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Sheng S, Chen B, Xu R, Han Y, Mao D, Chen Y, Li C, Su W, Hu X, Zhao Q, Lowe S, Huang Y, Shao W, Yao Y. A prognostic model for Schistosoma japonicum infection-associated liver hepatocellular carcinoma: strengthening the connection through initial biological experiments. Infect Agent Cancer 2024; 19:10. [PMID: 38515119 PMCID: PMC10956344 DOI: 10.1186/s13027-024-00569-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Numerous studies have shown that Schistosoma japonicum infection correlates with an increased risk of liver hepatocellular carcinoma (LIHC). However, data regarding the role of this infection in LIHC oncogenesis are scarce. This study aimed to investigate the potential mechanisms of hepatocarcinogenesis associated with Schistosoma japonicum infection. METHODS By examining chronic liver disease as a mediator, we identified the genes contributing to Schistosoma japonicum infection and LIHC. We selected 15 key differentially expressed genes (DEGs) using weighted gene co-expression network analysis (WGCNA) and random survival forest models. Consensus clustering revealed two subgroups with distinct prognoses. Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression identified six prognostic DEGs, forming an Schistosoma japonicum infection-associated signature for strong prognosis prediction. This signature, which is an independent LIHC risk factor, was significantly correlated with clinical variables. Four DEGs, including BMI1, were selected based on their protein expression levels in cancerous and normal tissues. We confirmed BMI1's role in LIHC using Schistosoma japonicum-infected mouse models and molecular experiments. RESULTS We identified a series of DEGs that mediate schistosomiasis, the parasitic disease caused by Schistosoma japonicum infection, and hepatocarcinogenesis, and constructed a suitable prognostic model. We analyzed the mechanisms by which these DEGs regulate disease and present the differences in prognosis between the different genotypes. Finally, we verified our findings using molecular biology experiments. CONCLUSION Bioinformatics and molecular biology analyses confirmed a relationship between schistosomiasis and liver hepatocellular cancer. Furthermore, we validated the role of a potential oncoprotein factor that may be associated with infection and carcinogenesis. These findings enhance our understanding of Schistosoma japonicum infection's role in LIHC carcinogenesis.
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Affiliation(s)
- Shuyan Sheng
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, 230032, China
| | - Bangjie Chen
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, 230032, China
| | - Ruiyao Xu
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Yanxun Han
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, 230032, China
| | - Deshen Mao
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, 230032, China
| | - Yuerong Chen
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, 230032, China
| | - Conghan Li
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, 230032, China
| | - Wenzhuo Su
- Second Clinical Medical College, Anhui Medical University, Hefei, 230032, China
| | - Xinyang Hu
- First Clinical Medical College (First Affiliated Hospital), Anhui Medical University, Hefei, 230032, China
| | - Qing Zhao
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Scott Lowe
- College of Osteopathic Medicine, Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
| | - Yuting Huang
- Division of Gastroenterology and Hepatology, Mayo Clinic in Florida, Jacksonville, FL, USA
| | - Wei Shao
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.
| | - Yong Yao
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China.
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He X, Chen X, Yang C, Wang W, Sun H, Wang J, Fu J, Dong H. Prognostic value of RNA methylation-related genes in gastric adenocarcinoma based on bioinformatics. PeerJ 2024; 12:e16951. [PMID: 38436027 PMCID: PMC10909369 DOI: 10.7717/peerj.16951] [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: 07/06/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024] Open
Abstract
Background Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer. Methods In this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR). Results In total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics. Conclusion Our study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy.
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Affiliation(s)
- Xionghui He
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Xiang Chen
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Changcheng Yang
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Wei Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Hening Sun
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Junjie Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Jincheng Fu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
| | - Huaying Dong
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Medical College, HaiNan, HaiKou, China
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Yuan Y, Zhang XF, Li YC, Chen HQ, Wen T, Zheng JL, Zhao ZY, Hu QY. VX-509 attenuates the stemness characteristics of colorectal cancer stem-like cells by regulating the epithelial-mesenchymal transition through Nodal/Smad2/3 signaling. World J Stem Cells 2024; 16:207-227. [PMID: 38455101 PMCID: PMC10915959 DOI: 10.4252/wjsc.v16.i2.207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/19/2023] [Accepted: 01/16/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Colorectal cancer stem cells (CCSCs) are heterogeneous cells that can self-renew and undergo multidirectional differentiation in colorectal cancer (CRC) patients. CCSCs are generally accepted to be important sources of CRC and are responsible for the progression, metastasis, and therapeutic resistance of CRC. Therefore, targeting this specific subpopulation has been recognized as a promising strategy for overcoming CRC. AIM To investigate the effect of VX-509 on CCSCs and elucidate the underlying mechanism. METHODS CCSCs were enriched from CRC cell lines by in conditioned serum-free medium. Western blot, Aldefluor, transwell and tumorigenesis assays were performed to verify the phenotypic characteristics of the CCSCs. The anticancer efficacy of VX-509 was assessed in HCT116 CCSCs and HT29 CCSCs by performing cell viability analysis, colony formation, sphere formation, flow cytometry, and western blotting assessments in vitro and tumor growth, immunohistochemistry and immunofluorescence assessments in vivo. RESULTS Compared with parental cells, sphere cells derived from HCT116 and HT29 cells presented increased expression of stem cell transcription factors and stem cell markers and were more potent at promoting migration and tumorigenesis, demonstrating that the CRC sphere cells displayed CSC features. VX-509 inhibited the tumor malignant biological behavior of CRC-stem-like cells, as indicated by their proliferation, migration and clonality in vitro, and suppressed the tumor of CCSC-derived xenograft tumors in vivo. Besides, VX-509 suppressed the CSC characteristics of CRC-stem-like cells and inhibited the progression of epithelial-mesenchymal transition (EMT) signaling in vitro. Nodal was identified as the regulatory factor of VX-509 on CRC stem-like cells through analyses of differentially expressed genes and CSC-related database information. VX-509 markedly downregulated the expression of Nodal and its downstream phosphorylated Smad2/3 to inhibit EMT progression. Moreover, VX-509 reversed the dedifferentiation of CCSCs and inhibited the progression of EMT induced by Nodal overexpression. CONCLUSION VX-509 prevents the EMT process in CCSCs by inhibiting the transcription and protein expression of Nodal, and inhibits the dedifferentiated self-renewal of CCSCs.
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Affiliation(s)
- Yun Yuan
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan Province, China
| | - Xu-Fan Zhang
- Department of Nuclear Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan Province, China
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan Province, China
| | - Yu-Chen Li
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan Province, China
| | - Hong-Qing Chen
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan Province, China
| | - Tian Wen
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan Province, China
| | - Jia-Lian Zheng
- Department of Hepatology, Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang 110032, Liaoning Province, China
| | - Zi-Yi Zhao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan Province, China
- Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Chengdu 610072, Sichuan Province, China
| | - Qiong-Ying Hu
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, Sichuan Province, China.
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Chatterjee D, Mou SI, Sultana T, Hosen MI, Faruk MO. Identification and validation of prognostic signature genes of bladder cancer by integrating methylation and transcriptomic analysis. Sci Rep 2024; 14:368. [PMID: 38172584 PMCID: PMC10764961 DOI: 10.1038/s41598-023-50740-x] [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: 11/05/2023] [Accepted: 12/24/2023] [Indexed: 01/05/2024] Open
Abstract
Being a frequent malignant tumor of the genitourinary system, Bladder Urothelial Carcinoma (BLCA) has a poor prognosis. This study focused on identifying and validating prognostic biomarkers utilizing methylation, transcriptomics, and clinical data from The Cancer Genome Atlas Bladder Urothelial Carcinoma (TCGA BLCA) cohort. The impact of altered differentially methylated hallmark pathway genes was subjected to clustering analysis to observe changes in the transcriptional landscape on BLCA patients and identify two subtypes of patients from the TCGA BLCA population where Subtype 2 was associated with the worst prognosis with a p-value of 0.00032. Differential expression and enrichment analysis showed that subtype 2 was enriched in immune-responsive and cancer-progressive pathways, whereas subtype 1 was enriched in biosynthetic pathways. Following, regression and network analyses revealed Epidermal Growth Factor Receptor (EGFR), Fos-related antigen 1 (FOSL1), Nuclear Factor Erythroid 2 (NFE2), ADP-ribosylation factor-like protein 4D (ARL4D), SH3 domain containing ring finger 2 (SH3RF2), and Cadherin 3 (CDH3) genes to be the most significant prognostic gene markers. These genes were used to construct a risk model that separated the BLCA patients into high and low-risk groups. The risk model was also validated in an external dataset by performing survival analysis between high and low-risk groups with a p-value < 0.001 and the result showed the high group was significantly associated with poor prognosis compared to the low group. Single-cell analyses revealed the elevated level of these genes in the tumor microenvironment and associated with immune response. High-grade patients also tend to have a high expression of these genes compared to low-grade patients. In conclusion, this research developed a six-gene signature that is pertinent to the prediction of overall survival (OS) and might contribute to the advancement of precision medicine in the management of bladder cancer.
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Affiliation(s)
- Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sadia Islam Mou
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Tamanna Sultana
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Md Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Md Omar Faruk
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh.
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Shen X, Su Z, Dou Y, Song X. A novel investigation into an E2F transcription factor-related prognostic model with seven signatures for colon cancer patients. IET Syst Biol 2023; 17:187-197. [PMID: 37431829 PMCID: PMC10439494 DOI: 10.1049/syb2.12069] [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: 01/13/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/12/2023] Open
Abstract
The pathogenesis of colon cancer, a common gastrointestinal tumour, involves complicated factors, especially a series of cell cycle-related genes. E2F transcription factors during the cell cycle play an essential role in the occurrence of colon cancer. It is meaningful to establish an efficient prognostic model of colon cancer targeting cellular E2F-associated genes. This has not been reported previously. The authors first aimed to explore the links of E2F genes with the clinical outcomes of colon cancer patients by integrating data from the TCGA-COAD (n = 521), GSE17536 (n = 177) and GSE39582 (n = 585) cohorts. The Cox regression and Lasso modelling approach to identify a novel colon cancer prognostic model involving several hub genes (CDKN2A, GSPT1, PNN, POLD3, PPP1R8, PTTG1 and RFC1) were utilised. Moreover, an E2F-related nomogram that efficiently predicted the survival rates of colon cancer patients was created. Additionally, the authors first identified two E2F tumour clusters, which showed distinct prognostic features. Interestingly, the potential links of E2F-based classification and 'protein secretion' issues of multiorgans and tumour infiltration of 'T-cell regulatory (Tregs)' and 'CD56dim natural killer cell' were detected. The authors' findings are of potential clinical significance for the prognosis assessment and mechanistic exploration of colon cancer.
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Affiliation(s)
- Xiaoyong Shen
- National Demonstration Center for Experimental Basic Medicine EducationSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Zheng Su
- National Demonstration Center for Experimental Basic Medicine EducationSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Yan Dou
- National Demonstration Center for Experimental Basic Medicine EducationSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Xin Song
- National Demonstration Center for Experimental Basic Medicine EducationSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
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Zheng Z, Li H, Yang R, Guo H. Role of the membrane-spanning 4A gene family in lung adenocarcinoma. Front Genet 2023; 14:1162787. [PMID: 37533433 PMCID: PMC10390740 DOI: 10.3389/fgene.2023.1162787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023] Open
Abstract
Lung adenocarcinoma, which is the second most prevalent cancer in the world, has a poor prognosis and a low 5-year survival rate. The MS4A protein family is crucial to disease development and progression, particularly for cancers, allergies, metabolic disorders, autoimmune diseases, infections, and neurodegenerative disorders. However, its involvement in lung adenocarcinoma remains unclear. In this study, we found that 11 MS4A family genes were upregulated or downregulated in lung adenocarcinoma. Furthermore, we described the genetic variation landscape of the MS4A family in lung adenocarcinoma. Notably, through functional enrichment analysis, we discovered that the MS4A family is involved in the immune response regulatory signaling pathway and the immune response regulatory cell surface receptor signaling pathway. According to the Kaplan-Meier curve, patients with lung adenocarcinoma having poor expression of MS4A2, MS4A7, MS4A14, and MS4A15 had a low overall survival rate. These four prognostic genes are substantially associated with immune-infiltrating cells, and a prognosis model incorporating them may more accurately predict the overall survival rate of patients with lung adenocarcinoma than current models. The findings of this study may offer creative suggestions and recommendations for the identification and management of lung adenocarcinoma.
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Boo HJ, Min HY, Park CS, Park JS, Jeong JY, Lee SY, Kim WY, Lee JW, Oh SR, Park RW, Lee HY. Dual Impact of IGF2 on Alveolar Stem Cell Function during Tobacco-Induced Injury Repair and Development of Pulmonary Emphysema and Cancer. Cancer Res 2023; 83:1782-1799. [PMID: 36971490 DOI: 10.1158/0008-5472.can-22-3543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/23/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Pulmonary emphysema is a destructive inflammatory disease primarily caused by cigarette smoking (CS). Recovery from CS-induced injury requires proper stem cell (SC) activities with a tightly controlled balance of proliferation and differentiation. Here we show that acute alveolar injury induced by two representative tobacco carcinogens, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone and benzo[a]pyrene (N/B), increased IGF2 expression in alveolar type 2 (AT2) cells to promote their SC function and facilitate alveolar regeneration. Autocrine IGF2 signaling upregulated Wnt genes, particularly Wnt3, to stimulate AT2 proliferation and alveolar barrier regeneration after N/B-induced acute injury. In contrast, repetitive N/B exposure provoked sustained IGF2-Wnt signaling through DNMT3A-mediated epigenetic control of IGF2 expression, causing a proliferation/differentiation imbalance in AT2s and development of emphysema and cancer. Hypermethylation of the IGF2 promoter and overexpression of DNMT3A, IGF2, and the Wnt target gene AXIN2 were seen in the lungs of patients with CS-associated emphysema and cancer. Pharmacologic or genetic approaches targeting IGF2-Wnt signaling or DNMT prevented the development of N/B-induced pulmonary diseases. These findings support dual roles of AT2 cells, which can either stimulate alveolar repair or promote emphysema and cancer depending on IGF2 expression levels. SIGNIFICANCE IGF2-Wnt signaling plays a key role in AT2-mediated alveolar repair after cigarette smoking-induced injury but also drives pathogenesis of pulmonary emphysema and cancer when hyperactivated.
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Affiliation(s)
- Hye-Jin Boo
- Creative Research Initiative Center for Concurrent Control of Emphysema and Lung Cancer, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hye-Young Min
- Creative Research Initiative Center for Concurrent Control of Emphysema and Lung Cancer, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Choon-Sik Park
- Soonchunhyang University Bucheon Hospital, Bucheon-si, Gyeonggi-do, Republic of Korea
| | - Jong-Sook Park
- Soonchunhyang University Bucheon Hospital, Bucheon-si, Gyeonggi-do, Republic of Korea
| | - Ji Yun Jeong
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Lung Cancer Center, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea
| | - Woo-Young Kim
- College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Jae-Won Lee
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Sei-Ryang Oh
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Rang-Woon Park
- Department of Biochemistry and Cell Biology, School of Medicine, and Cell and Matrix Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Ho-Young Lee
- Creative Research Initiative Center for Concurrent Control of Emphysema and Lung Cancer, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
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Pan B, Yue Y, Ding W, Sun L, Xu M, Wang S. A novel prognostic signatures based on metastasis- and immune-related gene pairs for colorectal cancer. Front Immunol 2023; 14:1161382. [PMID: 37180113 PMCID: PMC10169605 DOI: 10.3389/fimmu.2023.1161382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023] Open
Abstract
Background Metastasis remains the leading cause of mortality in patients diagnosed with colorectal cancer (CRC). The pivotal contribution of the immune microenvironment in the initiation and progression of CRC metastasis has gained significant attention. Methods A total of 453 CRC patients from The Cancer Genome Atlas (TCGA) were included as the training set, and GSE39582, GSE17536, GSE29621, GSE71187 were included as the validation set. The single-sample gene set enrichment analysis (ssGSEA) was performed to assess the immune infiltration of patients. Least absolute shrinkage and selection operator (LASSO) regression analysis, Time-dependent receiver operating characteristic (ROC) and Kaplan-Meier analysis were used to construct and validate risk models based on R package. CTSW and FABP4-knockout CRC cells were constructed via CRISPR-Cas9 system. Western-blot and Transwell assay were utilized to explore the role of fatty acid binding protein 4 (FABP4) / cathepsin W (CTSW) in CRC metastasis and immunity. Results Based on the normal/tumor, high-/low-immune cell infiltration, and metastatic/non-metastatic group, we identified 161 differentially expressed genes. After random assignment and LASSO regression analysis, a prognostic model containing 3 metastasis- and immune-related gene pairs was constructed and represented good prognostic prediction efficiency in the training set and 4 independent CRC cohorts. According to this model, we clustered patients and found that the high-risk group was associated with stage, T and M stage. In addition, the high-risk group also shown higher immune infiltration and high sensitivity to PARP inhibitors. Further, FABP4 and CTSW derived from the constitutive model were identified to be involved in metastasis and immunity of CRC. Conclusion In conclusion, a validated prognosis predictive model for CRC was constructed. CTSW and FABP4 are potential targets for CRC treatment.
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Affiliation(s)
- Bei Pan
- School of Medicine, Southeast University, Nanjing, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yanzhe Yue
- Division of Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Wenbo Ding
- Division of Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Li Sun
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Laboratory Medicine Center, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mu Xu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Shukui Wang
- School of Medicine, Southeast University, Nanjing, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
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Chatterjee D, Rahman MM, Saha AK, Siam MKS, Sharif Shohan MU. Transcriptomic analysis of esophageal cancer reveals hub genes and networks involved in cancer progression. Comput Biol Med 2023; 159:106944. [PMID: 37075603 DOI: 10.1016/j.compbiomed.2023.106944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/09/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023]
Abstract
Esophageal carcinoma (ESCA) has a 5-year survival rate of fewer than 20%. The study aimed to identify new predictive biomarkers for ESCA through transcriptomics meta-analysis to address the problems of ineffective cancer therapy, lack of efficient diagnostic tools, and costly screening and contribute to developing more efficient cancer screening and treatments by identifying new marker genes. Nine GEO datasets of three kinds of esophageal carcinoma were analyzed, and 20 differentially expressed genes were detected in carcinogenic pathways. Network analysis revealed four hub genes, namely RAR Related Orphan Receptor A (RORA), lysine acetyltransferase 2B (KAT2B), Cell Division Cycle 25B (CDC25B), and Epithelial Cell Transforming 2 (ECT2). Overexpression of RORA, KAT2B, and ECT2 was identified with a bad prognosis. These hub genes modulate immune cell infiltration. These hub genes modulate immune cell infiltration. Although this research needs lab confirmation, we found interesting biomarkers in ESCA that may aid in diagnosis and treatment.
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Affiliation(s)
- Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Mostafijur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Bangladesh
| | - Anik Kumar Saha
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
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Xiong Z, Li W, Luo X, Lin Y, Huang W, Zhang S. Seven bacterial response-related genes are biomarkers for colon cancer. BMC Bioinformatics 2023; 24:103. [PMID: 36941538 PMCID: PMC10026208 DOI: 10.1186/s12859-023-05204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Colon cancer (CC) is a common tumor that causes significant harm to human health. Bacteria play a vital role in cancer biology, particularly the biology of CC. Genes related to bacterial response were seldom used to construct prognosis models. We constructed a bacterial response-related risk model based on three Molecular Signatures Database gene sets to explore new markers for predicting CC prognosis. METHODS The Cancer Genome Atlas (TCGA) colon adenocarcinoma samples were used as the training set, and Gene Expression Omnibus (GEO) databases were used as the test set. Differentially expressed bacterial response-related genes were identified for prognostic gene selection. Univariate Cox regression analysis, least absolute shrinkage and selection operator-penalized Cox regression analysis, and multivariate Cox regression analysis were performed to construct a prognostic risk model. The individual diagnostic effects of genes in the prognostic model were also evaluated. Moreover, differentially expressed long noncoding RNAs (lncRNAs) were identified. Finally, the expression of these genes was validated using quantitative polymerase chain reaction (qPCR) in cell lines and tissues. RESULTS A prognostic signature was constructed based on seven bacterial response genes: LGALS4, RORC, DDIT3, NSUN5, RBCK1, RGL2, and SERPINE1. Patients were assigned a risk score based on the prognostic model, and patients in the TCGA cohort with a high risk score had a poorer prognosis than those with a low risk score; a similar finding was observed in the GEO cohort. These seven prognostic model genes were also independent diagnostic factors. Finally, qPCR validated the differential expression of the seven model genes and two coexpressed lncRNAs (C6orf223 and SLC12A9-AS1) in 27 pairs of CC and normal tissues. Differential expression of LGALS4 and NSUN5 was also verified in cell lines (FHC, COLO320DM, SW480). CONCLUSIONS We created a seven-gene bacterial response-related gene signature that can accurately predict the outcomes of patients with CC. This model can provide valuable insights for personalized treatment.
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Affiliation(s)
- Zuming Xiong
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wenxin Li
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiangrong Luo
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yirong Lin
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wei Huang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Sen Zhang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, No.6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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11
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Miao Y, Yuan Q, Wang C, Feng X, Ren J, Wang C. Comprehensive Characterization of RNA-Binding Proteins in Colon Adenocarcinoma Identifies a Novel Prognostic Signature for Predicting Clinical Outcomes and Immunotherapy Responses Based on Machine Learning. Comb Chem High Throughput Screen 2023; 26:163-182. [PMID: 35379120 DOI: 10.2174/1386207325666220404125228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND RNA-binding proteins (RBPs) are crucial factors that function in the posttranscriptional modification process and are significant in cancer. OBJECTIVE This research aimed for a multigene signature to predict the prognosis and immunotherapy response of patients with colon adenocarcinoma (COAD) based on the expression profile of RNA-binding proteins (RBPs). METHODS COAD samples retrieved from the TCGA and GEO datasets were utilized for a training dataset and a validation dataset. Totally, 14 shared RBP genes with prognostic significance were identified. Non-negative matrix factorization clusters defined by these RBPs could stratify COAD patients into two molecular subtypes. Cox regression analysis and identification of 8-gene signature categorized COAD patients into high- and low-risk populations with significantly different prognosis and immunotherapy responses. RESULTS Our prediction signature was superior to another five well-established prediction models. A nomogram was generated to quantificationally predict the overall survival (OS) rate, validated by calibration curves. Our findings also indicated that high-risk populations possessed an enhanced immune evasion capacity and low-risk populations might benefit immunotherapy, especially for the joint combination of PD-1 and CTLA4 immunosuppressants. DHX15 and LARS2 were detected with significantly different expressions in both datasets, which were further confirmed by qRTPCR and immunohistochemical staining. CONCLUSION Our observations supported an eight-RBP-related signature that could be applied for survival prediction and immunotherapy response of patients with COAD.
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Affiliation(s)
- Ye Miao
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of Neurosurgery, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Chao Wang
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xiaoshi Feng
- Department of Endocrinology, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Jie Ren
- Department of Oncology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Changmiao Wang
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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12
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Zhang G, Zhang K, Zhao Y, Yang Q, Lv X. A novel stemness-hypoxia-related signature for prognostic stratification and immunotherapy response in hepatocellular carcinoma. BMC Cancer 2022; 22:1103. [DOI: 10.1186/s12885-022-10195-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The specific differentiation potential, unlimited proliferation, and self-renewal capacity of cancer stem cells (CSCs) are closely related to the occurrence, recurrence, and drug resistance of hepatocellular carcinoma (HCC), as well as hypoxia. Therefore, an in-depth analysis of the relationship between HCC stemness, oxygenation status, and the effectiveness of immunotherapy is necessary to improve the poor prognosis of HCC patients.
Methods
The weighted gene co-expression network analysis (WGCNA) was utilized to find hypoxia-related genes, and the stemness index (mRNAsi) was evaluated using the one-class logistic regression (OCLR) technique. Based on stemness-hypoxia-related genes (SHRGs), population subgroup categorization using NMF cluster analysis was carried out. The relationship between SHRGs and survival outcomes was determined using univariate Cox regression. The LASSO-Cox regression strategy was performed to investigate the quality and establish the classifier associated with prognosis. The main effect of risk scores on the tumor microenvironment (TME) and its response to immune checkpoint drugs was also examined. Finally, qRT-PCR was performed to explore the expression and prognostic value of the signature in clinical samples.
Results
After identifying tumor stemness- and hypoxia-related genes through a series of bioinformatics analyses, we constructed a prognostic stratification model based on these SHRGs, which can be effectively applied to the prognostic classification of HCC patients and the prediction of immune checkpoint inhibitors (ICIs) efficacy. Independent validation of the model in the ICGC cohort yielded good results. In addition, we also constructed hypoxic cell models in Herp3B and Huh7 cells to verify the expression of genes in the prognostic model and found that C7, CLEC1B, and CXCL6 were not only related to the tumor stemness but also related to hypoxia. Finally, we found that the constructed signature had a good prognostic value in the clinical sample.
Conclusions
We constructed and validated a stemness-hypoxia-related prognostic signature that can be used to predict the efficacy of ICIs therapy. We also verified that C7, CLEC1B, and CXCL6 are indeed associated with stemness and hypoxia through a hypoxic cell model, which may provide new ideas for individualized immunotherapy.
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13
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Zhou R, Gao Z, Ju Y. Novel six-gene prognostic signature based on colon adenocarcinoma immune-related genes. BMC Bioinformatics 2022; 23:418. [PMID: 36221049 PMCID: PMC9552517 DOI: 10.1186/s12859-022-04909-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 12/05/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is one of the most common gastrointestinal tumors worldwide, and immunotherapy is one of the most promising treatments for it. Identifying immune genes involved in the development and maintenance of cancer is key to the use of tumor immunotherapy. This study aimed to determine the prognostic value of immune genes in patients with COAD and to establish an immune-related gene signature. Differentially expressed genes, immune-related genes (DEIGs), and transcription factors (DETFs) were screened using the following databases: Cistrome, The Cancer Genome Atlas (TCGA), the Immunology Database and Analysis Portal, and InnateDB. We constructed a network showing the regulation of DEIGs by DETFs. Using weighted gene co-expression network analysis, we prepared 5 co-expressed gene modules; 6 hub genes (CD1A, CD1B, FGF9, GRP, SERPINE1, and F2RL2) obtained using univariate and multivariate regression analysis were used to construct a risk model. Patients from TCGA database were divided into high- and low-risk groups based on whether their risk score was greater or less than the mean; the public dataset GSE40967, which contains gene expression profiles of 566 colon cancer patients, was used for validation. Results Survival analysis, somatic gene mutations, and tumor-infiltrating immune cells differed significantly between the high- and low-risk groups. Conclusions This immune-related gene signature could play an important role in guiding treatment, making prognoses, and potentially developing future clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04909-2.
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Affiliation(s)
- Rui Zhou
- Surgical Department of Gastrointestinal Surgery, Shunde Hospital of Southern Medical University, No. 1 Jiazi Road, Shunde District, Foshan, 528399, Guangdong, China
| | - Zhuowei Gao
- Medical Department of Traditional Chinese Medicine, Shunde Hospital of Guangzhou University of Traditional Chinese Medicine, No. 12, Jinsha Avenue, Shunde District, Foshan, 510006, Guangdong, China
| | - Yongle Ju
- Surgical Department of Gastrointestinal Surgery, Shunde Hospital of Southern Medical University, No. 1 Jiazi Road, Shunde District, Foshan, 528399, Guangdong, China.
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Cui G, Wang C, Liu J, Shon K, Gu R, Chang C, Ren L, Wei F, Sun Z. Development of an exosome-related and immune microenvironment prognostic signature in colon adenocarcinoma. Front Genet 2022; 13:995644. [PMID: 36176299 PMCID: PMC9513147 DOI: 10.3389/fgene.2022.995644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The correlation between exosomes and the tumor immune microenvironment has been proved to affect tumorigenesis and progression of colon adenocarcinoma (COAD). However, it remained unclear whether exosomes had an impact on the prognostic indications of COAD patients.Methods: Expression of exosome-related genes (ERGs) and clinical data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. The ERGs associated with prognosis were identified and exosome-related prognostic signature was constructed. Patients in two risk groups were classified according to the risk score calculation formula: Risk score = 1.0132 * CCKBR + 0.2416 * HOXC6 + 0.7618 * POU4F1. The expression of three ERGs was investigated by qRT-PCR. After that, we developed a nomogram predicting the likelihood of survival and verified its predictive efficiency. The differences of tumor immune microenvironment, immune cell infiltration, immune checkpoint and sensitivity to drugs in two risk groups were analyzed.Results: A prognostic signature was established based on the three ERGs (CCKBR, HOXC6, and POU4F1) and patients with different risk group were distinguished. Survival analysis revealed the negative associated of risk score and prognosis, ROC curve analyses showed the accuracy of this signature. Three ERGs expression was investigated by qRT-PCR in three colorectal cancer cell lines. Moreover, risk score was positively correlated with tumor mutational burden (TMB), immune activities, microsatellite instability level, the expression of immune checkpoint genes. Meanwhile, the expression level of three ERGs and the risk score were markedly related with the sensitive response to chemotherapy.Conclusion: The novel signature composed of three ERGs with precise predictive capabilities can be used to predict prognosis and provide a promising therapeutic target for improving the efficacy of immunotherapy.
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Affiliation(s)
- Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Can Wang
- Department of Colorectal Surgery, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kinyu Shon
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Fei Wei, ; Zhiguang Sun,
| | - Renjun Gu
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Cheng Chang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Lang Ren
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Fei Wei
- Department of Physiology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Fei Wei, ; Zhiguang Sun,
| | - Zhiguang Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Fei Wei, ; Zhiguang Sun,
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Liang XY, Zhang Y, He YN, Liu XY, Ding ZH, Zhang XD, Dong MY, Du RL. A cancer stem cell associated gene signature for predicting overall survival of hepatocellular carcinoma. Front Genet 2022; 13:888601. [PMID: 36171884 PMCID: PMC9511042 DOI: 10.3389/fgene.2022.888601] [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: 03/03/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most prevalent type of primary liver cancer characterized by high mortality and morbidity rate. The lack of effective treatments and the high frequency of recurrence lead to poor prognosis of patients with HCC. Therefore, it is important to develop robust prediction tools for predicting the prognosis of HCC. Recent studies have shown that cancer stem cells (CSC) participate in HCC progression. The aim of this study was to explore the prognostic value of CSC-related genes and establish a prediction model based on data from The Cancer Genome Atlas (TCGA) database. In this study, 475 CSC-related genes were obtained from the Molecular Signature Database and 160 differentially expressed CSC-related genes in HCC patients were identified using the limma R package in the TCGA database. A total of 79 CSC-related genes were found to be associated with overall survival (OS). Using the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regressions, a 3-gene signature (RAB10, TCOF1, and PSMD14) was constructed. Receiver operating characteristic (ROC) curves and Kaplan-Meier survival curves were constructed to test the prediction performance of the signature. Performance of the signature was validated using the International Cancer Genome Consortium (ICGC) dataset. In addition, immune feature and functional enrichment analyses were carried out to explore the underlying mechanisms. Moreover, a co-expression network was constructed using the weighted gene correlation network analysis (WGCNA) method to select genes significantly associated with risk scores in HCC in the TCGA dataset. The SGO2 gene was found to be significantly associated with risk scores of HCC. In vitro experiments revealed that it can promote HCC cell proliferation. Therefore, SGO2 may be a potential therapeutic target for HCC treatment. The constructed nomogram can help clinicians make decisions about HCC treatment.
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Affiliation(s)
- Xin-Yi Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yue Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ya-Nan He
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xue-Yi Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhi-Hao Ding
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao-Dong Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ming-You Dong
- The Key Laboratory of Molecular Pathology (For Hepatobiliary Diseases) of Guangxi, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Ming-You Dong, ; Run-Lei Du,
| | - Run-Lei Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- *Correspondence: Ming-You Dong, ; Run-Lei Du,
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16
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Li Z, Wang W, Wu J, Ye X. Identification of N7-methylguanosine related signature for prognosis and immunotherapy efficacy prediction in lung adenocarcinoma. Front Med (Lausanne) 2022; 9:962972. [PMID: 36091687 PMCID: PMC9449120 DOI: 10.3389/fmed.2022.962972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundLung adenocarcinoma (LUAD) is one of the most frequent causes of tumor-related mortality worldwide. Recently, the role of N7-methylguanosine (m7G) in tumors has begun to receive attention, but no investigation on the impact of m7G on LUAD. This study aims to elucidate the significance of m7G on the prognosis and immunotherapy in LUAD.MethodsConsensus clustering was employed to determine the molecular subtype according to m7G-related regulators extracted from The Cancer Genome Atlas (TCGA) database. Survival, clinicopathological features and tumor mutational burden (TMB) analysis were applied to research molecular characteristics of each subtype. Subsequently, “limma” package was used to screen differentially expressed genes (DEGs) between subtypes. In the TCGA train cohort (n = 245), a prognostic signature was established by univariate Cox regression, lasso regression and multivariate Cox regression analysis according to DEGs and survival analysis was employed to assess the prognosis. Then the prognostic value of the signature was verified by TCGA test cohort (n = 245), TCGA entire cohort (n = 490) and GSE31210 cohort (n = 226). Moreover, the association among immune infiltration, clinical features and the signature was investigated. The immune checkpoints, TMB and tumor immune dysfunction and exclusion (TIDE) were applied to predict the immunotherapy response.ResultsTwo novel molecular subtypes (C1 and C2) of LUAD were identified. Compared to C2 subtype, C1 subtype had poorer prognosis and higher TMB. Subsequently, the signature (called the “m7G score”) was constructed according to four key genes (E2F7, FAM83A, PITX3, and HOXA13). The distribution of m7G score were significantly different between two molecular subtypes. The patients with lower m7G score had better prognosis in TCGA train cohort and three verification cohort. The m7G score was intensively related to immune infiltration. Compared with the lower score, the higher m7G score was related to remarkable upregulation of the PD-1 and PD-L1, the higher TMB and the lower TIDE score.ConclusionThis study established a m7G-related signature for predicting prognosis and immunotherapy in LUAD, which may contribute to the development of new therapeutic strategies for LUAD.
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Liang Y, Wu X, Su Q, Liu Y, Xiao H. Identification and Validation of a Novel Inflammatory Response-Related Gene Signature for the Prognosis of Colon Cancer. J Inflamm Res 2021; 14:3809-3821. [PMID: 34408464 PMCID: PMC8364916 DOI: 10.2147/jir.s321852] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/14/2021] [Indexed: 01/10/2023] Open
Abstract
Purpose The inflammatory response plays a crucial role in the occurrence and development of colon cancer. In this study, we aimed to explore a novel prognostic model for patients with colon cancer (COAD) based on inflammatory response-related genes. Methods Inflammatory response-related genes were obtained from Molecular Signatures database. Univariate and multivariate Cox regression analyses were used for model construction based on TCGA dataset. GSE39582 dataset and qRT-PCR dataset were used for validation. Gene set variation analysis and gene set enrichment analysis were performed to explore the potential regulatory pathways. The immune cell infiltration level was analyzed via CIBERSORT. Immunohistochemistry analysis and experiments were used to explore the function of genes in model. Results In this study, a novel prognostic signature was identified using stepwise Cox proportional hazards regression analysis based on TCGA dataset. The results were subsequently validated in 562 patients from GSE39582 and a qRT-PCR data set from 70 tumor samples. Functional analysis indicated that the tumor microenvironment and immune cell infiltrate were different between high- and low-risk groups. Additionally, IHC results showed that the protein levels of prognostic genes were significantly different between COAD tissues and adjacent non-tumorous tissues, and prognostic genes could regulate the malignant phenotype of COAD cells. Conclusion Overall, the inflammation-related gene signature can be used for prognostic prediction in patients with COAD.
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Affiliation(s)
- Yichao Liang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Xin Wu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Qi Su
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yujie Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Hong Xiao
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
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Xiao J, Liu Q, Wu W, Yuan Y, Zhou J, Shi J, Zhou S. Elevated Ras related GTP binding B (RRAGB) expression predicts poor overall survival and constructs a prognostic nomogram for colon adenocarcinoma. Bioengineered 2021; 12:4620-4632. [PMID: 34320917 PMCID: PMC8806650 DOI: 10.1080/21655979.2021.1956402] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Currently, no articles have explored the roles of RRAGB gene in the occurrence and development of cancer. By means of The Cancer Genome Atlas (TCGA) data mining, we found that this gene might be a novel prognostic predictor for colon adenocarcinoma (COAD). Hence, this article was carried out to explore its roles in COAD and associations with immunity. RRAGB single-gene expression matrix and corresponding clinical information were extracted from TCGA database. Univariate/multivariate cox regression analyses and gene set enrichment analysis (GSEA) were utilized to identify independent prognostic factors and RRAGB related pathways, respectively. Relationships between RRAGB and immunity were also analyzed. Boxplot and K-M survival analysis indicated that RRAGB was not only differently expressed in COAD (P < 0.05), but also significantly associated with overall survival (OS; P < 0.05). Univariate and multivariate Cox hazard regression analyses indicated that RRAGB could serve as an independent prognostic factor for COAD (both P < 0.05). GSEA identified five signaling pathways significantly enriched in the high-RRAGB expression phenotype. Moreover, a RRAGB-based nomogram was successfully constructed and displayed a satisfactory performance. In addition, RRAGB expression was found to be significantly associated with microsatellite instability (MSI), tumor mutational burden (TMB) and immunity. Our results revealed that RRAGB could be a prognostic biomarker for COAD in terms of OS and markedly related to MSI, TMB, and immunity. We also constructed an RRAGB-based nomogram with a satisfactory performance. Further researches should be carried out to validate our findings.
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Affiliation(s)
- Jianjia Xiao
- Department of General Surgery, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, Jiangsu Province, China
| | - Qingqing Liu
- Department of Gastroenterology, Affiliated Hospital NO.2 Of Nantong University, Nantong, Jiangsu Province, China
| | - Weijie Wu
- Department of Orthopedics, The Sixth People's Hospital of Nantong, Medical College of Nantong University, Nantong, Jiangsu Province, China
| | - Ying Yuan
- Department of Geriatrics, Taizhou Second People's Hospital, Taizhou, Jiangsu Province, China
| | - Jie Zhou
- Department of General Surgery, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, Jiangsu Province, China
| | - Jieyu Shi
- Department of Neurology, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, Jiangsu Province, China
| | - Shaorong Zhou
- Department of General Surgery, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, Jiangsu Province, China
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