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Sharma A, Singh P, Jha R, Almatroodi SA, Alrumaihi F, Rahmani AH, Alharbi HO, Dohare R, Syed MA. Exploring the role of miR-200 family in regulating CX3CR1 and CXCR1 in lung adenocarcinoma tumor microenvironment: implications for therapeutic intervention. Sci Rep 2023; 13:16333. [PMID: 37770496 PMCID: PMC10539366 DOI: 10.1038/s41598-023-43484-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/25/2023] [Indexed: 09/30/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common malignant subtype of lung cancer (LC). miR-200 family is one of the prime miR regulators of epithelial-mesenchymal transition (EMT) and worst overall survival (OS) in LC patients. The study aimed to identify and validate the key differentially expressed immune-related genes (DEIRGs) regulated by miR-200 family which may serve for therapeutic aspects in LUAD tumor microenvironment (TME) by affecting cancer progression, invasion, and metastasis. The study identified differentially expressed miRNAs (DEMs) in LUAD, consisting of hsa-miR-200a-3p and hsa-miR-141-5p, respectively. Two highest-degree subnetwork motifs identified from 3-node miRNA FFL were: (i) miR-200a-3p-CX3CR1-SPIB and (ii) miR-141-5p-CXCR1-TBX21. TIMER analysis showed that the expression levels of CX3CR1 and CXCR1 were significantly positively correlated with infiltrating levels of M0-M2 macrophages and natural killer T (NKT) cells. The OS of LUAD patients was significantly affected by lower expression levels of hsa-miR-200a-3p, CX3CR1 and SPIB. These DEIRGs were validated using the human protein atlas (HPA) web server. Further, we validated the regulatory role of hsa-miR-200a-3p in an in-vitro indirect co-culture model using conditioned media from M0, M1 and M2 polarized macrophages (THP-1) and LUAD cell lines (A549 and H1299 cells). The results pointed out the essential role of hsa-miR-200a-3p regulated CX3CL1 and CX3CR1 expression in progression of LC TME. Thus, the study augments a comprehensive understanding and new strategies for LUAD treatment where miR-200 family regulated immune-related genes, especially chemokine receptors, which regulate the metastasis and invasion of LUAD, leading to the worst associated OS.
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Affiliation(s)
- Archana Sharma
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Rishabh Jha
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Saleh A Almatroodi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 51452, Buraydah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 51452, Buraydah, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 51452, Buraydah, Saudi Arabia
| | - Hajed Obaid Alharbi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 51452, Buraydah, Saudi Arabia
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
| | - Mansoor Ali Syed
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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Survival-Based Biomarker Module Identification Associated with Oral Squamous Cell Carcinoma (OSCC). BIOLOGY 2021; 10:biology10080760. [PMID: 34439992 PMCID: PMC8389591 DOI: 10.3390/biology10080760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022]
Abstract
Simple Summary In this study, four OSCC-specific hub genes were identified using high-throughput RNA-Seq data from TCGA cohort. The significant genes within tumor and normal samples were used for weighted PPI network construction based on survival of patients along with their expression profiles. The analysis revealed the most significant module in the training and test datasets. The genes from this module were used for pathway enrichment analysis followed by hub gene selection. These novel biomarkers might have clinical utility for diagnosis and prognosis prediction in OSCC, providing diagnosis at a very early stage. Moreover, a combination of all these biomarkers might distinguish the OSCC patients with low risk and high risk for cancer progression and recurrence, which will provide useful guidance for personalized and precision therapy. However, the results in the present study were obtained by integrative theoretical analysis, and the findings remain to be confirmed by further experimental validations. Abstract Head and neck squamous cell carcinoma (HNSC) is one of the most common malignant tumors worldwide with a high rate of morbidity and mortality, with 90% of predilections occurring for oral squamous cell carcinoma (OSCC). Cancers of the mouth account for 40% of head and neck cancers, including squamous cell carcinomas of the tongue, floor of the mouth, buccal mucosa, lips, hard and soft palate, and gingival. OSCC is the most devastating and commonly occurring oral malignancy, with a mortality rate of 500,000 deaths per year. This has imposed a strong necessity to discover driver genes responsible for its progression and malignancy. In the present study we filtered oral squamous cell carcinoma tissue samples from TCGA-HNSC cohort, which we followed by constructing a weighted PPI network based on the survival of patients and the expression profiles of samples collected from them. We found a total of 46 modules, with 18 modules having more than five edges. The KM and ME analyses revealed a single module (with 12 genes) as significant in the training and test datasets. The genes from this significant module were subjected to pathway enrichment analysis for identification of significant pathways and involved genes. Finally, the overlapping genes between gene sets ranked on the basis of weighted PPI module centralities (i.e., degree and eigenvector), significant pathway genes, and DEGs from a microarray OSCC dataset were considered as OSCC-specific hub genes. These hub genes were clinically validated using the IHC images available from the Human Protein Atlas (HPA) database.
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Wolska-Gawron K, Bartosińska J, Rusek M, Kowal M, Raczkiewicz D, Krasowska D. Circulating miRNA-181b-5p, miRNA-223-3p, miRNA-210-3p, let 7i-5p, miRNA-21-5p and miRNA-29a-3p in patients with localized scleroderma as potential biomarkers. Sci Rep 2020; 10:20218. [PMID: 33214624 PMCID: PMC7678876 DOI: 10.1038/s41598-020-76995-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022] Open
Abstract
Localized scleroderma (LoSc) is a rare disease manifested by an inflammation and sclerosis of the skin. The latest studies focused on glycoprotein Krebs von den Lungen-6, surfactant protein-D, chemokine ligand 18 and dipeptidylpeptidase 4 as potential biomarkers of skin fibrosis in systemic scleroderma. Our study aimed to identify 6 miRNAs with elevated or decreased levels in 38 LoSc patients (31 females, 7 males) compared to healthy volunteers (HVs) and to correlate the selected miRNAs' serum levels with the severity and the clinical symptoms of LoSc and some laboratory parameters with the selected miRNAs' serum levels. The serum levels of miRNAs, i.e. miRNA-181b-5p, miRNA-223-3p, miRNA-21-5p, let 7i-5p, miRNA-29a-3p and miRNA-210-3p were significantly increased in the LoSc patients compared to the HVs. The level of let-7i increase in the female LoSc patients correlated negatively with BSA (r = - 0.355, p = 0.049) and mLoSSI (r = - 0.432, p = 0.015). Moreover, the female patients with inactive LoSc had significantly higher level of let-7i (2.68-fold on average) in comparison to those with active disease (p = 0.045). The exact role of those molecules has not been revealed in LoSc and a long-term longitudinal research is pivotal to confirm their prognostic value.
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Affiliation(s)
- Katarzyna Wolska-Gawron
- Department of Dermatology, Venerology and Paediatric Dermatology, The Medical University of Lublin, 20-081 Lublin 11 Staszica St, Lublin, Poland.
| | - Joanna Bartosińska
- Department of Cosmetology and Aesthetic Medicine, The Medical University of Lublin, Lublin, Poland
| | - Marta Rusek
- Department of Dermatology, Venerology and Paediatric Dermatology, The Medical University of Lublin, 20-081 Lublin 11 Staszica St, Lublin, Poland
- Department of Pathophysiology, The Medical University of Lublin, Lublin, Poland
| | - Małgorzata Kowal
- Department of Dermatology, Venerology and Paediatric Dermatology, The Medical University of Lublin, 20-081 Lublin 11 Staszica St, Lublin, Poland
| | - Dorota Raczkiewicz
- SGH Warsaw School of Economics, Collegium of Economic Analysis, Institute of Statistics and Demography, Warsaw, Poland
| | - Dorota Krasowska
- Department of Dermatology, Venerology and Paediatric Dermatology, The Medical University of Lublin, 20-081 Lublin 11 Staszica St, Lublin, Poland
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Arora S, Singh P, Dohare R, Jha R, Ali Syed M. Unravelling host-pathogen interactions: ceRNA network in SARS-CoV-2 infection (COVID-19). Gene 2020; 762:145057. [PMID: 32805314 PMCID: PMC7428439 DOI: 10.1016/j.gene.2020.145057] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/13/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022]
Abstract
Bioinformatics analysis of mouse mRNA expression dataset for presumptive SARS-CoV-2 targets. Induction of ISGs-Isg15, Oasl1, Usp18 and Ddx58 with no marked changes in the expression of IFNs. No induction of ACE2 and TMPRSS2, raising implications for host factor limitations. Identification of ceRNA network including miR-124-3p, Ddx58, lncRNA (Gm26917) and circRNAs (Ppp1r10, C330019G07RiK). Virus regulates the expression of lnc and circRNAs, acting as sponges for miR-124-3p targeting Ddx58.
COVID-19 is a lurking calamitous disease caused by an unusual virus, SARS-CoV-2, causing massive deaths worldwide. Nonetheless, explicit therapeutic drugs or clinically approved vaccines are not available for COVID-19. Thus, a comprehensive research is crucially needed to decode the pathogenic tools, plausible drug targets, committed to the development of efficient therapy. Host-pathogen interactions via host cellular components is an emerging field of research in this respect. miRNAs have been established as vital players in host-virus interactions. Moreover, viruses have the capability to manoeuvre the host miRNA networks according to their own obligations. Besides protein coding mRNAs, noncoding RNAs might also be targeted in infected cells and viruses can exploit the host miRNA network via ceRNA effect. We have predicted a ceRNA network involving one miRNA (miR-124-3p), one mRNA (Ddx58), one lncRNA (Gm26917) and two circRNAs (Ppp1r10, C330019G07RiK) in SARS-CoV infected cells. We have identified 4 DEGs-Isg15, Ddx58, Oasl1, Usp18 by analyzing a mRNA GEO dataset. There is no notable induction of IFNs and IFN-induced ACE2, significant receptor responsible for S-protein binding mediated viral entry. Pathway enrichment and GO analysis conceded the enrichment of pathways associated with interferon signalling and antiviral-mechanism by IFN-stimulated genes. Further, we have identified 3 noncoding RNAs, playing as potential ceRNAs to the genes associated with immune mechanisms. This integrative analysis has identified noncoding RNAs and their plausible targets, which could effectively enhance the understanding of molecular mechanisms associated with viral infection. However, validation of these targets is further corroborated to determine their therapeutic efficacy.
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Affiliation(s)
- Shweta Arora
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Rishabh Jha
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mansoor Ali Syed
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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Arora S, Singh P, Rahmani AH, Almatroodi SA, Dohare R, Syed MA. Unravelling the Role of miR-20b-5p, CCNB1, HMGA2 and E2F7 in Development and Progression of Non-Small Cell Lung Cancer (NSCLC). BIOLOGY 2020; 9:biology9080201. [PMID: 32752229 PMCID: PMC7465122 DOI: 10.3390/biology9080201] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Lung cancer is a prime cause of worldwide cancer deaths, with non-small cell lung cancer (NSCLC) as a frequent subtype. Surgical resection, chemotherapy are the currently used treatment methods. Delayed detection, poor prognosis, tumor heterogeneity, and chemoresistance make them relatively ineffective. Genomic medicine is a budding aspect of cancer therapeutics, where miRNAs are impressively involved. miRNAs are short ncRNAs that bind to 3′UTR of target mRNA, causing its degradation or translational repression to regulate gene expression. This study aims to identify important miRNA-mRNA-TF interactions in NSCLC using bioinformatics analysis. GEO datasets containing mRNA expression data of NSCLC were used to determine differentially expressed genes (DEGs), and identification of hub genes-BIRC5, CCNB1, KIF11, KIF20A, and KIF4A (all functionally enriched in cell cycle). The FFL network involved, comprised of miR-20b-5p, CCNB1, HMGA2, and E2F7. KM survival analysis determines that these components may be effective prognostic biomarkers and would be a new contemplation in NSCLC therapeutics as they target cell cycle and immunosurveillance mechanisms via HMGA2 and E2F7. They provide survival advantage and evasion of host immune response (via downregulation of cytokines-IL6, IL1R1 and upregulation of chemokines-CXCL13, CXCL14) to NSCLC. The study has provided innovative targets, but further validation is needed to confirm the proposed mechanism.
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Affiliation(s)
- Shweta Arora
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India;
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.H.R.); (S.A.A.)
| | - Saleh A. Almatroodi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.H.R.); (S.A.A.)
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
- Correspondence: (R.D.); (M.A.S.); Tel.: +91-986-865-5958 (R.D.); +91-995-378-6440 (M.A.S.)
| | - Mansoor Ali Syed
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India;
- Correspondence: (R.D.); (M.A.S.); Tel.: +91-986-865-5958 (R.D.); +91-995-378-6440 (M.A.S.)
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