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Wang L, Chen A, Zhang L, Zhang J, Wei S, Chen Y, Hu M, Mo Y, Li S, Zeng M, Li H, Liang C, Ren Y, Xu L, Liang W, Zhu X, Wang X, Sun D. Deciphering the molecular nexus between Omicron infection and acute kidney injury: a bioinformatics approach. Front Mol Biosci 2024; 11:1340611. [PMID: 39027131 PMCID: PMC11254815 DOI: 10.3389/fmolb.2024.1340611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/07/2024] [Indexed: 07/20/2024] Open
Abstract
Background The ongoing global health crisis of COVID-19, and particularly the challenges posed by recurrent infections of the Omicron variant, have significantly strained healthcare systems worldwide. There is a growing body of evidence indicating an increased susceptibility to Omicron infection in patients suffering from Acute Kidney Injury (AKI). However, the intricate molecular interplay between AKI and Omicron variant of COVID-19 remains largely enigmatic. Methods This study employed a comprehensive analysis of human RNA sequencing (RNA-seq) and microarray datasets to identify differentially expressed genes (DEGs) associated with Omicron infection in the context of AKI. We engaged in functional enrichment assessments, an examination of Protein-Protein Interaction (PPI) networks, and advanced network analysis to elucidate the cellular signaling pathways involved, identify critical hub genes, and determine the relevant controlling transcription factors and microRNAs. Additionally, we explored protein-drug interactions to highlight potential pharmacological interventions. Results Our investigation revealed significant DEGs and cellular signaling pathways implicated in both Omicron infection and AKI. We identified pivotal hub genes, including EIF2AK2, PLSCR1, GBP1, TNFSF10, C1QB, and BST2, and their associated regulatory transcription factors and microRNAs. Notably, in the murine AKI model, there was a marked reduction in EIF2AK2 expression, in contrast to significant elevations in PLSCR1, C1QB, and BST2. EIF2AK2 exhibited an inverse relationship with the primary AKI mediator, Kim-1, whereas PLSCR1 and C1QB demonstrated strong positive correlations with it. Moreover, we identified potential therapeutic agents such as Suloctidil, Apocarotenal, 3'-Azido-3'-deoxythymidine, among others. Our findings also highlighted a correlation between the identified hub genes and diseases like myocardial ischemia, schizophrenia, and liver cirrhosis. To further validate the credibility of our data, we employed an independent validation dataset to verify the hub genes. Notably, the expression patterns of PLSCR1, GBP1, BST2, and C1QB were consistent with our research findings, reaffirming the reliability of our results. Conclusion Our bioinformatics analysis has provided initial insights into the shared genetic landscape between Omicron COVID-19 infections and AKI, identifying potential therapeutic targets and drugs. This preliminary investigation lays the foundation for further research, with the hope of contributing to the development of innovative treatment strategies for these complex medical conditions.
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Affiliation(s)
- Li Wang
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Anning Chen
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Lantian Zhang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Junwei Zhang
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Shuqi Wei
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yangxiao Chen
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Mingliang Hu
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Yihao Mo
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Sha Li
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Min Zeng
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Huafeng Li
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Caixing Liang
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Yi Ren
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Liting Xu
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Wenhua Liang
- Nephrology Department, Southern Medical University Affiliated Longhua People’s Hospital, Shenzhen, China
| | - Xuejiao Zhu
- Department of Anesthesiology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaokai Wang
- Xuzhou First People’s Hospital, Xuzhou, Jiangsu, China
| | - Donglin Sun
- Department of Urology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
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Bhattacharjya A, Islam MM, Uddin MA, Talukder MA, Azad AKM, Aryal S, Paul BK, Tasnim W, Almoyad MAA, Moni MA. Exploring gene regulatory interaction networks and predicting therapeutic molecules for hypopharyngeal cancer and EGFR-mutated lung adenocarcinoma. FEBS Open Bio 2024; 14:1166-1191. [PMID: 38783639 PMCID: PMC11216941 DOI: 10.1002/2211-5463.13807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 01/30/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
Hypopharyngeal cancer is a disease that is associated with EGFR-mutated lung adenocarcinoma. Here we utilized a bioinformatics approach to identify genetic commonalities between these two diseases. To this end, we examined microarray datasets from GEO (Gene Expression Omnibus) to identify differentially expressed genes, common genes, and hub genes between the selected two diseases. Our analyses identified potential therapeutic molecules for the selected diseases based on 10 hub genes with the highest interactions according to the degree topology method and the maximum clique centrality (MCC). These therapeutic molecules may have the potential for simultaneous treatment of these diseases.
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Affiliation(s)
- Abanti Bhattacharjya
- Department of Computer Science and EngineeringJagannath UniversityDhakaBangladesh
| | - Md Manowarul Islam
- Department of Computer Science and EngineeringJagannath UniversityDhakaBangladesh
| | - Md Ashraf Uddin
- School of Information TechnologyDeakin UniversityGeelongAustralia
| | - Md Alamin Talukder
- Department of Computer Science and EngineeringInternational University of Business Agriculture and TechnologyDhakaBangladesh
| | - AKM Azad
- Department of Mathematics and Statistics, Faculty of ScienceImam Mohammad Ibn Saud Islamic University (IMSIU)RiyadhSaudi Arabia
| | - Sunil Aryal
- School of Information TechnologyDeakin UniversityGeelongAustralia
| | - Bikash Kumar Paul
- Department of Information and Communication TechnologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
- Department of Software EngineeringDaffodil International UniversityDhakaBangladesh
| | - Wahia Tasnim
- Department of Information and Communication TechnologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | | | - Mohammad Ali Moni
- Artificial Intelligence & Data Science, Faculty of Health and Behavioural SciencesThe University of QueenslandBrisbaneAustralia
- AI & Digital Health Technology, Artificial Intelligence and Cyber Futures InstituteCharles Sturt UniversityBathurstAustralia
- Rural Health Research InstituteCharles Sturt UniversityOrangeAustralia
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Tang Z, Han Y, Meng Y, Li J, Qiu X, Bajinka O, Wu G, Tan Y. A bioinformatics approach to systematically analyze the molecular patterns of monkeypox virus-host cell interactions. Heliyon 2024; 10:e30483. [PMID: 38737277 PMCID: PMC11088324 DOI: 10.1016/j.heliyon.2024.e30483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 04/20/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024] Open
Abstract
Monkeypox has been spreading worldwide since May 2022, when the World Health Organization (WHO) declared the outbreak a "public health emergency of international concern." The spread of monkeypox has posed a serious threat to the health of people around the world, but few studies have been conducted, and the molecular mechanism of monkeypox after infection remains unclear. We therefore implemented a transcriptome analysis to identify signaling pathways and biomarkers in monkeypox-infected cells to help understand monkeypox-host cell interactions. In this study, datasets GSE36854 and GSE11234 were obtained from GEO. Of these, 84 significantly different genes were identified in the dataset GSE36854, followed by KEGG, GO analysis protein-protein interaction (PPI) construction, and Hub gene extraction. We also analyzed the expression regulation of hub genes and screened for drugs targeting hub genes. The results showed that monkeypox-infected cells significantly activated the cellular immune response. The top 10 hub genes are IER3, IFIT2, IL11, ZC3H12A, EREG, IER2, NFKBIE, FST, IFIT1 and AREG. AP-26113 and itraconazole can be used to counteract the inhibitory effect of monkeypox on IFIT1 and IFIT2 and serve as candidate drugs for the treatment of monkeypox virus infection. IRF1 may also be a transcription factor of IFIT. Our results provide a new entry point for understanding how monkeypox virus interacts with its host.
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Affiliation(s)
- Zhongxiang Tang
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Ying Han
- Department of Stomatology, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yuting Meng
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Jiani Li
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Xiangjie Qiu
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Ousman Bajinka
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
- China-Africa Research Center for Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Guojun Wu
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
- China-Africa Research Center for Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yurong Tan
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
- China-Africa Research Center for Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
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Tang Z, Mao Y, Ruan P, Li J, Qiu X, Meng Y, Wang M, Wu G, Wang L, Tan Y. Drugs targeting CMPK2 inhibit pyroptosis to alleviate severe pneumonia caused by multiple respiratory viruses. J Med Virol 2024; 96:e29643. [PMID: 38695269 DOI: 10.1002/jmv.29643] [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: 11/16/2023] [Revised: 03/05/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024]
Abstract
Severe pneumonia caused by respiratory viruses has become a major threat to humans, especially with the SARS-CoV-2 outbreak and epidemic. The aim of this study was to investigate the universal molecular mechanism of severe pneumonia induced by multiple respiratory viruses and to search for therapeutic strategies targeting this universal molecular mechanism. The common differential genes of four respiratory viruses, including respiratory syncytial virus (RSV), rhinovirus, influenza, and SARS-CoV-2, were screened by GEO database, and the hub gene was obtained by Sytohubba in Cytoscape. Then, the effect of hub genes on inflammasome and pyrodeath was investigated in the model of RSV infection in vitro and in vivo. Finally, through virtual screening, drugs targeting the hub gene were obtained, which could alleviate severe viral pneumonia in vitro and in vivo. The results showed that CMPK2 is one of the hub genes after infection by four respiratory viruses. CMPK2 activates the inflammasome by activating NLRP3, and promotes the releases of inflammatory factors interleukin (IL)-1β and IL-18 to induce severe viral pneumonia. Z25 and Z08 can reduce the expression level of CMPK2 mRNA and protein, thereby inhibiting NLRP3 and alleviating the development of severe viral pneumonia. In conclusion, the inflammatory response mediated by CMPK2 is the common molecular mechanism of severe pneumonia induced by viral infection, and Z25 and Z08 can effectively alleviate viral infection and severe pneumonia through this mechanism.
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Affiliation(s)
- Zhongxiang Tang
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu Mao
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Pinglang Ruan
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiani Li
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Xiangjie Qiu
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuting Meng
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Mengyu Wang
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Guojun Wu
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Lili Wang
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yurong Tan
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
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Zhou X, Huang T, Pan H, Du A, Wu T, Lan J, Song Y, Lv Y, He F, Yuan K. Bioinformatics and system biology approaches to determine the connection of SARS-CoV-2 infection and intrahepatic cholangiocarcinoma. PLoS One 2024; 19:e0300441. [PMID: 38648205 PMCID: PMC11034673 DOI: 10.1371/journal.pone.0300441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/27/2024] [Indexed: 04/25/2024] Open
Abstract
INTRODUCTION Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease 2019 (COVID-19), has infected millions of individuals worldwide, which poses a severe threat to human health. COVID-19 is a systemic ailment affecting various tissues and organs, including the lungs and liver. Intrahepatic cholangiocarcinoma (ICC) is one of the most common liver cancer, and cancer patients are particularly at high risk of SARS-CoV-2 infection. Nonetheless, few studies have investigated the impact of COVID-19 on ICC patients. METHODS With the methods of systems biology and bioinformatics, this study explored the link between COVID-19 and ICC, and searched for potential therapeutic drugs. RESULTS This study identified a total of 70 common differentially expressed genes (DEGs) shared by both diseases, shedding light on their shared functionalities. Enrichment analysis pinpointed metabolism and immunity as the primary areas influenced by these common genes. Subsequently, through protein-protein interaction (PPI) network analysis, we identified SCD, ACSL5, ACAT2, HSD17B4, ALDOA, ACSS1, ACADSB, CYP51A1, PSAT1, and HKDC1 as hub genes. Additionally, 44 transcription factors (TFs) and 112 microRNAs (miRNAs) were forecasted to regulate the hub genes. Most importantly, several drug candidates (Periodate-oxidized adenosine, Desipramine, Quercetin, Perfluoroheptanoic acid, Tetrandrine, Pentadecafluorooctanoic acid, Benzo[a]pyrene, SARIN, Dorzolamide, 8-Bromo-cAMP) may prove effective in treating ICC and COVID-19. CONCLUSION This study is expected to provide valuable references and potential drugs for future research and treatment of COVID-19 and ICC.
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Affiliation(s)
- Xinyi Zhou
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Tengda Huang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongyuan Pan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ao Du
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Tian Wu
- NHC Key Laboratory of Transplant Engineering and Immunology, Regenerative Medicine Research Center, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, China
| | - Jiang Lan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yujia Song
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Lv
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Fang He
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Kefei Yuan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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Park J, Park IS, Kim JH, Ji JH, Park SJ, Park JJ, Kim TI, Kim SW, Cheon JH. New genetic biomarkers predicting 5-aminosalicylate-induced adverse events in patients with inflammatory bowel diseases. Therap Adv Gastroenterol 2024; 17:17562848241227029. [PMID: 38282956 PMCID: PMC10822078 DOI: 10.1177/17562848241227029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024] Open
Abstract
Background Notably, 5-aminosalicylates (5-ASA) are vital in treating inflammatory bowel diseases (IBD). The adverse events of 5-ASA rarely occur but they could be fatal. Objectives We aimed to discover new genetic biomarkers predicting 5-ASA-induced adverse events in patients with IBD. Design This was a retrospective observational study. Methods We performed a genome-wide association study on patients with IBD in South Korea. We defined subset 1 as 39 all adverse events and 272 controls; subset 2 as 20 severe adverse events and 291 controls (mild adverse events and control); subset 3 as 20 severe adverse events and 272 controls; and subset 4 as 19 mild adverse events and 272 controls. Logistic regression analysis was performed and commonly found associated genes were determined as candidate single-nucleotide polymorphisms predicting 5-ASA adverse events. Results Patients with Crohn's disease (CD) were significantly negatively associated with the development of adverse events compared to patients with ulcerative colitis (UC) (5.3% versus 22.9%). However, sex and age at diagnosis were unassociated with the adverse events of 5-ASA. rs13898676 [odds ratio (OR), 20.33; 95% confidence interval (CI), 5.69-72.67; p = 3.57 × e-6], rs12681590 (OR, 7.35; 95% CI, 2.85-19.00; p = 3.78 × e-5), rs10967320 (OR, 4.51; 95% CI, 2.18-9.31; p = 4.72 × e-5), and rs78726924 (OR, 3.54; 95% CI, 1.69-7.40; p = 7.96 × e-5) were genetic biomarkers predicting 5-ASA-induced severe adverse events in patients with IBD. Conclusion The adverse events of 5-ASA were more common in patients with UC than those with CD in our study. We found that novel rs13898676 nearby WSB2 was the most significant genetic locus contributing to 5-ASA's adverse event risk.
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Affiliation(s)
- Jihye Park
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Center of Inflammatory Bowel Disease, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - I. Seul Park
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Ji Hyung Kim
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jung Hyun Ji
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Center of Inflammatory Bowel Disease, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Soo Jung Park
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Center of Inflammatory Bowel Disease, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae Jun Park
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Center of Inflammatory Bowel Disease, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Tae Il Kim
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Center of Inflammatory Bowel Disease, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung Won Kim
- Department of Severance Biomedical Science Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae Hee Cheon
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
- Institute of Gastroenterology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Center of Inflammatory Bowel Disease, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
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Huang T, He J, Zhou X, Pan H, He F, Du A, Yu B, Jiang N, Li X, Yuan K, Wang Z. Discovering common pathogenetic processes between COVID-19 and tuberculosis by bioinformatics and system biology approach. Front Cell Infect Microbiol 2023; 13:1280223. [PMID: 38162574 PMCID: PMC10757339 DOI: 10.3389/fcimb.2023.1280223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/07/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction The coronavirus disease 2019 (COVID-19) pandemic, stemming from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has persistently threatened the global health system. Meanwhile, tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis) still continues to be endemic in various regions of the world. There is a certain degree of similarity between the clinical features of COVID-19 and TB, but the underlying common pathogenetic processes between COVID-19 and TB are not well understood. Methods To elucidate the common pathogenetic processes between COVID-19 and TB, we implemented bioinformatics and systematic research to obtain shared pathways and molecular biomarkers. Here, the RNA-seq datasets (GSE196822 and GSE126614) are used to extract shared differentially expressed genes (DEGs) of COVID-19 and TB. The common DEGs were used to identify common pathways, hub genes, transcriptional regulatory networks, and potential drugs. Results A total of 96 common DEGs were selected for subsequent analyses. Functional enrichment analyses showed that viral genome replication and immune-related pathways collectively contributed to the development and progression of TB and COVID-19. Based on the protein-protein interaction (PPI) network analysis, we identified 10 hub genes, including IFI44L, ISG15, MX1, IFI44, OASL, RSAD2, GBP1, OAS1, IFI6, and HERC5. Subsequently, the transcription factor (TF)-gene interaction and microRNA (miRNA)-gene coregulatory network identified 61 TFs and 29 miRNAs. Notably, we identified 10 potential drugs to treat TB and COVID-19, namely suloctidil, prenylamine, acetohexamide, terfenadine, prochlorperazine, 3'-azido-3'-deoxythymidine, chlorophyllin, etoposide, clioquinol, and propofol. Conclusion This research provides novel strategies and valuable references for the treatment of tuberculosis and COVID-19.
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Affiliation(s)
- Tengda Huang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jinyi He
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xinyi Zhou
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongyuan Pan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Fang He
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ao Du
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Bingxuan Yu
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Nan Jiang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoquan Li
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kefei Yuan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen Wang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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Patra R, Dey AK, Mukherjee S. Identification of genes critical for inducing ulcerative colitis and exploring their tumorigenic potential in human colorectal carcinoma. PLoS One 2023; 18:e0289064. [PMID: 37535606 PMCID: PMC10399749 DOI: 10.1371/journal.pone.0289064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 07/11/2023] [Indexed: 08/05/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease leading to continuous mucosal inflammation in the rectum extending proximally towards the colon. Chronic and/or recurrent UC is one of the critical predisposing mediators of the oncogenesis of human colorectal carcinoma (CRC). Perturbations of the differential expression of the UC-critical genes exert an intense impact on the neoplastic transformation of the affected tissue(s). Herein, a comprehensive exploration of the UC-critical genes from the transcriptomic profiles of UC patients was conducted to study the differential expression, functional enrichment, genomic alterations, signal transduction pathways, and immune infiltration level encountered by these genes concerning the oncogenesis of CRC. The study reveals that WFDC2, TTLL12, THRA, and EPHB3 play crucial roles as UC-CRC critical genes and are positively correlated with the molecular transformation of UC to CRC. Taken together, these genes can be used as potential biomarkers and therapeutic targets for combating UC-induced human CRC.
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Affiliation(s)
- Ritwik Patra
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Amit Kumar Dey
- Biomedical Research Centre, Translational Geroproteomics Unit, National Institute on Aging, National Institute of Health (NIH), Baltimore, MD, United States of America
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
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9
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Sarkar MS, Mia MM, Amin MA, Hossain MS, Islam MZ. Bioinformatics and network biology approach to identifying type 2 diabetes genes and pathways that influence the progression of breast cancer. Heliyon 2023; 9:e16151. [PMID: 37234659 PMCID: PMC10205526 DOI: 10.1016/j.heliyon.2023.e16151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/28/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Breast cancer is the second most prevalent malignancy affecting women. Postmenopausal women breast tumor is one of the top causes of death in women, accounting for 23% of cancer cases. Type 2 diabetes, a worldwide pandemic, has been connected to a heightened risk of several malignancies, although its association with breast cancer is still uncertain. In comparison to non-diabetic women, women with T2DM had a 23% elevated likelihood of developing breast cancer. It is difficult to determine causative or genetic susceptibility that connect T2DM and breast cancer. We created a large-scale network-based quantitative approach employing unbiased methods to discover abnormally amplified genes in both T2DM and breast cancer, to solve these issues. We performed transcriptome analysis to uncover identical genetic biomarkers and pathways to clarify the connection between T2DM and breast cancer patients. In this study, two RNA-seq datasets (GSE103001 and GSE86468) from the Gene Expression Omnibus (GEO) are used to identify mutually differentially expressed genes (DEGs) for breast cancer and T2DM, as well as common pathways and prospective medicines. Firstly, 45 shared genes (30 upregulated and 15 downregulated) between T2D and breast cancer were detected. We employed gene ontology and pathway enrichment to characterize prevalent DEGs' molecular processes and signal transduction pathways and observed that T2DM has certain connections to the progression of breast cancer. Using several computational and statistical approaches, we created a protein-protein interactions (PPI) network and revealed hub genes. These hub genes can be potential biomarkers, which may also lead to new therapeutic strategies for investigated diseases. We conducted TF-gene interactions, gene-microRNA interactions, protein-drug interactions, and gene-disease associations to find potential connections between T2DM and breast cancer pathologies. We assume that the potential drugs that emerged from this study could be useful therapeutic values. Researchers, doctors, biotechnologists, and many others may benefit from this research.
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Affiliation(s)
- Md Sumon Sarkar
- Department of Pharmacy, Islamic University, Kushtia-7003, Bangladesh
| | - Md Misor Mia
- Department of Pharmacy, Islamic University, Kushtia-7003, Bangladesh
| | - Md Al Amin
- Department of Computer Science & Engineering, Prime University, Dhaka-1216, Bangladesh
| | - Md Sojib Hossain
- Department of Mathematics, Govt. Bangla College, Dhaka-1216, Bangladesh
| | - Md Zahidul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia-7003, Bangladesh
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10
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Chen L, Li Y, Deng X. Comprehensive analysis of pan-cancer reveals the potential of SLC16A1 as a prognostic and immunological biomarker. Medicine (Baltimore) 2023; 102:e33242. [PMID: 36930112 PMCID: PMC10019278 DOI: 10.1097/md.0000000000033242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
SLC16A1 plays an important role in the development of multiple cancer types. Pan-cancer analysis may have significant impacts on the exploration of the relationship between SLC16A1 gene expression, prognosis and the molecular mechanisms of tumorigenesis. In this study, through the analysis of TCGA and GEO datasets, we explored the expression level and survival prognosis of SLC16A1 in pan-cancer, and further explored the differences in SLC16A1 gene mutation, methylation, and phosphorylation between tumor and normal tissues. In addition, we focused on the biological function of this gene and the relationship between the prognosis and immune infiltration by immune infiltration analysis and enrichment analysis, in order to evaluate the diagnostic and prognostic significance of SLC16A1 in carcinomas. The study found that SLC16A1 was highly expressed in 14 kinds of tumors, and there were statistically significant differences in the prognosis of 9 tumors. The phosphorylation level of S467 increased in OV, RCC, and UCEC. There was a statistically negative correlation between the CD8+ T-cell infiltration level and the SLC16A1 expression in HNSC, LUSC, SARC, TGCT, and KIRC. The cancer-related fibroblasts were positively correlated with SLC16A1 expression in BLCA, BRCA, KIRC, KIRP, PAAD, PCPG, and THCA. The enrichment analysis indicated that the tumorigenesis mechanism of this gene was mainly related to "glycolysis and glucose metabolism synthesis." SLC16A1 was a promising prognostic and immunological biomarker in pan-cancer.
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Affiliation(s)
- Lingyun Chen
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, China
- Department of Oncology, Hebei General Hospital, Shijiazhuang, China
| | - Yang Li
- Department of Oncology, Hebei General Hospital, Shijiazhuang, China
| | - Xinna Deng
- Department of Oncology, Hebei General Hospital, Shijiazhuang, China
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11
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Stibbe JA, Hoogland P, Achterberg FB, Holman DR, Sojwal RS, Burggraaf J, Vahrmeijer AL, Nagengast WB, Rogalla S. Highlighting the Undetectable - Fluorescence Molecular Imaging in Gastrointestinal Endoscopy. Mol Imaging Biol 2023; 25:18-35. [PMID: 35764908 PMCID: PMC9971088 DOI: 10.1007/s11307-022-01741-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Flexible high-definition white-light endoscopy is the current gold standard in screening for cancer and its precursor lesions in the gastrointestinal tract. However, miss rates are high, especially in populations at high risk for developing gastrointestinal cancer (e.g., inflammatory bowel disease, Lynch syndrome, or Barrett's esophagus) where lesions tend to be flat and subtle. Fluorescence molecular endoscopy (FME) enables intraluminal visualization of (pre)malignant lesions based on specific biomolecular features rather than morphology by using fluorescently labeled molecular probes that bind to specific molecular targets. This strategy has the potential to serve as a valuable tool for the clinician to improve endoscopic lesion detection and real-time clinical decision-making. This narrative review presents an overview of recent advances in FME, focusing on probe development, techniques, and clinical evidence. Future perspectives will also be addressed, such as the use of FME in patient stratification for targeted therapies and potential alliances with artificial intelligence. KEY MESSAGES: • Fluorescence molecular endoscopy is a relatively new technology that enables safe and real-time endoscopic lesion visualization based on specific molecular features rather than on morphology, thereby adding a layer of information to endoscopy, like in PET-CT imaging. • Recently the transition from preclinical to clinical studies has been made, with promising results regarding enhancing detection of flat and subtle lesions in the colon and esophagus. However, clinical evidence needs to be strengthened by larger patient studies with stratified study designs. • In the future fluorescence molecular endoscopy could serve as a valuable tool in clinical workflows to improve detection in high-risk populations like patients with Barrett's esophagus, Lynch syndrome, and inflammatory bowel syndrome, where flat and subtle lesions tend to be malignant up to five times more often. • Fluorescence molecular endoscopy has the potential to assess therapy responsiveness in vivo for targeted therapies, thereby playing a role in personalizing medicine. • To further reduce high miss rates due to human and technical factors, joint application of artificial intelligence and fluorescence molecular endoscopy are likely to generate added value.
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Affiliation(s)
- Judith A Stibbe
- Department of Surgery, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Petra Hoogland
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Friso B Achterberg
- Department of Surgery, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Derek R Holman
- Department of Medicine, Division of Gastroenterology, Stanford University School of Medicine, Stanford, CA, USA
| | - Raoul S Sojwal
- Department of Medicine, Division of Gastroenterology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacobus Burggraaf
- Department of Surgery, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
- Centre for Human Drug Research, Leiden, The Netherlands
| | - Alexander L Vahrmeijer
- Department of Surgery, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Wouter B Nagengast
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Stephan Rogalla
- Department of Medicine, Division of Gastroenterology, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Zhang W, Liu L, Xiao X, Zhou H, Peng Z, Wang W, Huang L, Xie Y, Xu H, Tao L, Nie W, Yuan X, Liu F, Yuan Q. Identification of common molecular signatures of SARS-CoV-2 infection and its influence on acute kidney injury and chronic kidney disease. Front Immunol 2023; 14:961642. [PMID: 37026010 PMCID: PMC10070855 DOI: 10.3389/fimmu.2023.961642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the main cause of COVID-19, causing hundreds of millions of confirmed cases and more than 18.2 million deaths worldwide. Acute kidney injury (AKI) is a common complication of COVID-19 that leads to an increase in mortality, especially in intensive care unit (ICU) settings, and chronic kidney disease (CKD) is a high risk factor for COVID-19 and its related mortality. However, the underlying molecular mechanisms among AKI, CKD, and COVID-19 are unclear. Therefore, transcriptome analysis was performed to examine common pathways and molecular biomarkers for AKI, CKD, and COVID-19 in an attempt to understand the association of SARS-CoV-2 infection with AKI and CKD. Three RNA-seq datasets (GSE147507, GSE1563, and GSE66494) from the GEO database were used to detect differentially expressed genes (DEGs) for COVID-19 with AKI and CKD to search for shared pathways and candidate targets. A total of 17 common DEGs were confirmed, and their biological functions and signaling pathways were characterized by enrichment analysis. MAPK signaling, the structural pathway of interleukin 1 (IL-1), and the Toll-like receptor pathway appear to be involved in the occurrence of these diseases. Hub genes identified from the protein-protein interaction (PPI) network, including DUSP6, BHLHE40, RASGRP1, and TAB2, are potential therapeutic targets in COVID-19 with AKI and CKD. Common genes and pathways may play pathogenic roles in these three diseases mainly through the activation of immune inflammation. Networks of transcription factor (TF)-gene, miRNA-gene, and gene-disease interactions from the datasets were also constructed, and key gene regulators influencing the progression of these three diseases were further identified among the DEGs. Moreover, new drug targets were predicted based on these common DEGs, and molecular docking and molecular dynamics (MD) simulations were performed. Finally, a diagnostic model of COVID-19 was established based on these common DEGs. Taken together, the molecular and signaling pathways identified in this study may be related to the mechanisms by which SARS-CoV-2 infection affects renal function. These findings are significant for the effective treatment of COVID-19 in patients with kidney diseases.
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Affiliation(s)
- Weiwei Zhang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Leping Liu
- Department of Pediatrics, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiangcheng Xiao
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Hongshan Zhou
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhangzhe Peng
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Wei Wang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Ling Huang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Yanyun Xie
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Hui Xu
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Lijian Tao
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Wannian Nie
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Xiangning Yuan
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Fang Liu
- Health Management Center, Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Fang Liu, ; Qiongjing Yuan,
| | - Qiongjing Yuan
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
- National Clinical Medical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, China
- Research Center for Medical Metabolomics, Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Fang Liu, ; Qiongjing Yuan,
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13
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Li C, Zhang Y, Xiao Y, Luo Y. Identifying the Effect of COVID-19 Infection in Multiple Myeloma and Diffuse Large B-Cell Lymphoma Patients Using Bioinformatics and System Biology. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7017317. [PMID: 36466549 PMCID: PMC9711963 DOI: 10.1155/2022/7017317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/05/2022] [Accepted: 11/12/2022] [Indexed: 09/29/2023]
Abstract
The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), also referred to as COVID-19, has spread to several countries and caused a serious threat to human health worldwide. Patients with confirmed COVID-19 infection spread the disease rapidly throughout the region. Multiple myeloma (MM) and diffuse large B-cell lymphoma (DLBCL) are risk factors for COVID-19, although the molecular mechanisms underlying the relationship among MM, DLBCL, and COVID-19 have not been elucidated so far. In this context, transcriptome analysis was performed in the present study to identify the shared pathways and molecular indicators of MM, DLBCL, and COVID-19, which benefited the overall understanding of the effect of COVID-19 in patients with MM and DLBCL. Three datasets (GSE16558, GSE56315, and GSE152418) were downloaded from the Gene Expression Omnibus (GEO) and searched for the shared differentially expressed genes (DEGs) in patients with MM and DLBCL who were infected with SARS-CoV-2. The objective was to detect similar pathways and prospective medicines. A total of 29 DEGs that were common across these three datasets were selected. A protein-protein interaction (PPI) network was constructed using data from the STRING database followed by the identification of hub genes. In addition, the association of MM and DLBCL with COVID-19 infection was analyzed through functional analysis using ontologies terms and pathway analysis. Three relationships were observed in the evaluated datasets: transcription factor-gene interactions, protein-drug interactions, and an integrated regulatory network of DEGs and miRNAs with mutual DEGs. The findings of the present study revealed potential pharmaceuticals that could be beneficial in the treatment of COVID-19.
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Affiliation(s)
- Chengcheng Li
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Life Science, Chongqing Medical University, Chongqing, China
| | - Ying Zhang
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yingying Xiao
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Life Science, Chongqing Medical University, Chongqing, China
| | - Yun Luo
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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14
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Yang K, Liu J, Gong Y, Li Y, Liu Q. Bioinformatics and systems biology approaches to identify molecular targeting mechanism influenced by COVID-19 on heart failure. Front Immunol 2022; 13:1052850. [DOI: 10.3389/fimmu.2022.1052850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a contemporary hazard to people. It has been known that COVID-19 can both induce heart failure (HF) and raise the risk of patient mortality. However, the mechanism underlying the association between COVID-19 and HF remains unclear. The common molecular pathways between COVID-19 and HF were identified using bioinformatic and systems biology techniques. Transcriptome analysis was performed to identify differentially expressed genes (DEGs). To identify gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways, common DEGs were used for enrichment analysis. The results showed that COVID-19 and HF have several common immune mechanisms, including differentiation of T helper (Th) 1, Th 2, Th 17 cells; activation of lymphocytes; and binding of major histocompatibility complex class I and II protein complexes. Furthermore, a protein-protein interaction network was constructed to identify hub genes, and immune cell infiltration analysis was performed. Six hub genes (FCGR3A, CD69, IFNG, CCR7, CCL5, and CCL4) were closely associated with COVID-19 and HF. These targets were associated with immune cells (central memory CD8 T cells, T follicular helper cells, regulatory T cells, myeloid-derived suppressor cells, plasmacytoid dendritic cells, macrophages, eosinophils, and neutrophils). Additionally, transcription factors, microRNAs, drugs, and chemicals that are closely associated with COVID-19 and HF were identified through the interaction network.
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15
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Han X, Wang F, Yang P, Di B, Xu X, Zhang C, Yao M, Sun Y, Lin Y. A Bioinformatic Approach Based on Systems Biology to Determine the Effects of SARS-CoV-2 Infection in Patients with Hypertrophic Cardiomyopathy. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5337380. [PMID: 36203534 PMCID: PMC9532139 DOI: 10.1155/2022/5337380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/18/2022]
Abstract
Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has infected millions of individuals worldwide. While COVID-19 generally affects the lungs, it also damages other organs, including those of the cardiovascular system. Hypertrophic cardiomyopathy (HCM) is a common genetic cardiovascular disorder. Studies have shown that HCM patients with COVID-19 have a higher mortality rate; however, the reason for this phenomenon is not yet elucidated. Herein, we conducted transcriptomic analyses to identify shared biomarkers between HCM and COVID-19 to bridge this knowledge gap. Differentially expressed genes (DEGs) were obtained using the Gene Expression Omnibus ribonucleic acid (RNA) sequencing datasets, GSE147507 and GSE89714, to identify shared pathways and potential drug candidates. We discovered 30 DEGs that were common between these two datasets. Using a combination of statistical and biological tools, protein-protein interactions were constructed in response to these findings to support hub genes and modules. We discovered that HCM is linked to COVID-19 progression based on a functional analysis under ontology terms. Based on the DEGs identified from the datasets, a coregulatory network of transcription factors, genes, proteins, and microRNAs was also discovered. Lastly, our research suggests that the potential drugs we identified might be helpful for COVID-19 therapy.
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Affiliation(s)
- Xiao Han
- Department of Cardiology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Fei Wang
- Department of Emergency Medicine, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Ping Yang
- Department of Pharmacy, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Bin Di
- Department of Cardiology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xiangdong Xu
- Department of Cardiology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Chunya Zhang
- Department of Cardiology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Man Yao
- Department of Cardiology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Yaping Sun
- Department of Cardiology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Yangyi Lin
- Department of Pulmonary Vascular Disease, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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16
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Fang H, Sun Z, Chen Z, Chen A, Sun D, Kong Y, Fang H, Qian G. Bioinformatics and systems-biology analysis to determine the effects of Coronavirus disease 2019 on patients with allergic asthma. Front Immunol 2022; 13:988479. [PMID: 36211429 PMCID: PMC9537444 DOI: 10.3389/fimmu.2022.988479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/30/2022] [Indexed: 12/05/2022] Open
Abstract
Background The coronavirus disease (COVID-19) pandemic has posed a significant challenge for global health systems. Increasing evidence shows that asthma phenotypes and comorbidities are major risk factors for COVID-19 symptom severity. However, the molecular mechanisms underlying the association between COVID-19 and asthma are poorly understood. Therefore, we conducted bioinformatics and systems biology analysis to identify common pathways and molecular biomarkers in patients with COVID-19 and asthma, as well as potential molecular mechanisms and candidate drugs for treating patients with both COVID-19 and asthma. Methods Two sets of differentially expressed genes (DEGs) from the GSE171110 and GSE143192 datasets were intersected to identify common hub genes, shared pathways, and candidate drugs. In addition, murine models were utilized to explore the expression levels and associations of the hub genes in asthma and lung inflammation/injury. Results We discovered 157 common DEGs between the asthma and COVID-19 datasets. A protein–protein-interaction network was built using various combinatorial statistical approaches and bioinformatics tools, which revealed several hub genes and critical modules. Six of the hub genes were markedly elevated in murine asthmatic lungs and were positively associated with IL-5, IL-13 and MUC5AC, which are the key mediators of allergic asthma. Gene Ontology and pathway analysis revealed common associations between asthma and COVID-19 progression. Finally, we identified transcription factor–gene interactions, DEG–microRNA coregulatory networks, and potential drug and chemical-compound interactions using the hub genes. Conclusion We identified the top 15 hub genes that can be used as novel biomarkers of COVID-19 and asthma and discovered several promising candidate drugs that might be helpful for treating patients with COVID-19 and asthma.
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Affiliation(s)
- Hongwei Fang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhun Sun
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Zhouyi Chen
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Anning Chen
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Donglin Sun
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yan Kong
- Department of Anesthesiology (High-Tech Branch), The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hao Fang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Anesthesiology, Minhang Hospital, Fudan University, Shanghai, China
- *Correspondence: Guojun Qian, ; Hao Fang,
| | - Guojun Qian
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Guojun Qian, ; Hao Fang,
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Network-Based Data Analysis Reveals Ion Channel-Related Gene Features in COVID-19: A Bioinformatic Approach. Biochem Genet 2022; 61:471-505. [PMID: 36104591 PMCID: PMC9473477 DOI: 10.1007/s10528-022-10280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 09/01/2022] [Indexed: 11/02/2022]
Abstract
Coronavirus disease 2019 (COVID-19) seriously threatens human health and has been disseminated worldwide. Although there are several treatments for COVID-19, its control is currently suboptimal. Therefore, the development of novel strategies to treat COVID-19 is necessary. Ion channels are located on the membranes of all excitable cells and many intracellular organelles and are key components involved in various biological processes. They are a target of interest when searching for drug targets. This study aimed to reveal the relevant molecular features of ion channel genes in COVID-19 based on bioinformatic analyses. The RNA-sequencing data of patients with COVID-19 and healthy subjects (GSE152418 and GSE171110 datasets) were obtained from the Gene Expression Omnibus (GEO) database. Ion channel genes were selected from the Hugo Gene Nomenclature Committee (HGNC) database. The RStudio software was used to process the data based on the corresponding R language package to identify ion channel-associated differentially expressed genes (DEGs). Based on the DEGs, Gene Ontology (GO) functional and pathway enrichment analyses were performed using the Enrichr web tool. The STRING database was used to generate a protein-protein interaction (PPI) network, and the Cytoscape software was used to screen for hub genes in the PPI network based on the cytoHubba plug-in. Transcription factors (TF)-DEG, DEG-microRNA (miRNA) and DEG-disease association networks were constructed using the NetworkAnalyst web tool. Finally, the screened hub genes as drug targets were subjected to enrichment analysis based on the DSigDB using the Enrichr web tool to identify potential therapeutic agents for COVID-19. A total of 29 ion channel-associated DEGs were identified. GO functional analysis showed that the DEGs were integral components of the plasma membrane and were mainly involved in inorganic cation transmembrane transport and ion channel activity functions. Pathway analysis showed that the DEGs were mainly involved in nicotine addiction, calcium regulation in the cardiac cell and neuronal system pathways. The top 10 hub genes screened based on the PPI network included KCNA2, KCNJ4, CACNA1A, CACNA1E, NALCN, KCNA5, CACNA2D1, TRPC1, TRPM3 and KCNN3. The TF-DEG and DEG-miRNA networks revealed significant TFs (FOXC1, GATA2, HINFP, USF2, JUN and NFKB1) and miRNAs (hsa-mir-146a-5p, hsa-mir-27a-3p, hsa-mir-335-5p, hsa-let-7b-5p and hsa-mir-129-2-3p). Gene-disease association network analysis revealed that the DEGs were closely associated with intellectual disability and cerebellar ataxia. Drug-target enrichment analysis showed that the relevant drugs targeting the hub genes CACNA2D1, CACNA1A, CACNA1E, KCNA2 and KCNA5 were gabapentin, gabapentin enacarbil, pregabalin, guanidine hydrochloride and 4-aminopyridine. The results of this study provide a valuable basis for exploring the mechanisms of ion channel genes in COVID-19 and clues for developing therapeutic strategies for COVID-19.
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Al-Mustanjid M, Mahmud SMH, Akter F, Rahman MS, Hossen MS, Rahman MH, Moni MA. Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. INFORMATICS IN MEDICINE UNLOCKED 2022; 32:101003. [PMID: 35818398 PMCID: PMC9259025 DOI: 10.1016/j.imu.2022.101003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating since 2019, and its global dominance is rising. Evidences suggest the respiratory illness SARS-CoV-2 has a sensitive affect on causing organ damage and other complications to the patients with autoimmune diseases (AD), posing a significant risk factor. The genetic interrelationships and molecular appearances between SARS-CoV-2 and AD are yet unknown. We carried out the transcriptomic analytical framework to delve into the SARS-CoV-2 impacts on AD progression. We analyzed both gene expression microarray and RNA-Seq datasets from SARS-CoV-2 and AD affected tissues. With neighborhood-based benchmarks and multilevel network topology, we obtained dysfunctional signaling and ontological pathways, gene disease (diseasesome) association network and protein-protein interaction network (PPIN), uncovered essential shared infection recurrence connectivities with biological insights underlying between SARS-CoV-2 and AD. We found a total of 77, 21, 9, 54 common DEGs for SARS-CoV-2 and inflammatory bowel disorder (IBD), SARS-CoV-2 and rheumatoid arthritis (RA), SARS-CoV-2 and systemic lupus erythematosus (SLE) and SARS-CoV-2 and type 1 diabetes (T1D). The enclosure of these common DEGs with bimolecular networks revealed 10 hub proteins (FYN, VEGFA, CTNNB1, KDR, STAT1, B2M, CD3G, ITGAV, TGFB3). Drugs such as amlodipine besylate, vorinostat, methylprednisolone, and disulfiram have been identified as a common ground between SARS-CoV-2 and AD from drug repurposing investigation which will stimulate the optimal selection of medications in the battle against this ongoing pandemic triggered by COVID-19.
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Affiliation(s)
- Md Al-Mustanjid
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - S M Hasan Mahmud
- Department of Computer Science, American International University-Bangladesh, Dhaka, 1229, Bangladesh
| | - Farzana Akter
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Shazzadur Rahman
- Department of Computer Science & Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Sajid Hossen
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia-7003, Bangladesh
| | - Mohammad Ali Moni
- Department of Computer Science and Engineering, Pabna Science & Technology University, Pabna, 6600, Bangladesh
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19
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Yuan S, Wang Q, Li J, Xue JC, Li Y, Meng H, Hou XT, Nan JX, Zhang QG. Inflammatory bowel disease: an overview of Chinese herbal medicine formula-based treatment. Chin Med 2022; 17:74. [PMID: 35717380 PMCID: PMC9206260 DOI: 10.1186/s13020-022-00633-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/02/2022] [Indexed: 12/14/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic recurrent inflammatory disease of the intestine, including Crohn’s disease (CD) and ulcerative colitis (UC), whose etiology and pathogenesis have not been fully understood. Due to its prolonged course and chronic recurrence, IBD imposes a heavy economic burden and psychological stress on patients. Traditional Chinese Herbal Medicine has unique advantages in IBD treatment because of its symptomatic treatment. However, the advantages of the Chinese Herbal Medicine Formula (CHMF) have rarely been discussed. In recent years, many scholars have conducted fundamental studies on CHMF to delay IBD from different perspectives and found that CHMF may help maintain intestinal integrity, reduce inflammation, and decrease oxidative stress, thus playing a positive role in the treatment of IBD. Therefore, this review focuses on the mechanisms associated with CHMF in IBD treatment. CHMF has apparent advantages. In addition to the exact composition and controlled quality of modern drugs, it also has multi-component and multi-target synergistic effects. CHMF has good prospects in the treatment of IBD, but its multi-agent composition and wide range of targets exacerbate the difficulty of studying its treatment of IBD. Future research on CHMF-related mechanisms is needed to achieve better efficacy.
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Affiliation(s)
- Shuo Yuan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, 133002, Jilin, China.,Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Qi Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Jiao Li
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China.,Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, 133002, Jilin, China
| | - Jia-Chen Xue
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China.,Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, 133002, Jilin, China
| | - You Li
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Huan Meng
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Xiao-Ting Hou
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China
| | - Ji-Xing Nan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, 133002, Jilin, China.
| | - Qing-Gao Zhang
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, 133002, Jilin, China. .,Chronic Disease Research Center, Medical College, Dalian University, Dalian, 116622, Liaoning, China. .,Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, 133002, Jilin, China.
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20
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Huang S, Xiang C, Song Y. Identification of the shared gene signatures and pathways between sarcopenia and type 2 diabetes mellitus. PLoS One 2022; 17:e0265221. [PMID: 35271662 PMCID: PMC8912249 DOI: 10.1371/journal.pone.0265221] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
Background Sarcopenia is characterized by the age-associated loss of skeletal muscle mass and strength that develops progressively and plays an important role in the disability of the elderly. It has received growing attention over the last decade and has been implicated as both a cause and consequence of type 2 diabetes mellitus (T2DM). The existence of T2DM could increase the risk of developing sarcopenia through multiple mechanisms including advanced glycation end-product accumulation. Meanwhile, sarcopenia would alter glucose disposal and may contribute to the development and progression of T2DM due to reduced muscle mass. Methods We implemented transcriptomic analysis of skeletal muscle biopsy specimens in sarcopenia patients and proliferating myoblasts or differentiated myotubes from individuals with T2DM. Related microarray data were selected from Gene Expression Omnibus (GEO) to screen the genes, which were differentially expressed for sarcopenia and T2DM. Multiple combinatorial statistical methods and bioinformatics tools were used to analyze the common DEGs. Meanwhile, functional enrichment analysis was also carried out. Furthermore, we constructed the protein-protein interaction (PPI), as well as transcription factor (TF)-gene interactions network and TF-miRNA coregulatory network. Finally, based on the common DEGs, drug compounds were speculated using the Drug Signatures database (DSigDB). Results A total of 1765 and 2155 DEGs of sarcopenia and T2DM were screened, respectively. 15 common genes (LXN, CIB2, PEA15, KANK2, FGD1, NMRK1, PLCB1, SEMA4G, ADARB1, UPF3A, CSTB, COL3A1, CD99, ETV3, FJX1) correlated with sarcopenia and T2DM simultaneously were then identified, and 3 genes (UPF3A, CSTB and PEA15) of them were regarded as hub genes. Functional enrichment analysis revealed several shared pathways between two diseases. In addition, according to the TF-gene interactions network and TF-miRNA coregulatory network, part of TF and miRNA may be identified as key regulator in sarcopenia and T2DM at the same time (e.g., CREM and miR-155). Notably, drug compounds for T2DM and sarcopenia were also suggested, such as coenzyme Q10. Conclusion This study revealed that sarcopenia and T2DM may share similar pathogenesis and provided new biological targets and ideas for early diagnosis and effective treatment of sarcopenia and T2DM.
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Affiliation(s)
- Shiyuan Huang
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunhua Xiang
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Song
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail:
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21
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Immune-related biomarkers shared by inflammatory bowel disease and liver cancer. PLoS One 2022; 17:e0267358. [PMID: 35452485 PMCID: PMC9032416 DOI: 10.1371/journal.pone.0267358] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
It has been indicated that there is an association between inflammatory bowel disease (IBD) and hepatocellular carcinoma (HCC). However, the molecular mechanism underlying the risk of developing HCC among patients with IBD is not well understood. The current study aimed to identify shared genes and potential pathways and regulators between IBD and HCC using a system biology approach. By performing the different gene expression analyses, we identified 871 common differentially expressed genes (DEGs) between IBD and HCC. Of these, 112 genes overlapped with immune genes were subjected to subsequent bioinformatics analyses. The results revealed four hub genes (CXCL2, MMP9, SPP1 and SRC) and several other key regulators including six transcription factors (FOXC1, FOXL1, GATA2, YY1, ZNF354C and TP53) and five microRNAs (miR-124-3p, miR-34a-5p, miR-1-3p, miR-7-5p and miR-99b-5p) for these disease networks. Protein-drug interaction analysis discovered the interaction of the hub genes with 46 SRC-related and 11 MMP9- related drugs that may have a therapeutic effect on IBD and HCC. In conclusion, this study sheds light on the potential connecting mechanisms of HCC and IBD.
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22
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Shen Y, Lin H, Chen K, Ge W, Xia D, Wu Y, Lu W. High expression of RIPK2 is associated with Taxol resistance in serous ovarian cancer. J Ovarian Res 2022; 15:48. [PMID: 35477477 PMCID: PMC9044796 DOI: 10.1186/s13048-022-00986-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/19/2022] [Indexed: 12/30/2022] Open
Abstract
Background Taxol resistance in serous ovarian cancer is responsible for its poor prognosis, yet the underlying mechanism is still poorly understood. Thus, we probed the mechanism of Taxol resistance in serous ovarian cancer with multiple bioinformatic methods to provide novel insights into potential therapies. Methods The differentially expressed genes (DEGs) in Taxol-sensitive and Taxol-resistant cell lines and their relationship with the overall survival (OS) and progression-free interval (PFI) of ovarian cancer patients were analyzed using gene expression datasets from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The role of receptor interacting serine/threonine kinase 2 (RIPK2) was validated via identification of its coexpressed genes, functional analysis and generation of a protein-protein interaction (PPI) network. The single sample gene set enrichment analysis (ssGSEA) was used to explore immune infiltration, and genomic alterations of RIPK2 were also analyzed via cBio Cancer Genomics Portal (cBioProtal). Results RIPK2 was highly expressed in Taxol resistant ovarian cancer cell lines, and its high expression was also linked with shorter OS and PFI in serous ovarian cancer patients. The PPI network analysis and pathway analysis demonstrated that RIPK2 might participate in the positive regulation of NF-κB transcription factor activity. RIPK2 expression was related to tumor microenvironment alterations, which might participate in the formation of Taxol resistance. Conclusions Our studies suggested that high expression of RIPK2 is related to Taxol resistance in serous ovarian cancer, and that RIPK2 induces Taxol resistance through NOD1/RIPK2/NF-κB inflammatory pathway activation and tumor microenvironment changes. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-022-00986-2.
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Affiliation(s)
- Yuqing Shen
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310006, China.,Department of Gynecologic Oncology of Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Hui Lin
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310006, China.,Department of Gynecologic Oncology of Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kelie Chen
- Department of Toxicology of School of Public Health, and Department of Gynecologic Oncology of Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China.,Institute of Genetics and Department of Genetics School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Dajing Xia
- Department of Toxicology of School of Public Health, and Department of Gynecologic Oncology of Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China.,Institute of Genetics and Department of Genetics School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yihua Wu
- Department of Toxicology of School of Public Health, and Department of Gynecologic Oncology of Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China.,Institute of Genetics and Department of Genetics School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Weiguo Lu
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310006, China. .,Department of Gynecologic Oncology of Women's Hospital School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China. .,Institute of Genetics and Department of Genetics School of Medicine Zhejiang University, Hangzhou, 310058, Zhejiang, China. .,Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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23
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Systems Biology and Bioinformatics approach to Identify blood based signatures molecules and drug targets of patient with COVID-19. INFORMATICS IN MEDICINE UNLOCKED 2022; 28:100840. [PMID: 34981034 PMCID: PMC8716147 DOI: 10.1016/j.imu.2021.100840] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection results in the development of a highly contagious respiratory ailment known as new coronavirus disease (COVID-19). Despite the fact that the prevalence of COVID-19 continues to rise, it is still unclear how people become infected with SARS-CoV-2 and how patients with COVID-19 become so unwell. Detecting biomarkers for COVID-19 using peripheral blood mononuclear cells (PBMCs) may aid in drug development and treatment. This research aimed to find blood cell transcripts that represent levels of gene expression associated with COVID-19 progression. Through the development of a bioinformatics pipeline, two RNA-Seq transcriptomic datasets and one microarray dataset were studied and discovered 102 significant differentially expressed genes (DEGs) that were shared by three datasets derived from PBMCs. To identify the roles of these DEGs, we discovered disease-gene association networks and signaling pathways, as well as we performed gene ontology (GO) studies and identified hub protein. Identified significant gene ontology and molecular pathways improved our understanding of the pathophysiology of COVID-19, and our identified blood-based hub proteins TPX2, DLGAP5, NCAPG, CCNB1, KIF11, HJURP, AURKB, BUB1B, TTK, and TOP2A could be used for the development of therapeutic intervention. In COVID-19 subjects, we discovered effective putative connections between pathological processes in the transcripts blood cells, suggesting that blood cells could be used to diagnose and monitor the disease’s initiation and progression as well as developing drug therapeutics.
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24
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Wang C, Jiang H. Long non-coding RNA PCAT19 regulates the malignant progression of bladder cancer through the miR-335-5p/IER2 axis. Crit Rev Eukaryot Gene Expr 2022; 32:81-94. [DOI: 10.1615/critreveukaryotgeneexpr.2022043175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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25
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Identification of molecular signatures and pathways common to blood cells and brain tissue based RNA-Seq datasets of bipolar disorder: Insights from comprehensive bioinformatics approach. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100881] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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26
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Grillo TG, Quaglio AEV, Beraldo RF, Lima TB, Baima JP, Di Stasi LC, Sassaki LY. MicroRNA expression in inflammatory bowel disease-associated colorectal cancer. World J Gastrointest Oncol 2021; 13:995-1016. [PMID: 34616508 PMCID: PMC8465441 DOI: 10.4251/wjgo.v13.i9.995] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/30/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNA molecules composed of 19–25 nucleotides that regulate gene expression and play a central role in the regulation of several immune-mediated disorders, including inflammatory bowel diseases (IBD). IBD, represented by ulcerative colitis and Crohn’s disease, is characterized by chronic intestinal inflammation associated with an increased risk of colorectal cancer (CRC). CRC is one of the most prevalent tumors in the world, and its main risk factors are obesity, physical inactivity, smoking, alcoholism, advanced age, and some eating habits, in addition to chronic intestinal inflammatory processes and the use of immunosuppressants administered to IBD patients. Recent studies have identified miRNAs associated with an increased risk of developing CRC in this population. The identification of miRNAs involved in this tumorigenic process could be useful to stratify cancer risk development for patients with IBD and to monitor and assess prognosis. Thus, the present review aimed to summarize the role of miRNAs as biomarkers for the diagnosis and prognosis of IBD-associated CRC. In the future, therapies based on miRNA modulation could be used both in clinical practice to achieve remission of the disease and restore the quality of life for patients with IBD, and to identify the patients with IBD at high risk for tumor development.
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Affiliation(s)
- Thais Gagno Grillo
- Department of Internal Medicine, São Paulo State University (Unesp), Medical School, Botucatu 18618-686, São Paulo, Brazil
| | - Ana Elisa Valencise Quaglio
- Department of Biophysics and Pharmacology, São Paulo State University (Unesp), Institute of Biosciences, Botucatu 18618-689, São Paulo, Brazil
| | - Rodrigo Fedatto Beraldo
- Department of Internal Medicine, São Paulo State University (Unesp), Medical School, Botucatu 18618-686, São Paulo, Brazil
| | - Talles Bazeia Lima
- Department of Internal Medicine, São Paulo State University (Unesp), Medical School, Botucatu 18618-686, São Paulo, Brazil
| | - Julio Pinheiro Baima
- Department of Internal Medicine, São Paulo State University (Unesp), Medical School, Botucatu 18618-686, São Paulo, Brazil
| | - Luiz Claudio Di Stasi
- Department of Biophysics and Pharmacology, São Paulo State University (Unesp), Institute of Biosciences, Botucatu 18618-689, São Paulo, Brazil
| | - Ligia Yukie Sassaki
- Department of Internal Medicine, São Paulo State University (Unesp), Medical School, Botucatu 18618-686, São Paulo, Brazil
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27
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Mahmud SMH, Al-Mustanjid M, Akter F, Rahman MS, Ahmed K, Rahman MH, Chen W, Moni MA. Bioinformatics and system biology approach to identify the influences of SARS-CoV-2 infections to idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease patients. Brief Bioinform 2021; 22:6224261. [PMID: 33847347 PMCID: PMC8083324 DOI: 10.1093/bib/bbab115] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/25/2021] [Accepted: 03/13/2021] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), better known as COVID-19, has become a current threat to humanity. The second wave of the SARS-CoV-2 virus has hit many countries, and the confirmed COVID-19 cases are quickly spreading. Therefore, the epidemic is still passing the terrible stage. Having idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) are the risk factors of the COVID-19, but the molecular mechanisms that underlie IPF, COPD, and CVOID-19 are not well understood. Therefore, we implemented transcriptomic analysis to detect common pathways and molecular biomarkers in IPF, COPD, and COVID-19 that help understand the linkage of SARS-CoV-2 to the IPF and COPD patients. Here, three RNA-seq datasets (GSE147507, GSE52463, and GSE57148) from Gene Expression Omnibus (GEO) is employed to detect mutual differentially expressed genes (DEGs) for IPF, and COPD patients with the COVID-19 infection for finding shared pathways and candidate drugs. A total of 65 common DEGs among these three datasets were identified. Various combinatorial statistical methods and bioinformatics tools were used to build the protein–protein interaction (PPI) and then identified Hub genes and essential modules from this PPI network. Moreover, we performed functional analysis under ontologies terms and pathway analysis and found that IPF and COPD have some shared links to the progression of COVID-19 infection. Transcription factors–genes interaction, protein–drug interactions, and DEGs-miRNAs coregulatory network with common DEGs also identified on the datasets. We think that the candidate drugs obtained by this study might be helpful for effective therapeutic in COVID-19.
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Affiliation(s)
- S M Hasan Mahmud
- Computer Science and Technology from the University of Electronic Science and Technology of China, China
| | | | - Farzana Akter
- Computer Science and Engineering from Daffodil International University, Bangladesh
| | | | - Kawsar Ahmed
- Information and Communication Technology (ICT) at Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md Habibur Rahman
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Wenyu Chen
- University of Electronic Science and Technology of China, China
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28
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Taz TA, Ahmed K, Paul BK, Al-Zahrani FA, Mahmud SMH, Moni MA. Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. Brief Bioinform 2021; 22:1451-1465. [PMID: 33611340 PMCID: PMC7929374 DOI: 10.1093/bib/bbab026] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
This study aimed to identify significant gene expression profiles of the human lung epithelial cells caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We performed a comparative genomic analysis to show genomic observations between SARS-CoV and SARS-CoV-2. A phylogenetic tree has been carried for genomic analysis that confirmed the genomic variance between SARS-CoV and SARS-CoV-2. Transcriptomic analyses have been performed for SARS-CoV-2 infection responses and pulmonary arterial hypertension (PAH) patients' lungs as a number of patients have been identified who faced PAH after being diagnosed with coronavirus disease 2019 (COVID-19). Gene expression profiling showed significant expression levels for SARS-CoV-2 infection responses to human lung epithelial cells and PAH lungs as well. Differentially expressed genes identification and integration showed concordant genes (SAA2, S100A9, S100A8, SAA1, S100A12 and EDN1) for both SARS-CoV-2 and PAH samples, including S100A9 and S100A8 genes that showed significant interaction in the protein-protein interactions network. Extensive analyses of gene ontology and signaling pathways identification provided evidence of inflammatory responses regarding SARS-CoV-2 infections. The altered signaling and ontology pathways that have emerged from this research may influence the development of effective drugs, especially for the people with preexisting conditions. Identification of regulatory biomolecules revealed the presence of active promoter gene of SARS-CoV-2 in Transferrin-micro Ribonucleic acid (TF-miRNA) co-regulatory network. Predictive drug analyses provided concordant drug compounds that are associated with SARS-CoV-2 infection responses and PAH lung samples, and these compounds showed significant immune response against the RNA viruses like SARS-CoV-2, which is beneficial in therapeutic development in the COVID-19 pandemic.
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Affiliation(s)
- Tasnimul Alam Taz
- Department of Software Engineering, Daffodil International University, Bangladesh
| | - Kawsar Ahmed
- Department of Information and Communication Technology (ICT) at Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Bikash Kumar Paul
- Department of ICT at Mawlana Bhashani Science and Technology University, Bangladesh
| | | | - S M Hasan Mahmud
- Department of Software Engineering, Daffodil International University, Bangladesh
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29
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Wang H, Xing J, Wang W, Lv G, He H, Lu Y, Sun M, Chen H, Li X. Molecular Characterization of the Oncogene BTF3 and Its Targets in Colorectal Cancer. Front Cell Dev Biol 2021; 8:601502. [PMID: 33644029 PMCID: PMC7905040 DOI: 10.3389/fcell.2020.601502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/26/2020] [Indexed: 01/12/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed and leading causes of cancer mortality worldwide, and the prognosis of patients with CRC remains unsatisfactory. Basic transcription factor 3 (BTF3) is an oncogene and hazardous prognosticator in CRC. Although two distinct functional mechanisms of BTF3 in different cancer types have been reported, its role in CRC is still unclear. In this study, we aimed to molecularly characterize the oncogene BTF3 and its targets in CRC. Here, we first identified the transcriptional targets of BTF3 by applying combined RNA-Seq and ChIP-Seq analysis, identifying CHD1L as a transcriptional target of BTF3. Thereafter, we conducted immunoprecipitation (IP)-MS and E3 ubiquitin ligase analysis to identify potential interacting targets of BTF3 as a subunit of the nascent-polypeptide-associated complex (NAC). The analysis revealed that BTF3 might also inhibit E3 ubiquitin ligase HERC2-mediated p53 degradation. Finally, miRNAs targeting BTF3 were predicted and validated. Decreased miR-497-5p expression is responsible for higher levels of BTF3 post-transcriptionally. Collectively, we concluded that BTF3 is an oncogene, and there may exist a transcription factor and NAC-related proteolysis mechanism in CRC. This study provides a comprehensive basis for understanding the oncogenic mechanisms of BTF3 in CRC.
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Affiliation(s)
- Hantao Wang
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Junjie Xing
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Wei Wang
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Guifen Lv
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Haiyan He
- Department of Digestive Endoscopy, Changhai Hospital, Shanghai, China
| | - Yeqing Lu
- Department of Anesthesiology, Changhai Hospital, Shanghai, China
| | - Mei Sun
- Department of Anesthesiology, Changhai Hospital, Shanghai, China
| | - Haiyan Chen
- Department of Endocrinology, Changzheng Hospital, Shanghai, China
| | - Xu Li
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
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