Lu
- The Key Laboratory of Sepsis Translational Medicine, The Intensive Care Unit, The Second Affiliated Hospital of Guangdong Medical University, Minyou Road 12, Xiashan District, Zhanjiang City, 524001, Guangdong Province, People's Republic of China
| | - Hongpeng Chen
- The Department of Chemotherapy, Jieyang Affiliated Hospital, SunYat-Sen University, Jieyang, Guangdong, People's Republic of China
| | - Yuan Hong
- The Key Laboratory of Sepsis Translational Medicine, The Intensive Care Unit, The Second Affiliated Hospital of Guangdong Medical University, Minyou Road 12, Xiashan District, Zhanjiang City, 524001, Guangdong Province, People's Republic of China
| | - Yao Lin
- The Clinical Medicine Research Laboratory, The Intensive Care Unit, Jieyang Affiliated Hospital, SunYat-Sen University, Tianfu Road 107, Rongcheng District, Jieyang City, 522000, Guangdong Province, People's Republic of China
| | - Lizhen Liu
- The Key Laboratory of Sepsis Translational Medicine, The Intensive Care Unit, The Second Affiliated Hospital of Guangdong Medical University, Minyou Road 12, Xiashan District, Zhanjiang City, 524001, Guangdong Province, People's Republic of China.,The Intensive Care Unit, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, People's Republic of China
| | - Ning Wei
- The Key Laboratory of Sepsis Translational Medicine, The Intensive Care Unit, The Second Affiliated Hospital of Guangdong Medical University, Minyou Road 12, Xiashan District, Zhanjiang City, 524001, Guangdong Province, People's Republic of China
| | - Qinyan Wu
- The Key Laboratory of Sepsis Translational Medicine, The Intensive Care Unit, The Second Affiliated Hospital of Guangdong Medical University, Minyou Road 12, Xiashan District, Zhanjiang City, 524001, Guangdong Province, People's Republic of China
| | - Shuanglin Liao
- The Key Laboratory of Sepsis Translational Medicine, The Intensive Care Unit, The Second Affiliated Hospital of Guangdong Medical University, Minyou Road 12, Xiashan District, Zhanjiang City, 524001, Guangdong Province, People's Republic of China
| | - Shuai Yang
- The Key Laboratory of Sepsis Translational Medicine, The Intensive Care Unit, The Second Affiliated Hospital of Guangdong Medical University, Minyou Road 12, Xiashan District, Zhanjiang City, 524001, Guangdong Province, People's Republic of China
| | - Junbing He
- The Clinical Medicine Research Laboratory, The Intensive Care Unit, Jieyang Affiliated Hospital, SunYat-Sen University, Tianfu Road 107, Rongcheng District, Jieyang City, 522000, Guangdong Province, People's Republic of China.
| | - Yiming Shao
- The Key Laboratory of Sepsis Translational Medicine, The Intensive Care Unit, The Second Affiliated Hospital of Guangdong Medical University, Minyou Road 12, Xiashan District, Zhanjiang City, 524001, Guangdong Province, People's Republic of China. .,The Intensive Care Unit, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524023, Guangdong, People's Republic of China.
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Safdar M, Khan MS, Karim AY, Omar SA, Smail SW, Saeed M, Zaheer S, Ali M, Ahmad B, Tasleem M, Junejo Y. 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. Mamm Genome 2021; 32:389-400. [PMID: 34089082 PMCID: PMC8177038 DOI: 10.1007/s00335-021-09880-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/24/2021] [Indexed: 01/04/2023]
Abstract
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, SLC6A19, IL-6,10,18, chemokine (C–C motif) ligand 5, SWT1, NFYB, BRF1, HES2, NFYB, MED12L, MAFG, GTF2H5, TRAF3, angiotensin II receptor-associated protein, PRSS23) by evaluating online software in the binding sites of the miR-6741-3p. miR-6741-3p has not previously shown any association with kidney diseases and SARS-COV-2 infection. It assures that APOL1 can have a significant consequence in kidney-associated diseases by different pathways. Henceforth, this study represents and demonstrates an effective association between miR-6741-3p and kidney diseases, i.e., collapsing glomerulopathy, chronic kidney disease (CKD), acute kidney injury (AKI), and tubulointerstitial lesions susceptibility to SARS-COV-2 infection via in silico and in vitro exploration and recommended to have better insight.
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Affiliation(s)
- Muhammad Safdar
- Department of Breeding and Genetics, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Muhammad Sajjad Khan
- Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Abdulkarim Yasin Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, Iraq
- Department of Medical Analysis, Faculty of Science, Tishk International University-Erbil, Kurdistan Region, Erbil, Iraq
| | - Shwan Ali Omar
- Ministry of Health, Kurdistan Regional Government, Erbil, Iraq
| | - Shukur Wasman Smail
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, Iraq
- Department of Biology, College of Science, Cihan University-Erbil, Kurdistan Region, Erbil, Iraq
| | - Muhammad Saeed
- Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Sana Zaheer
- Department of Biotechnology, Virtual University of Pakistan, Lahore, Pakistan
| | - Mazhar Ali
- Consultant Urologist, Recep Tayyip Erdogan Hospital (RTEH), Muzaffargarh, Pakistan
| | | | - Muhammad Tasleem
- Senior Medical Officer, Shah Bhittaai Govt Hospital Latifabad, Hyderabad, Pakistan
| | - Yasmeen Junejo
- Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan.
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