1
|
Tang B, Liu B, Zeng Z. A new TGF-β risk score predicts clinical and immune landscape in colorectal cancer patients. Ann Gastroenterol Surg 2024; 8:927-941. [PMID: 39229560 PMCID: PMC11368510 DOI: 10.1002/ags3.12802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/06/2024] [Accepted: 03/26/2024] [Indexed: 09/05/2024] Open
Abstract
Background Aberrant TGF-β signaling pathway can lead to invasive phenotype of colorectal cancer (CRC), resulting in poor prognosis. It is pivotal to develop an effective prognostic factor on the basis of TGF-β-related genes to accurately identify risk of CRC patients. Methods We performed differential analysis of TGF-β-related genes in CRC patients from databases and previous literature to obtain TGF-β-related differentially expressed genes (TRDEGs). LASSO-Cox regression was utilized to build a CRC prognostic feature model based on TRDEGs. The model was validated using two GEO validation sets. Wilcoxon rank-sum test was utilized to test correlation of model with clinical factors. ESTIMATE algorithm and ssGSEA and tumor mutation burden (TMB) analysis were used to analyze immune landscape and mutation burden of high-risk (HR) and low-risk (LR) groups. CellMiner database was utilized to identify therapeutic drugs with high sensitivity to the feature genes. Results We established a six-gene risk prognostic model with good predictive accuracy, which independently predicted CRC patients' prognoses. The HR group was more likely to experience immunotherapy benefits due to higher immune infiltration and TMB. The feature gene TGFB2 could inhibit the efficacy of drugs such as XAV-939, Staurosporine, and Dasatinib, but promote the efficacy of drugs such as CUDC-305 and by-product of CUDC-305. Similarly, RBL1 could inhibit the drug action of Fluphenazine and Imiquimod but promote that of Irofulven. Conclusion A CRC risk prognostic signature was developed on basis of TGF-β-related genes, which provides a reference for risk and further therapeutic selection of CRC patients.
Collapse
Affiliation(s)
- Bing Tang
- Department of Gastrointestinal SurgeryCentral Hospital of YongzhouYongzhouHunanChina
| | - Binggang Liu
- Department of Gastrointestinal SurgeryCentral Hospital of YongzhouYongzhouHunanChina
| | - Zhiyao Zeng
- Department of Gastrointestinal SurgeryCentral Hospital of YongzhouYongzhouHunanChina
| |
Collapse
|
2
|
Zhou W, Lin L, Chen D, Wang J, Chen J. Construction of a Liver Cancer Prognostic Model Based on Interferon-Gamma-Related Genes for Revealing the Immune Landscape. J Environ Pathol Toxicol Oncol 2024; 43:25-42. [PMID: 39016139 DOI: 10.1615/jenvironpatholtoxicoloncol.2024049848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024] Open
Abstract
Inferferon-gamma (LFN-γ) exerts anti-tumor effects, but there is currently no reliable and comprehensive study on prognostic function of IFN-γ-related genes in liver cancer. In this study, IFN-γ-related differentially expressed genes (DEGs) in liver cancer were identified through GO/KEGG databases and open-access literature. Based on these genes, individuals with liver cancer were clustered. A prognostic model was built based on the intersection genes between differential genes in clusters and in liver cancer. Then, model predictive performance was analyzed and validated in GEO dataset. Regression analysis was fulfilled on the model, and a nomogram was utilized to evaluate model ability as an independent prognostic factor and its clinical application value. An immune-related analysis was conducted on both the H- and L-groups, with an additional investigation into link of model genes to drug sensitivity. Significant differential expression of IFN-γ-related genes was observed between the liver cancer and control groups. Subsequently, individuals with liver cancer were classified into two subtypes based on these genes, which displayed a notable difference in survival between the two subtypes. A 10-gene liver cancer prognostic model was constructed, with good prognostic performance and was an independent prognosticator for patient analysis. L-group patients possessed higher immune infiltration levels, immune checkpoint expression levels, and immunophenoscore, as well as lower TIDE scores. Drugs that had high correlations with the feature genes included SPANXB1: PF-04217903, SGX-523, MMP1: PF-04217903, DUSP13: Imatinib, TFF1: KHK-Indazole, and Fulvestrant. We built a 10-gene liver cancer prognostic model. It was found that L-group patients were more suitable for immunotherapy. This study provided valuable information on the prognosis of liver cancer.
Collapse
Affiliation(s)
- Wuhan Zhou
- Department of Hepatobiliary Surgery, The First Hospital of Putian City, Putian, Fujian 351100, P.R. China
| | - Liang Lin
- Department of Hepatobiliary Surgery, The First Hospital of Putian City, Putian, Fujian 351100, P.R. China
| | - Dongxing Chen
- Department of Hepatobiliary Surgery, The First Hospital of Putian City, Putian, Fujian 351100, P.R. China
| | - Jingui Wang
- Department of Hepatobiliary Surgery, The First Hospital of Putian City, Putian, Fujian 351100, P.R. China; Department of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian 350122, P.R. China
| | | |
Collapse
|
3
|
Wang Y, Wan X, Du S. Integrated analysis revealing a novel stemness-metabolism-related gene signature for predicting prognosis and immunotherapy response in hepatocellular carcinoma. Front Immunol 2023; 14:1100100. [PMID: 37622118 PMCID: PMC10445950 DOI: 10.3389/fimmu.2023.1100100] [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: 11/16/2022] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant lethal tumor and both cancer stem cells (CSCs) and metabolism reprogramming have been proven to play indispensable roles in HCC. This study aimed to reveal the connection between metabolism reprogramming and the stemness characteristics of HCC, established a new gene signature related to stemness and metabolism and utilized it to assess HCC prognosis and immunotherapy response. The clinical information and gene expression profiles (GEPs) of 478 HCC patients came from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA). The one-class logistic regression (OCLR) algorithm was employed to calculate the messenger ribonucleic acid expression-based stemness index (mRNAsi), a new stemness index quantifying stemness features. Differentially expressed analyses were done between high- and low-mRNAsi groups and 74 differentially expressed metabolism-related genes (DEMRGs) were identified with the help of metabolism-related gene sets from Molecular Signatures Database (MSigDB). After integrated analysis, a risk score model based on the three most efficient prognostic DEMRGs, including Recombinant Phosphofructokinase Platelet (PFKP), phosphodiesterase 2A (PDE2A) and UDP-glucuronosyltransferase 1A5 (UGT1A5) was constructed and HCC patients were divided into high-risk and low-risk groups. Significant differences were found in pathway enrichment, immune cell infiltration patterns, and gene alterations between the two groups. High-risk group patients tended to have worse clinical outcomes and were more likely to respond to immunotherapy. A stemness-metabolism-related model composed of gender, age, the risk score model and tumor-node-metastasis (TNM) staging was generated and showed great discrimination and strong ability in predicting HCC prognosis and immunotherapy response.
Collapse
Affiliation(s)
| | | | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| |
Collapse
|
4
|
Jou E. Type 1 and type 2 cytokine-mediated immune orchestration in the tumour microenvironment and their therapeutic potential. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:474-497. [PMID: 37455828 PMCID: PMC10345208 DOI: 10.37349/etat.2023.00146] [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: 02/27/2023] [Accepted: 04/25/2023] [Indexed: 07/18/2023] Open
Abstract
Cancer remains the second leading cause of death worldwide despite modern breakthroughs in medicine, and novel treatments are urgently needed. The revolutionary success of immune checkpoint inhibitors in the past decade serves as proof of concept that the immune system can be effectively harnessed to treat cancer. Cytokines are small signalling proteins with critical roles in orchestrating the immune response and have become an attractive target for immunotherapy. Type 1 immune cytokines, including interferon γ (IFNγ), interleukin-12 (IL-12), and tumour necrosis factor α (TNFα), have been shown to have largely tumour suppressive roles in part through orchestrating anti-tumour immune responses mediated by natural killer (NK) cells, CD8+ T cells and T helper 1 (Th1) cells. Conversely, type 2 immunity involving group 2 innate lymphoid cells (ILC2s) and Th2 cells are involved in tissue regeneration and wound repair and are traditionally thought to have pro-tumoural effects. However, it is found that the classical type 2 immune cytokines IL-4, IL-5, IL-9, and IL-13 may have conflicting roles in cancer. Similarly, type 2 immunity-related cytokines IL-25 and IL-33 with recently characterised roles in cancer may either promote or suppress tumorigenesis in a context-dependent manner. Furthermore, type 1 cytokines IFNγ and TNFα have also been found to have pro-tumoural effects under certain circumstances, further complicating the overall picture. Therefore, the dichotomy of type 1 and type 2 cytokines inhibiting and promoting tumours respectively is not concrete, and attempts of utilising these for cancer immunotherapy must take into account all available evidence. This review provides an overview summarising the current understanding of type 1 and type 2 cytokines in tumour immunity and discusses the prospects of harnessing these for immunotherapy in light of previous and ongoing clinical trials.
Collapse
Affiliation(s)
- Eric Jou
- Queens’ College, University of Cambridge, CB3 9ET Cambridge, UK
- MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| |
Collapse
|
5
|
Xiong Z, Han Z, Pan W, Zhu X, Liu C. Correlation between chromatin epigenetic-related lncRNA signature (CELncSig) and prognosis, immune microenvironment, and immunotherapy in non-small cell lung cancer. PLoS One 2023; 18:e0286122. [PMID: 37224123 DOI: 10.1371/journal.pone.0286122] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Chromatin regulators drive cancer epigenetic changes, and lncRNA can play an important role in epigenetic changes as chromatin regulators. We used univariate Cox, LASSO, and multivariate Cox regression analysis to select epigenetic-associated lncRNA signatures. Twenty-five epigenetic-associated lncRNA signatures (CELncSig) were identified to establish the immune prognostic model. According to Kaplan-Meier analysis, the overall survival of the high-risk group was significantly lower than the low-risk group. Receiver operating characteristic (ROC) curves, C-index, survival curve, nomogram, and principal component analysis (PCA) were performed to validate the risk model. In GO/KEGG analysis, differentially expressed lncRNAs were correlated with the PI3K-Akt pathway, suggesting that they were highly associated with the metastasis of LUAD. Interestingly, in the immune escape analysis, the TIDE score was lower, and the possibility of immune dysfunction is also slighter in the high-risk group, which means they still have the potential to receive immunotherapy. And CELncsig is highly correlated with immune pathways T_cell_co-inhibition and Check-point. Also, the IMvigor210 cohort analysis indicated that our risk-scoring model has significant potential clinical application value in lung cancer immunotherapy. And we also screened out ten potential chemotherapy agents using the 'pRRophetic' package.
Collapse
Affiliation(s)
- Zhuolong Xiong
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Computational Systems Biology Lab (CSBL), Institute of Bioinformatics, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Zenglei Han
- Department of Pathology, Qingdao Municipal Hospital, Qingdao, China
| | - Weiyi Pan
- Computational Systems Biology Lab (CSBL), Institute of Bioinformatics, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), Institute of Bioinformatics, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou Medical College, Hangzhou, China
| | - Caixin Liu
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| |
Collapse
|
6
|
Gupta S, Singh P, Tasneem A, Almatroudi A, Rahmani AH, Dohare R, Parveen S. Integrative Multiomics and Regulatory Network Analyses Uncovers the Role of OAS3, TRAFD1, miR-222-3p, and miR-125b-5p in Hepatitis E Virus Infection. Genes (Basel) 2022; 14:42. [PMID: 36672782 PMCID: PMC9859139 DOI: 10.3390/genes14010042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The hepatitis E virus (HEV) is a long-ignored virus that has spread globally with time. It ranked 6th among the top risk-ranking viruses with high zoonotic spillover potential; thus, considering its viral threats is a pressing priority. The molecular pathophysiology of HEV infection or the underlying cause is limited. Therefore, we incorporated an unbiased, systematic methodology to get insights into the biological heterogeneity associated with the HEV. Our study fetched 93 and 2016 differentially expressed genes (DEGs) from chronic HEV (CHEV) infection in kidney-transplant patients, followed by hub module selection from a weighted gene co-expression network (WGCN). Most of the hub genes identified in this study were associated with interferon (IFN) signaling pathways. Amongst the genes induced by IFNs, the 2'-5'-oligoadenylate synthase 3 (OAS3) protein was upregulated. Protein-protein interaction (PPI) modular, functional enrichment, and feed-forward loop (FFL) analyses led to the identification of two key miRNAs, i.e., miR-222-3p and miR-125b-5p, which showed a strong association with the OAS3 gene and TRAF-type zinc finger domain containing 1 (TRAFD1) transcription factor (TF) based on essential centrality measures. Further experimental studies are required to substantiate the significance of these FFL-associated genes and miRNAs with their respective functions in CHEV. To our knowledge, it is the first time that miR-222-3p has been described as a reference miRNA for use in CHEV sample analyses. In conclusion, our study has enlightened a few budding targets of HEV, which might help us understand the cellular and molecular pathways dysregulated in HEV through various factors. Thus, providing a novel insight into its pathophysiology and progression dynamics.
Collapse
Affiliation(s)
- Sonam Gupta
- Molecular Virology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Prithvi Singh
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Alvea Tasneem
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ravins Dohare
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Shama Parveen
- Molecular Virology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| |
Collapse
|
7
|
Wang J, Chen S, Wang H, Cao J, Fan X, Man J, Li Q, Yang L. Integrated molecular analyses of an interferon-γ based subtype with regard to outcome, immune characteristics, and immunotherapy in bladder cancer and experimental verification. Heliyon 2022; 8:e12102. [PMID: 36582677 PMCID: PMC9792807 DOI: 10.1016/j.heliyon.2022.e12102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
This study attempted to explore the role of interferon-γ related genes (IRGs) in the prognosis and immunotherapy of bladder cancer (BC). Based on data downloaded from public databases, molecular subtypes with different IRG expression patterns were determined via nonnegative matrix factorization clustering. On the basis of IRGs, interferon-γ related gene signature (IRGS) was developed through Cox regression analyses. We identified that two molecular subgroups with different outcome and immune profiles. It was proved that IRGS possessed prediction efficiency for BC prognosis. Compared with low IRGS group, high IRGS group was related to less anti-cancer immune cells infiltration, less tumor mutation burden score, more cancer stem cell index, and less benefit from immunotherapy. Differential expression of six model genes (IRF5, LATS2, MTHFD2, VAMP8, HLA-G and PTPN6) was validated between paired tissues by RT-qPCR. This study presents a prognostic model, which could serve as an indicator for the benefit of BC immunotherapy.
Collapse
Affiliation(s)
- Jirong Wang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Siyu Chen
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Huabin Wang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Jinlong Cao
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Xinpeng Fan
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Jiangwei Man
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Qingchao Li
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Li Yang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| |
Collapse
|
8
|
Ye Z, Song P, Zheng D, Zhang X, Wu J. A Naive Bayes model on lung adenocarcinoma projection based on tumor microenvironment and weighted gene co-expression network analysis. Infect Dis Model 2022; 7:498-509. [PMID: 36091346 PMCID: PMC9403296 DOI: 10.1016/j.idm.2022.07.009] [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: 06/22/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/23/2022] Open
Abstract
Based on the lung adenocarcinoma (LUAD) gene expression data from the cancer genome atlas (TCGA) database, the Stromal score, Immune score and Estimate score in tumor microenvironment (TME) were computed by the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) algorithm. And gene modules significantly related to the three scores were identified by weighted gene co-expression network analysis (WGCNA). Based on the correlation coefficients and P values, 899 key genes affecting tumor microenvironment were obtained by selecting the two most correlated modules. It was suggested through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis that these key genes were significantly involved in immune-related or cancer-related terms. Through univariate cox regression and elastic network analysis, genes associated with prognosis of the LUAD patients were screened out and their prognostic values were further verified by the survival analysis and the University of ALabama at Birmingham CANcer (UALCAN) database. The results indicated that eight genes were significantly related to the overall survival of LUAD. Among them, six genes were found differentially expressed between tumor and control samples. And immune infiltration analysis further verified that all the six genes were significantly related to tumor purity and immune cells. Therefore, these genes were used eventually for constructing a Naive Bayes projection model of LUAD. The model was verified by the receiver operating characteristic (ROC) curve where the area under curve (AUC) reached 92.03%, which suggested that the model could discriminate the tumor samples from the normal accurately. Our study provided an effective model for LUAD projection which improved the clinical diagnosis and cure of LUAD. The result also confirmed that the six genes in the model construction could be the potential prognostic biomarkers of LUAD.
Collapse
|
9
|
Gu C, Lin C, Zhu Z, Hu L, Wang F, Wang X, Ruan J, Zhao X, Huang S. The IFN-γ-related long non-coding RNA signature predicts prognosis and indicates immune microenvironment infiltration in uterine corpus endometrial carcinoma. Front Oncol 2022; 12:955979. [PMID: 35957871 PMCID: PMC9360323 DOI: 10.3389/fonc.2022.955979] [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: 05/29/2022] [Accepted: 06/30/2022] [Indexed: 12/01/2022] Open
Abstract
Background One of the most common diseases that have a negative impact on women’s health is endometrial carcinoma (EC). Advanced endometrial cancer has a dismal prognosis and lacks solid prognostic indicators. IFN-γ is a key cytokine in the inflammatory response, and it has also been suggested that it has a role in the tumor microenvironment. The significance of IFN-γ-related genes and long non-coding RNAs in endometrial cancer, however, is unknown. Methods The Cancer Genome Atlas (TCGA) database was used to download RNA-seq data from endometrial cancer tissues and normal controls. Genes associated with IFN-γ were retrieved from the gene set enrichment analysis (GSEA) website. Co-expression analysis was performed to find lncRNAs linked to IFN-γ gene. The researchers employed weighted co-expression network analysis (WGCNA) to find lncRNAs that were strongly linked to survival. The prognostic signature was created using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression. The training cohort, validation cohort, and entire cohort of endometrial cancer patients were then split into high-risk and low-risk categories. To investigate variations across different risk groups, we used survival analysis, enrichment analysis, and immune microenvironment analysis. The platform for analysis is R software (version X64 3.6.1). Results Based on the transcript expression of IFN-γ-related lncRNAs, two distinct subgroups of EC from TCGA cohort were formed, each with different outcomes. Ten IFN-γ-related lncRNAs were used to build a predictive signature using Cox regression analysis and the LASSO regression, including CFAP58, LINC02014, UNQ6494, AC006369.1, NRAV, BMPR1B-DT, AC068134.2, AP002840.2, GS1-594A7.3, and OLMALINC. The high-risk group had a considerably worse outcome (p < 0.05). In the immunological microenvironment, there were also substantial disparities across different risk categories. Conclusion Our findings give a reference for endometrial cancer prognostic type and immunological status assessment, as well as prospective molecular markers for the disease.
Collapse
Affiliation(s)
- Chunyan Gu
- Department of Obstetrics and Gynecology, Nantong Haimen People’s Hospital, Nantong, China
| | - Chen Lin
- Vectors and Parasitosis Control and Prevention Section, Center of Disease Prevention and Control in Pudong New Area of Shanghai, Shanghai, China
| | - Zheng Zhu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Hu
- Department of Medicine, Kangda College of Nanjing Medical University, Lianyungang, China
| | - Fengxu Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xuehai Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Junpu Ruan
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xinyuan Zhao
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
- *Correspondence: Xinyuan Zhao, ; Sen Huang,
| | - Sen Huang
- Department of Obstetrics and Gynecology, Nantong Haimen People’s Hospital, Nantong, China
- *Correspondence: Xinyuan Zhao, ; Sen Huang,
| |
Collapse
|
10
|
Liu C, Liu D, Wang F, Xie J, Liu Y, Wang H, Rong J, Xie J, Wang J, Zeng R, Xie Y. The Interferon Gamma-Related Long Noncoding RNA Signature Predicts Prognosis and Indicates Immune Microenvironment Infiltration in Colon Adenocarcinoma. Front Oncol 2022; 12:876660. [PMID: 35747790 PMCID: PMC9211770 DOI: 10.3389/fonc.2022.876660] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 12/17/2022] Open
Abstract
Colon adenocarcinoma (COAD) is one of the most common clinically malignant tumours of the digestive system, with high incidence and mortality and poor prognosis. Interferon-gamma (IFN-γ) and long noncoding RNAs (lncRNAs) have prognostic values and were closely associated with immune microenvironment in COAD. Thus, identifying IFN-γ-related lncRNAs may be valuable in predicting the survival of patients with COAD. In this study, we identified IFN-γ-related lncRNAs and divided COAD patients from the Cancer Genome Atlas (TCGA) database into training and validation sets. Pearson’s correlation analysis and least absolute shrinkage and selection operator (LASSO) Cox regression were performed to select IFN-γ-related lncRNA-associated prognoses. Thirteen lncRNAs (AC025165.8, AC091633.3, FENDRR, LINC00882, LINC01828, LINC01829, MYOSLID, RP11-154H23.4, RP11-20J15.3, RP11-324L17.1, RP11-342A23.2, RP11-805I24.3, SERTAD4-AS1) were identified to construct an IFN-γ-related lncRNA prognostic signature in TCGA training (n =213) and validation (n =213) cohorts. COAD patient risk scores were calculated and classified into high- and low-risk groups based on the median value of the risk scores in each dataset. We compared the overall survival (OS) of patients stratified by age, gender, and stage. The OS in the high-risk group was significantly shorter than that in the low-risk group. In addition, the clinical nomogram incorporating the prognostic signature and clinical features showed a high concordance index of 0.78 and accurately predicted 1-, 3-, and 5-year survival times among COAD patients in the high- and low-risk groups. Based on the risk model, the high- and low-risk groups exhibited distinct differences in the immune system by gene set enrichment analysis (GSEA) functional annotation, and differentially expressed genes (DEGs) between the high- and low-risk groups were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. We investigated the expression of multiple immune checkpoint genes in the high- and low-risk groups and plotted Kaplan-Meier survival curves, indicating that immune checkpoint genes, such as LAG3 and PD. L1, STING and TIM 3, were also expressed differently between the two risk groups. Subsequently, there were dramatic differences in mutated genes, SNV (single nucleotide variants) classes, variant types and variant allele frequencies between low- and high-risk patients with COAD. Patients stratified by risk scores had different sensitivities to common chemotherapeutic agents. Finally, we used quantitative real-time polymerase chain reaction (qRT-PCR) assays to demonstrate that three lncRNAs were significantly differentially expressed in COAD tissues and adjacent normal tissues. Considered together, a thirteen-lncRNA prognostic signature has great potential to be a prognostic biomarker and could play an essential role in the immune microenvironment of COAD.
Collapse
Affiliation(s)
- Cong Liu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Dingwei Liu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Fangfei Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Jun Xie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Yang Liu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Huan Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Jianfang Rong
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Jinliang Xie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Jinyun Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Rong Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
| | - Yong Xie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, China
- *Correspondence: Yong Xie,
| |
Collapse
|
11
|
Liu X, Quan J, Shen Z, Zhang Z, Chen Z, Li L, Li X, Hu G, Deng X. Metallothionein 2A (MT2A) controls cell proliferation and liver metastasis by controlling the MST1/LATS2/YAP1 signaling pathway in colorectal cancer. Cancer Cell Int 2022; 22:205. [PMID: 35642057 PMCID: PMC9158144 DOI: 10.1186/s12935-022-02623-w] [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: 12/18/2021] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the three major cancers in the world and is the cancer with the most liver metastasis. The present study aimed to investigate the role of metallothionein 2A (MT2A) in the modulation of CRC cell proliferation and liver metastasis, as well as its molecular mechanisms. METHODS The expression profile of metallothionein 2A (MT2A) in colorectal cancer retrieved from TCGA, GEO and Oncomine database. The biological effect of MT2A overexpression was investigated mainly involving cell proliferation and migration in CRC cells as well as growth and metastasis in CRC animal models. To explore the specific mechanism of MT2A metastasis in CRC, transcriptome sequencing was used to compare the overall expression difference between the control group and the MT2A overexpression group. RESULTS Metallothionein 2A (MT2A) was downregulated in the tumor tissues of patients with CRC compared to adjacent normal tissues and was related to the tumor M stage of patients. MT2A overexpression inhibited CRC cell proliferation and migration in cells, as well as growth and metastasis in CRC animal models. While knockdown of MT2A had the opposite effect in cells. Western blotting confirmed that MT2A overexpression promoted the phosphorylation of MST1, LAST2 and YAP1, thereby inhibiting the Hippo signaling pathway. Additionally, specific inhibitors of MST1/2 inhibited MT2A overexpression-mediated phosphorylation and relieved the inhibition of the Hippo signaling pathway, thus promoting cell proliferation. Immunohistochemistry in subcutaneous grafts and liver metastases further confirmed this result. CONCLUSIONS Our results suggested that MT2A is involved in CRC growth and liver metastasis. Therefore, MT2A and MST1 may be potential therapeutic targets for patients with CRC, especially those with liver metastases.
Collapse
Affiliation(s)
- Xi Liu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Jun Quan
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Zhaolong Shen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Zequn Zhang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
| | - Zhijian Chen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Liang Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Gui Hu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Xiaofeng Deng
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Renmin Road, Changsha, 410000, Hunan, People's Republic of China.
| |
Collapse
|
12
|
Chen CW, Huang NK, Lee YL, Fan CK, Chen YC, Liu CW, Huang HM. Activin A downregulates the CD69-MT2A axis via p38MAPK to induce erythroid differentiation that sensitizes BCR-ABL-positive cells to imatinib. Exp Cell Res 2022; 417:113219. [DOI: 10.1016/j.yexcr.2022.113219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/25/2022] [Accepted: 05/19/2022] [Indexed: 11/04/2022]
|
13
|
Liu L, Du X, Fang J, Zhao J, Guo Y, Zhao Y, Zou C, Yan X, Li W. Development of an Interferon Gamma Response-Related Signature for Prediction of Survival in Clear Cell Renal Cell Carcinoma. J Inflamm Res 2021; 14:4969-4985. [PMID: 34611422 PMCID: PMC8485924 DOI: 10.2147/jir.s334041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022] Open
Abstract
Background Interferon plays a crucial role in the pathogenesis and progression of tumors. Clear cell renal cell carcinoma (ccRCC) represents a prevalent malignant urinary system tumor. An effective predictive model is required to evaluate the prognosis of patients to optimize treatment. Materials and Methods RNA-sequencing data and clinicopathological data from TCGA were involved in this retrospective study. The IFN-γ response genes with significantly different gene expression were screened out. Univariate Cox regression, LASSO regression and multivariate Cox regression were used to establish a new prognostic scoring model for the training group. Survival curves and ROC curves were drawn, and nomogram was constructed. At the same time, we conducted subgroup analysis and experimental verification using our own samples. Finally, we evaluated the relatedness between the prognostic signature and immune infiltration landscapes. In addition, the sensitivity of different risk groups to six drugs and immune checkpoint inhibitors was calculated. Results The IFN-γ response-related signature included 7 genes: C1S, IFI44, ST3GAL5, NUP93, TDRD7, DDX60, and ST8SIA4. The survival curves of the training and testing groups showed the model's effectiveness (P = 4.372e-11 and P = 1.08e-08, respectively), the ROC curves showed that the signature was stable, and subgroup analyses showed the wide applicability of the model (P<0.001). Multivariate Cox regression analysis showed that the risk model was an independent prognostic factor of ccRCC. A high-risk score may represent an immunosuppressive microenvironment, while the high-risk group exhibited poor sensitivity to drugs. Conclusion Our findings strongly indicate that the IFN-γ response-related signature can be used as an effective prognostic indicator of ccRCC.
Collapse
Affiliation(s)
- Lixiao Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xuedan Du
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Jintao Fang
- Department of Urinary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Jinduo Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Yong Guo
- Department of Urinary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Ye Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Chengyang Zou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xiaojian Yan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Wenfeng Li
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| |
Collapse
|