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Kadhim DJ, Azari H, Sokhangouy SK, Hassanian SM, Alshekarchi HI, Goshayeshi L, Goshayeshi L, Abbaszadegan MR, Khojasteh-Leylakoohi F, Khazaei M, Gataa IS, Peters GJ, A. Ferns G, Batra J, Lam AKY, Giovannetti E, Avan A. G-Protein Signaling Modulator 2 as a Potential Biomarker in Colorectal Cancer: Integrative Analysis Using Genetic Profiling and Pan-Cancer Studies. Genes (Basel) 2024; 15:474. [PMID: 38674408 PMCID: PMC11050220 DOI: 10.3390/genes15040474] [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: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
Colorectal cancer (CRC) imposes a significant healthcare burden globally, prompting the quest for innovative biomarkers to enhance diagnostic and therapeutic strategies. This study investigates the G-protein signaling modulator (GPSM) family across several cancers and presents a comprehensive pan-cancer analysis of the GPSM2 gene across several gastrointestinal (GI) cancers. Leveraging bioinformatics methodologies, we investigated GPSM2 expression patterns, protein interactions, functional enrichments, prognostic implications, genetic alterations, and immune infiltration associations. Furthermore, the expression of the GPSM2 gene was analyzed using real-time analysis. Our findings reveal a consistent upregulation of GPSM2 expression in all GI cancer datasets analyzed, suggesting its potential as a universal biomarker in GI cancers. Functional enrichment analysis underscores the involvement of GPSM2 in vital pathways, indicating its role in tumor progression. The prognostic assessment indicates that elevated GPSM2 expression correlates with adverse overall and disease-free survival outcomes across multiple GI cancer types. Genetic alteration analysis highlights the prevalence of mutations, particularly missense mutations, in GPSM2. Furthermore, significant correlations between GPSM2 expression and immune cell infiltration are observed, suggesting its involvement in tumor immune evasion mechanisms. Collectively, our study underscores the multifaceted role of GPSM2 in GI cancers, particularly in CRC, emphasizing its potential as a promising biomarker for prognosis and therapeutic targeting. Further functional investigations are warranted to elucidate its clinical utility and therapeutic implications in CRC management.
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Affiliation(s)
- Doaa Jawad Kadhim
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran (H.A.); (S.M.H.); (F.K.-L.); (M.K.)
| | - Hanieh Azari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran (H.A.); (S.M.H.); (F.K.-L.); (M.K.)
| | - Saeideh Khorshid Sokhangouy
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad 91886-17871, Iran; (S.K.S.); (M.R.A.)
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran (H.A.); (S.M.H.); (F.K.-L.); (M.K.)
| | - Hawraa Ibrahim Alshekarchi
- Al-Zahraa Center for Medical and Pharmaceutical Research Sciences (ZCMRS), Al-Zahraa University for Women, Kerbala 56001, Iraq
| | - Ladan Goshayeshi
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran;
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48954, Iran
| | - Lena Goshayeshi
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48954, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad 91886-17871, Iran; (S.K.S.); (M.R.A.)
| | - Fatemeh Khojasteh-Leylakoohi
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran (H.A.); (S.M.H.); (F.K.-L.); (M.K.)
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran (H.A.); (S.M.H.); (F.K.-L.); (M.K.)
| | | | - Godefridus J. Peters
- Department of Biochemistry, Medical University of Gdansk, 80-211 Gdansk, Poland;
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam UMC, Vrije Universiteit, Department of Medical Oncology, 1081 HV Amsterdam, The Netherlands
| | - Gordon A. Ferns
- Department of Medical Education, Brighton & Sussex Medical School, Falmer, Brighton BN1 9PH, UK;
| | - Jyotsna Batra
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia;
| | - Alfred King-Yin Lam
- Pathology, School of Medicine and Dentistry, Gold Coast Campus, Griffith University, Gold Coast, QLD 4222, Australia;
| | - Elisa Giovannetti
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam UMC, Vrije Universiteit, Department of Medical Oncology, 1081 HV Amsterdam, The Netherlands
- Cancer Pharmacology Laboratory, AIRC Start Up Unit, Fondazione Pisana per La Scienza, 56017 Pisa, Italy
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran (H.A.); (S.M.H.); (F.K.-L.); (M.K.)
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia;
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Nassani R, Bokhari Y, Alrfaei BM. Molecular signature to predict quality of life and survival with glioblastoma using Multiview omics model. PLoS One 2023; 18:e0287448. [PMID: 37972206 PMCID: PMC10653472 DOI: 10.1371/journal.pone.0287448] [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: 02/21/2023] [Accepted: 06/05/2023] [Indexed: 11/19/2023] Open
Abstract
Glioblastoma multiforme (GBM) patients show a variety of signs and symptoms that affect their quality of life (QOL) and self-dependence. Since most existing studies have examined prognostic factors based only on clinical factors, there is a need to consider the value of integrating multi-omics data including gene expression and proteomics with clinical data in identifying significant biomarkers for GBM prognosis. Our research aimed to isolate significant features that differentiate between short-term (≤ 6 months) and long-term (≥ 2 years) GBM survival, and between high Karnofsky performance scores (KPS ≥ 80) and low (KPS ≤ 60), using the iterative random forest (iRF) algorithm. Using the Cancer Genomic Atlas (TCGA) database, we identified 35 molecular features composed of 19 genes and 16 proteins. Our findings propose molecular signatures for predicting GBM prognosis and will improve clinical decisions, GBM management, and drug development.
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Affiliation(s)
- Rayan Nassani
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Yahya Bokhari
- Department of AI and Bioinformatics, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- Department of Health Informatics, College of Public Health and Health Informatics, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Bahauddeen M. Alrfaei
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
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3
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Dang HH, Ta HDK, Nguyen TTT, Wang CY, Lee KH, Le NQK. Identification of a Novel Eight-Gene Risk Model for Predicting Survival in Glioblastoma: A Comprehensive Bioinformatic Analysis. Cancers (Basel) 2023; 15:3899. [PMID: 37568715 PMCID: PMC10417140 DOI: 10.3390/cancers15153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Glioblastoma (GBM) is one of the most progressive and prevalent cancers of the central nervous system. Identifying genetic markers is therefore crucial to predict prognosis and enhance treatment effectiveness in GBM. To this end, we obtained gene expression data of GBM from TCGA and GEO datasets and identified differentially expressed genes (DEGs), which were overlapped and used for survival analysis with univariate Cox regression. Next, the genes' biological significance and potential as immunotherapy candidates were examined using functional enrichment and immune infiltration analysis. Eight prognostic-related DEGs in GBM were identified, namely CRNDE, NRXN3, POPDC3, PTPRN, PTPRN2, SLC46A2, TIMP1, and TNFSF9. The derived risk model showed robustness in identifying patient subgroups with significantly poorer overall survival, as well as those with distinct GBM molecular subtypes and MGMT status. Furthermore, several correlations between the expression of the prognostic genes and immune infiltration cells were discovered. Overall, we propose a survival-derived risk score that can provide prognostic significance and guide therapeutic strategies for patients with GBM.
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Affiliation(s)
- Huy-Hoang Dang
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan; (H.D.K.T.); (C.-Y.W.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Truc Tran Thanh Nguyen
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 115, Taiwan;
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan; (H.D.K.T.); (C.-Y.W.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Kuen-Haur Lee
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 110, Taiwan; (H.D.K.T.); (C.-Y.W.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 110, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- AIBioMed Research Group, Taipei Medical University, Taipei 110, Taiwan
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 110, Taiwan
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
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Hu M, Wei J, Hao J, Jin T, Li B. Impact of TREM1 Variants on the Risk and Prognosis of Glioma in the Chinese Han Population. Pharmgenomics Pers Med 2023; 16:707-715. [PMID: 37426899 PMCID: PMC10327902 DOI: 10.2147/pgpm.s403870] [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] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/21/2023] [Indexed: 07/11/2023] Open
Abstract
Background Glioma is the main pathological subtype of brain tumors with high mortality. Objective This study aimed to elucidate the correlation between TREM1 variants and glioma risk in the Chinese Han population. Methods Genotyping of six variants of TREM1 was completed by Agena MassARRAY platform in 1061 subjects (503 controls and 558 glioma patients). The relationship between TREM1 polymorphisms and glioma risk was calculated using the logistic regression model, with odds ratio (OR) and 95% confidence intervals (CIs). A multifactor dimensionality reduction (MDR) method was performed to assess SNP-SNP interactions to predict glioma risk. Results In this research, overall analysis illustrated an association between TREM1 rs9369269 and an increased risk of glioma. Rs9369269 was also related to the risk of glioma in patients aged ≤40 years and females. Subjects with rs9369269 AC genotype were likely to obtain glioma compared to people with CC genotype (patients with astroglioma vs healthy people). Compared to TT genotype carriers, carriers with AT genotype of rs1351835 were significantly associated with overall survival (OS). Conclusion Taken together, the study identified the association between TREM1 variants and glioma risk and TREM1 variants were significantly associated with the prognosis of glioma. In the future, larger samples are needed to verify the results.
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Affiliation(s)
- Mingjun Hu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Department of Neurosurgery, Xi’an Chang’an District Hospital, Xi’an, Shaanxi Province, People’s Republic of China
| | - Jie Wei
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Jie Hao
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Tianbo Jin
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Bin Li
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi Province, People’s Republic of China
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Dai L, Han Y, Yang Z, Zeng Y, Liang W, Shi Z, Tao Y, Liang X, Liu W, Zhou S, Xing Z, Hu W, Wang X. Identification and validation of SOCS1/2/3/4 as potential prognostic biomarkers and correlate with immune infiltration in glioblastoma. J Cell Mol Med 2023. [PMID: 37315184 PMCID: PMC10399539 DOI: 10.1111/jcmm.17807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/11/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
Suppressor of cytokine signalling (SOCS) 1/2/3/4 are involved in the occurrence and progression of multiple malignancies; however, their prognostic and developmental value in patients with glioblastoma (GBM) remains unclear. The present study used TCGA, ONCOMINE, SangerBox3.0, UALCAN, TIMER2.0, GENEMANIA, TISDB, The Human Protein Atlas (HPA) and other databases to analyse the expression profile, clinical value and prognosis of SOCS1/2/3/4 in GBM, and to explore the potential development mechanism of action of SOCS1/2/3/4 in GBM. The majority of analyses showed that SOCS1/2/3/4 transcription and translation levels in GBM tissues were significantly higher than those in normal tissues. qRT-PCR, western blotting (WB) and immunohistochemical staining were used to verify that SOCS3 was expressed at higher mRNA and protein levels in GBM than in normal tissues or cells. High SOCS1/2/3/4 mRNA expression was associated with poor prognosis in patients with GBM, especially SOCS3. SOCS1/2/3/4 were highly contraindicated, which had few mutations, and were not associated with clinical prognosis. Furthermore, SOCS1/2/3/4 were associated with the infiltration of specific immune cell types. In addition, SOCS3 may affect the prognosis of patients with GBM through JAK/STAT signalling pathway. Analysis of the GBM-specific protein interaction (PPI) network showed that SOCS1/2/3/4 were involved in multiple potential carcinogenic mechanisms of GBM. In addition, colony formation, Transwell, wound healing and western blotting assays revealed that inhibition of SOCS3 decreased the proliferation, migration and invasion of GBM cells. In conclusion, the present study elucidated the expression profile and prognostic value of SOCS1/2/3/4 in GBM, which may provide potential prognostic biomarkers and therapeutic targets for GBM, especially SOCS3.
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Affiliation(s)
- Lirui Dai
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yongjie Han
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zhuo Yang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yuling Zeng
- Department of Blood Transfusion, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wulong Liang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zimin Shi
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yiran Tao
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Xianyin Liang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Wanqing Liu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Shaolong Zhou
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Weihua Hu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Xinjun Wang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
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Zhao N, Xu H. Pan-cancer analysis of aldolase B gene as a novel prognostic biomarker for human cancers. Medicine (Baltimore) 2023; 102:e33577. [PMID: 37083815 PMCID: PMC10118374 DOI: 10.1097/md.0000000000033577] [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: 11/21/2022] [Accepted: 03/30/2023] [Indexed: 04/22/2023] Open
Abstract
Aldolase B (ALDOB) gene is essential for the process of glycolysis and differentially expressed in cancers. The aims of this study were to explore the potential role of ALDOB in pan-cancer, in order to deepen the research on the pathological mechanism of cancer. Hence, we used several online tools (TIMER2, GEPIA2, UALCAN, cBioPortal, and MXPRESS) and R language to identify the correlation between the ALDOB expression and survival analysis, genetic alteration, DNA methylation, and immune cell infiltration based on The Cancer Genome Atlas project. The results showed that ALDOB was lowly expressed in pan-cancer. Survival analysis revealed that low expression of ALDOB was markedly related with poor clinical prognosis, while the genetic alteration within ALDOB changed along with the difference of overall survival (OS) and disease-free survival (DFS) prognosis in several cancers. A possible relationship between DNA methylation and ALDOB expression for several tumors was found. Besides, ALDOB expression was confirmed to be associated with tumor immune cell infiltration, especially in breast invasive carcinoma (BRCA), esophageal carcinoma (ESCA), and testicular germ cell tumors (TGCT) cases. Further, the enrichment analysis demonstrated that metabolic pathway was closely related to ALDOB expression. Our results provide a comprehensive pan-cancer analysis and suggest ALDOB could act as a promising tumor predictive biomarker for human cancer.
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Affiliation(s)
- Nannan Zhao
- School of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, China
| | - Haixu Xu
- School of Food and Biology Engineering, Xuzhou University of Technology, Xuzhou, China
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7
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Liu X, Xie F, Ding J, Li S, Li J. Systematic pan-cancer analysis identifies gasdermin B as an immunological and prognostic biomarker for kidney renal clear cell carcinoma. Front Oncol 2023; 13:1164214. [PMID: 37064151 PMCID: PMC10101337 DOI: 10.3389/fonc.2023.1164214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
Gasdermin (GSDM)-mediated cell lytic death plays an essential role in immunity and tumorigenesis. Despite the association of gasdermin B (GSDMB) with the tumorigenesis of various cancers, whether GSDMB functions as a prognostic biomarker in renal cell carcinoma remains poorly understood. Here, we explored the potential immunological functions and the prognostic value of GSDMB across multiple tumors with The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, including analyzing the relationship between GSDMB expression and prognosis, tumor–immune system interactions, immunomodulators, and immune cell infiltration of different tumors. Importantly, elevated expression of GSDMB is an essential factor for the poor prognosis of kidney renal clear cell carcinoma (KIRC) patients, suggesting that it might be helpful to predict a survival benefit from a clinical therapy regimen. Furthermore, GSDMB expression promoted the level of CD4+ T-cell infiltration of the tumors but is significantly negatively associated with immature dendritic cells (iDCs) in KIRC. Additionally, we identified TNFRSF25 and TNFSF14 as immunostimulators highly correlated with GSDMB expression. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses showed that GSDMB and its interacting proteins might affect tumor growth through the serine metabolism pathway. Our current results demonstrate a promising therapeutic strategy targeting GSDMB and provide new insights into GSDMB as an immunological and prognostic biomarker for KIRC.
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Affiliation(s)
- Xuehe Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
| | - Feiyan Xie
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Suhua Li
- Division of Natural Science, Duke Kunshan University, Jiangsu, China
- *Correspondence: Jixi Li, ; Suhua Li,
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
- *Correspondence: Jixi Li, ; Suhua Li,
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8
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Wadapurkar RM, Sivaram A, Vyas R. RNA-Seq Analysis of Clinical Samples from TCGA Reveal Molecular Signatures for Ovarian Cancer. Cancer Invest 2023; 41:394-404. [PMID: 36797673 DOI: 10.1080/07357907.2023.2182123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Identifying differentially expressed genes and co-expression modules lead to novel biomarkers. GO, pathway enrichment, network, and tumor stage analysis of 318 ovarian cancer samples from TCGA, categorised into primary and recurrent, pre-menopause and post-menopause, and early and late stage tumors was performed. Upregulated and downregulated genes in primary vs recurrent, early stage vs late-stage and pre-menopause vs post-menopause tumors were 84 and 62, 84 and 35, and 88 and 14, respectively. IRAK2 and CXCL8 had higher expression in recurrent tumors while REG1A had higher expression in post-menopause samples. In late stage tumors constant expression of IRAK2 and REG1A was observed, while that of CXCL8 and EGF decreased. These genes may be potential biomarkers for the diagnosis of the disease.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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9
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Dai L, Guo X, Xing Z, Tao Y, Liang W, Shi Z, Hu W, Zhou S, Wang X. Multi-omics analyses of CD276 in pan-cancer reveals its clinical prognostic value in glioblastoma and other major cancer types. BMC Cancer 2023; 23:102. [PMID: 36717836 PMCID: PMC9885708 DOI: 10.1186/s12885-023-10575-1] [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: 10/19/2022] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND CD276 (also known as B7-H3) is one of the most important immune checkpoints of the CD28 and B7 superfamily, and its abnormal expression is closely associated with various types of cancer. It has been shown that CD276 is able to inhibit the function of T cells, and that this gene may potentially be a promising immunotherapy target for different types of cancer. METHODS Since few systematic studies have been published on the role of CD276 in cancer to date, the present study has employed single-cell sequencing and bioinformatics methods to analyze the expression patterns, clinical significance, prognostic value, epigenetic alterations, DNA methylation level, tumor immune cell infiltration and immune functions of CD276 in different types of cancer. In order to analyze the potential underlying mechanism of CD276 in glioblastoma (GBM) to assess its prognostic value, the LinkedOmics database was used to explore the biological function and co-expression pattern of CD276 in GBM, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. In addition, a simple validation of the above analyses was performed using reverse transcription-quantitative (RT-q)PCR assay. RESULTS The results revealed that CD276 was highly expressed, and was often associated with poorer survival and prognosis, in the majority of different types of cancer. In addition, CD276 expression was found to be closely associated with T cell infiltration, immune checkpoint genes and immunoregulatory interactions between lymphoid and a non-lymphoid cell. It was also shown that the CD276 expression network exerts a wide influence on the immune activation of GBM. The expression of CD276 was found to be positively correlated with neutrophil-mediated immunity, although it was negatively correlated with the level of neurotransmitters, neurotransmitter transport and the regulation of neuropeptide signaling pathways in GBM. It is noteworthy that CD276 expression was found to be significantly higher in GBM compared with normal controls according to the RT-qPCR analysis, and the co-expression network, biological function and chemotherapeutic drug sensitivity of CD276 in GBM were further explored. In conclusion, the findings of the present study have revealed that CD276 is strongly expressed and associated with poor prognosis in most types of cancer, including GBM, and its expression is strongly associated with T-cell infiltration, immune checkpoint genes, and immunomodulatory interactions between lymphocytes and non-lymphoid cells. CONCLUSIONS Taken together, based on our systematic analysis, our findings have revealed important roles for CD276 in different types of cancers, especially GBM, and CD276 may potentially serve as a biomarker for cancer.
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Affiliation(s)
- Lirui Dai
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Xuyang Guo
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Zhe Xing
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Yiran Tao
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Wulong Liang
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Zimin Shi
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Weihua Hu
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Shaolong Zhou
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
| | - Xinjun Wang
- grid.460069.dDepartment of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Institute of Neuroscience, Zhengzhou University, Zhengzhou, 450052 China ,Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan China
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Liu S, Miao M, Kang L. Upregulation of MAD2L1 mediated by ncRNA axis is associated with poor prognosis and tumor immune infiltration in hepatocellular carcinoma: A review. Medicine (Baltimore) 2023; 102:e32625. [PMID: 36637946 PMCID: PMC9839239 DOI: 10.1097/md.0000000000032625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The mortality rate and prognosis of patients with hepatocellular carcinoma (HCC) are well known. A variety of highly malignant human cancers express mitotic arrest deficient 2 like 1 (MAD2L1), a transcription factor that plays a critical role in their development and progression. However, MAD2L1's particular mechanisms and effects on HCC remain uncertain. METHODS We performed a pan-cancer analysis for MAD2L1 prognosis and expression using The Cancer Genome Atlas and Genotype-Tissue Expression data in the present study. MAD2L1 may act as an oncogene in HCC, and a combination of in silico analyses, including expression, survival, and correlation analyses, were performed to identify non-coding ribonucleic acids (ncRNAs) that contribute to MAD2L1 overexpression. RESULTS In conclusion, MAD2L1 is most likely regulated by HCP5/miRNA-139-5p/MAD2L1 in HCC based on its upstream ncRNA-related pathway. A significant positive association was also found between MAD2L1 levels and tumor immune cell infiltration, immune cell biomarkers, and immune checkpoint expression. CONCLUSION Our findings demonstrate that ncRNA-mediated upregulation of MAD2L1 in HCC is closely related to poor prognosis and tumor infiltration.
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Affiliation(s)
- Sizhe Liu
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Mingsan Miao
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
- * Correspondence: Mingsan Miao, School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, No. 156, Jinshuidong Road, Zhengzhou, Henan 450046, China (e-mail: )
| | - Le Kang
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
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11
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Hu LM, Ou XH, Shi SY. A comprehensive analysis of G-protein-signaling modulator 2 as a prognostic and diagnostic marker for pan-cancer. Front Genet 2022; 13:984714. [PMID: 36186420 PMCID: PMC9523219 DOI: 10.3389/fgene.2022.984714] [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: 07/02/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Background: G-protein signaling modulator 2 (GPSM2) maintains cell polarization and regulates the cell cycle. Recent studies have shown that it is highly expressed in various tumors, but its pan-cancer analysis has not been reported.Methods: First, we analyzed the differential GPSM2 expression in normal and cancer tissues by the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) and Human Protein Atlas databases and investigated its expression effect on the survival of cancer patients by gene expression profiling interactive analysis 2 (GEPIA2). Second, we analyzed the GPSM2 phosphorylation level using the clinical proteomic tumor analysis consortium dataset. In addition, we investigated GPSM2 gene mutations in human tumor specimens and the impact of gene mutations on patient survival. Finally, we analyzed the relationship between GPSM2 expression and cellular immune infiltration through the TIMER 2.0 database. Meanwhile, the possible signaling pathway of the gene was analyzed by the Gene Ontology (GO)| Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway to explore its potential mechanism.Results:GPSM2 is overexpressed in most cancers, which leads to reduced overall survival (OS) and disease-free survival in patients. The results of phosphorylation analysis suggest that tumor development involves a complex GPSM2 phosphorylation process. We identified GPSM2 mutation loci with the highest frequency of mutations in uterine corpus endometrial carcinoma (UCEC), and this mutation increased progression-free survival and overall survival in uterine corpus endometrial carcinoma patients. Finally, we found that the role of GPSM2 in tumors may be associated with cellular immune infiltration. Gene Ontology|KEGG pathway analysis showed that the enrichment pathways were mainly “mitotic nuclear division,” “chromosome segregation,” and “spindle.”Conclusions: Our pan-cancer analysis provides a comprehensive overview of the oncogenic roles and potential mechanisms of GPSM2 in multiple human cancers.
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Wang Z, He Z, Xuan Q, Zhang Y, Xu J, Lin J, Li H, Chen W, Jiang T. Analysis of the potential ferroptosis mechanism and multitemporal expression change of central ferroptosis-related genes in cardiac ischemia–reperfusion injury. Front Physiol 2022; 13:934901. [PMID: 36091399 PMCID: PMC9461145 DOI: 10.3389/fphys.2022.934901] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/29/2022] [Indexed: 12/15/2022] Open
Abstract
Acute myocardial infraction is the most severe type of coronary artery disease and remains a substantial burden to the health care system globally. Although myocardial reperfusion is critical for ischemic cardiac tissue survival, the reperfusion itself could cause paradoxical injury. This paradoxical phenomenon is known as ischemia–reperfusion injury (IRI), and the exact molecular mechanism of IRI is still far from being elucidated and is a topic of controversy. Meanwhile, ferroptosis is a nonapoptotic form of cell death that has been reported to be associated with various cardiovascular diseases. Thus, we explored the potential ferroptosis mechanism and target in cardiac IRI via bioinformatics analysis and experiment. GSE4105 data were obtained from the GEO database and consist of a rat IRI model and control. After identifying differentially expressed ferroptosis-related genes (DEFRGs) and hub genes of cardiac IRI, we performed enrichment analysis, coexpression analysis, drug–gene interaction prediction, and mRNA–miRNA regulatory network construction. Moreover, we validated and explored the multitemporal expression of hub genes in a hypoxia/reoxygenation (H/R)-induced H9C2 cell injury model under different conditions via RT-qPCR. A total of 43 DEFRGs and 7 hub genes (tumor protein p53 [Tp53], tumor necrosis factor [Tnf], hypoxia-inducible factor 1 subunit alpha [Hif1a], interleukin 6 [Il6], heme oxygenase 1 [Hmox1], X-box binding protein 1 [Xbp1], and caspase 8 [Casp8]) were screened based on bioinformatics analysis. The functional annotation of these genes revealed apoptosis, and the related signaling pathways could have association with the pathogenesis of ferroptosis in cardiac IRI. In addition, the expression of the seven hub genes in IRI models were found higher than that of control under different H/R conditions and time points. In conclusion, the analysis of 43 DEFRGs and 7 hub genes could reveal the potential biological pathway and mechanism of ferroptosis in cardiac IRI. In addition, the multitemporal expression change of hub genes in H9C2 cells under different H/R conditions could provide clues for further ferroptosis mechanism exploring, and the seven hub genes could be potential biomarkers or therapeutic targets in cardiac IRI.
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Affiliation(s)
- Zuoxiang Wang
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Medicine, Soochow University, Suzhou, Jiangsu, China
| | - Zhisong He
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qinkao Xuan
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yue Zhang
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jialiang Xu
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jia Lin
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hongxia Li
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Weixiang Chen
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- *Correspondence: Weixiang Chen, ; Tingbo Jiang,
| | - Tingbo Jiang
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- *Correspondence: Weixiang Chen, ; Tingbo Jiang,
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13
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Liao L, Gao Y, Su J, Feng Y. By characterizing metabolic and immune microenvironment reveal potential prognostic markers in the development of colorectal cancer. Front Bioeng Biotechnol 2022; 10:822835. [PMID: 35992347 PMCID: PMC9390973 DOI: 10.3389/fbioe.2022.822835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Colon adenocarcinoma (COAD) is one of the deadliest cancers in the world and survival rates vary significantly between early and advanced stage patients. Therefore, the identification of the pathogenesis in the development of COAD and prognostic markers is urgently demanded. Herein, we collected RNA-seq and somatic mutation data of COAD for statistical analysis. Clinical stage-specific differentially expressed genes (DEGs) and tumor development-dependent DEGs were identified. By characterizing the metabolic and immune features of COAD between stages, we found that the energy supply and inflammatory response of advanced tumors were suppressed. Next, the ETS1, AR, GATA1, GATA2, SREBF1, FOXP3, STAT4, and NFKB1 were identified to drive the metabolic and immune-related pathways in the development of COAD. The three potential prognostic markers (HOXC8, IRF7, and CXCL13) were identified based on Cox regression analysis. Additionally, immune infiltration analysis revealed that the resting CD4+ T cell was significantly related to the overall survival (OS) of COAD patients. Collectively, the specific metabolic and immune characteristics of advanced patients and the identified prognostic biomarkers will contribute to the development of precision medicine.
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Affiliation(s)
- Liangliang Liao
- China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yongjian Gao
- China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jie Su
- The First Hospital of Jilin University, Changchun, China
| | - Ye Feng
- China-Japan Union Hospital of Jilin University, Changchun, China
- *Correspondence: Ye Feng,
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Gao W, Li Y, Zhang T, Lu J, Pan J, Qi Q, Dong S, Chen X, Su Z, Li J. Systematic Analysis of Chemokines Reveals CCL18 is a Prognostic Biomarker in Glioblastoma. J Inflamm Res 2022; 15:2731-2743. [PMID: 35509325 PMCID: PMC9059990 DOI: 10.2147/jir.s357787] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/12/2022] [Indexed: 12/30/2022] Open
Abstract
Background Glioblastoma (GBM) is the most common and aggressive brain tumor in adults, in which chemokines are often upregulated and may play pivotal roles in their development and progression. Chemokines are a large subfamily of cytokines with leukocyte chemotactic activities involved in various tumor progression. However, gene expression patterns of the chemokines on a global scale were not known in GBM. Methods Differentially expressed chemokine genes in glioma and normal samples were screened by using The Cancer Genome Atlas (TCGA) database. Cox regression identified the prognosis-related genes in each glioma subtype. The protein expression levels of chemokines in 72 glioma tissues were detected by ELISA. Results We found that the transcripts of seven chemokines, including CCL2, CCL8, CCL18, CCL28, CXCL1, CXCL5, and CXCL13, were highly expressed in GBM that evidenced by involving immune cell infiltration regulation and accompanied with worse outcomes of GBM patients. The prognostic nomogram construction demonstrated that CCL18 held the highest risk score in patients with GBM. Furthermore, experiments on 72 glioma tissue samples confirmed that CCL18 protein expression was positively associated with tumor grade and IDH1 status but inversely with glioma patients’ overall survival (OS). Conclusion Our study reveals comprehensive and comparable roles of chemokine members in glioblastoma, and identified CCL18 as a critical driver of GBM malignant behaviors, therefore providing a potential target for developing prognosis and therapy in human glioblastoma.
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Affiliation(s)
- Wenqing Gao
- State Key Laboratory of Genetic Engineering, Department of Neurology, Huashan Hospital and Institute of Neurology, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, People's Republic of China
| | - Yuanyuan Li
- State Key Laboratory of Genetic Engineering, Department of Neurology, Huashan Hospital and Institute of Neurology, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, People's Republic of China
| | - Teng Zhang
- State Key Laboratory of Genetic Engineering, Department of Neurology, Huashan Hospital and Institute of Neurology, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, People's Republic of China
| | - Jianglong Lu
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, People's Republic of China
| | - Jiasong Pan
- State Key Laboratory of Genetic Engineering, Department of Neurology, Huashan Hospital and Institute of Neurology, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, People's Republic of China
| | - Qi Qi
- State Key Laboratory of Genetic Engineering, Department of Neurology, Huashan Hospital and Institute of Neurology, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, People's Republic of China
| | - Siqi Dong
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040, People's Republic of China
| | - Xiangjun Chen
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, Shanghai, 200040, People's Republic of China.,National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, 200040, People's Republic of China
| | - Zhipeng Su
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, People's Republic of China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Department of Neurology, Huashan Hospital and Institute of Neurology, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, People's Republic of China.,National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, 200040, People's Republic of China
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Zhang W, Zhang Q, Che L, Xie Z, Cai X, Gong L, Li Z, Liu D, Liu S. Using biological information to analyze potential miRNA-mRNA regulatory networks in the plasma of patients with non-small cell lung cancer. BMC Cancer 2022; 22:299. [PMID: 35313857 PMCID: PMC8939143 DOI: 10.1186/s12885-022-09281-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Background Lung cancer is the most common malignant tumor, and it has a high mortality rate. However, the study of miRNA-mRNA regulatory networks in the plasma of patients with non-small cell lung cancer (NSCLC) is insufficient. Therefore, this study explored the differential expression of mRNA and miRNA in the plasma of NSCLC patients. Methods The Gene Expression Omnibus (GEO) database was used to download microarray datasets, and the differentially expressed miRNAs (DEMs) were analyzed. We predicted transcription factors and target genes of the DEMs by using FunRich software and the TargetScanHuman database, respectively. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used for GO annotation and KEGG enrichment analysis of downstream target genes. We constructed protein-protein interaction (PPI) and DEM-hub gene networks using the STRING database and Cytoscape software. The GSE20189 dataset was used to screen out the key hub gene. Using The Cancer Genome Atlas (TCGA) and UALCAN databases to analyze the expression and prognosis of the key hub gene and DEMs. Then, GSE17681 and GSE137140 datasets were used to validate DEMs expression. Finally, the receiver operating characteristic (ROC) curve was used to verify the ability of the DEMs to distinguish lung cancer patients from healthy patients. Results Four upregulated candidate DEMs (hsa-miR199a-5p, hsa-miR-186-5p, hsa-miR-328-3p, and hsa-let-7d-3p) were screened from 3 databases, and 6 upstream transcription factors and 2253 downstream target genes were predicted. These genes were mainly enriched in cancer pathways and PI3k-Akt pathways. Among the top 30 hub genes, the expression of KLHL3 was consistent with the GSE20189 dataset. Except for let-7d-3p, the expression of other DEMs and KLHL3 in tissues were consistent with those in plasma. LUSC patients with high let-7d-3p expression had poor overall survival rates (OS). External validation demonstrated that the expression of hsa-miR-199a-5p and hsa-miR-186-5p in peripheral blood of NSCLC patients was higher than the healthy controls. The ROC curve confirmed that the DEMs could better distinguish lung cancer patients from healthy people. Conclusion The results showed that miR-199a-5p and miR-186-5p may be noninvasive diagnostic biomarkers for NSCLC patients. MiR-199a-5p-KLHL3 may be involved in the occurrence and development of NSCLC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09281-1.
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Affiliation(s)
- Wei Zhang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China.,Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), No. 98, Fenghuang Road North, Zunyi, 563000, Guizhou, China
| | - Qian Zhang
- Department of Renal Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China
| | - Li Che
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China
| | - Zhefan Xie
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China
| | - Xingdong Cai
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China
| | - Ling Gong
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China.,Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), No. 98, Fenghuang Road North, Zunyi, 563000, Guizhou, China
| | - Zhu Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), No. 98, Fenghuang Road North, Zunyi, 563000, Guizhou, China
| | - Daishun Liu
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), No. 98, Fenghuang Road North, Zunyi, 563000, Guizhou, China.
| | - Shengming Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, No. 613, Huangpu Road West, Tianhe District, Guangzhou, 510630, China.
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Identification of MAD2L1 as a Potential Biomarker in Hepatocellular Carcinoma via Comprehensive Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9868022. [PMID: 35132379 PMCID: PMC8817109 DOI: 10.1155/2022/9868022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/19/2021] [Accepted: 01/15/2022] [Indexed: 11/17/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is widely acknowledged as a malignant tumor with rapid progression, high recurrence rate, and poor prognosis. At present, there is a paucity of reliable biomarkers at the clinical level to guide the management of HCC and improve patient outcomes. Our research is aimed at assessing the prognostic value of MAD2L1 in HCC. Methods Four datasets, GSE121248, GSE101685, GSE85598, and GSE62232, were selected from the GEO database to analyze differentially expressed genes (DEGs) between HCC and normal liver tissues. After functional analysis, we constructed a protein-protein interaction network (PPI) for DEGs and identified core genes in this network with high connectivity with other genes. We assessed the relationship between core genes and the pathogenesis and prognosis of HCC. Finally, we explored the gene regulatory signaling mechanisms involved in HCC pathogenesis. Results 145 DEGs were screened from the intersection of the four GEO datasets. MAD2L1 was associated with most genes according to the PPI network and was selected as a candidate gene for further study. Survival analysis suggested that high MAD2L1 expression in HCC correlated with a worse prognosis. In addition, real-time quantitative PCR (RT-qPCR), western blot (WB), and immunohistochemistry (IHC) findings suggested that the expression of MAD2L1 was abnormally increased in HCC tissues and cells compared to paraneoplastic tissues and normal hepatocytes. Conclusion We found that high MAD2L1 expression in HCC was significantly associated with overall patient survival and clinical features. We also explored the potential biological properties of this gene.
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