1
|
Li S, Wang M, Liu B, Lv Y, Man J, Liang M, Qiao H. Analysis of lncRNA-miRNA-mRNA interactions identified a novel biomarker LINC00657 to improve prognosis prediction of papillary thyroid carcinoma. Int Immunopharmacol 2024; 137:112432. [PMID: 38865751 DOI: 10.1016/j.intimp.2024.112432] [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: 03/04/2024] [Revised: 05/21/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most common type of thyroid cancer. Identification of novel biomarkers can potentially help explore the underlying molecular mechanisms of PTC. Long non-coding RNAs (lncRNAs) are involved in cancer development. However, understanding the role of lncRNA in PTC remains challenging. METHODS Based on the competitive endogenous RNA (ceRNA) theory, we constructed a comprehensive PTC-related lncRNA-miRNA-mRNA network using data from The Cancer Genome Atlas. To evaluate the prognostic power, we performed survival analysis for patients with PTC with low and high lncRNA expression levels, and examined the relationship between lncRNA and immune-related functions. RESULTS We identified a hub node, long intergenic non-coding RNA, LINC00657, as a novel prognostic biomarker in PTC. LINC00657 was differentially expressed between tumor and adjacent normal samples. Low LINC00657 expression levels was significantly associated with better survival outcome. Our functional analyses showed that LINC00657 was related with infiltration of CD8+ T cell and macrophage; immune check point molecules; and immune metagenes such as IgG, LCK, MHC_I/II and etc. These results suggest that LINC00657 is an immune-related biomarker with potential clinical applicability. Additionally, cancer-related signaling pathway and high frequency of gene BRAF mutation were found in PTC samples with high LINC00657 expression level, which were consistent with previous findings. CONCLUSION LINC00657 is an immune-related biomarker that can potentially improve prognosis prediction in PTC. Our study provided new treatment target of PTC in clinical practice and offered the novel insights in elucidating the functional role of lncRNAs.
Collapse
Affiliation(s)
- Shuang Li
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China; Department of Endocrinology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Mingli Wang
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Liu
- The Fourth Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yichen Lv
- The Fourth Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jianting Man
- The Fourth Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meihua Liang
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Hong Qiao
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| |
Collapse
|
2
|
Zhang C, Lin Q, Li C, Chen Z, Deng M, Weng H, Zhu X. Analysis of endoplasmic reticulum stress-related gene signature for the prognosis and pattern in diffuse large B cell lymphoma. Sci Rep 2023; 13:13894. [PMID: 37626099 PMCID: PMC10457392 DOI: 10.1038/s41598-023-38568-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/11/2023] [Indexed: 08/27/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma in adults. This study aimed to determine the prognostic significance of endoplasmic reticulum (ER) stress-related genes in DLBCL. ER stress-related genes were obtained from the molecular signatures database. Gene expression data and clinical outcomes from the gene expression omnibus and TCGA datasets were collected, and differentially expressed genes (DEGs) were screened out. Gene ontology enrichment analysis, the kyoto encyclopaedia of genes and genomes pathway analysis, and geneset enrichment analysis were used to analyse the possible biological function of ER stress-related DEGs in DLBCL. Protein-protein interaction network construction using the STRING online and hub genes were identified by cytoHubba on Cytoscape software. The significant prognosis-related genes were screened, and the differential expression was validated. The immune microenvironment assessment of significant genes were evaluated. Next, the nomogram was built using univariate and multivariate Cox regression analysis. 26 ER stress-related DEGs were screened. Functional enrichment analysis showed them to be involved in the regulation of the endoplasmic reticulum mainly. NUPR1 and TRIB3 were identified as the most significant prognostic-related genes by comparison with the GSE10846, GSE11318, and TCGA datasets. NUPR1 was correlated with a good prognosis and immune infiltration in DLBCL; on the other hand, high expression of TRIB3 significantly correlated with a poor prognosis, which was an independent prognostic factor for DLBCL. In summary, we identified NUPR1 and TRIB3 as critical ER stress-related genes in DLBCL. NUPR1 might be involved in immune infiltration in DLBCL, and TRIB3 might serve as a potential therapeutic target and prognostic factor in DLBCL.
Collapse
Affiliation(s)
- Chaofeng Zhang
- Department of Hematology and Rheumatology, The Affiliated Hospital of Putian University, Putian, Fujian Province, China
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Qi Lin
- Department of Pharmacy, The Affiliated Hospital of Putian University, Putian, Fujian Province, China
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Chaoqi Li
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Zhimin Chen
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Mengmeng Deng
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Huixin Weng
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Xiongpeng Zhu
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian Province, China.
- Department of Haematology, Quanzhou First Hospital of Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China.
| |
Collapse
|
3
|
Tang W, Shao Q, He Z, Zhang X, Li X, Wu R. Clinical significance of nonerythrocytic spectrin Beta 1 (SPTBN1) in human kidney renal clear cell carcinoma and uveal melanoma: a study based on Pan-Cancer Analysis. BMC Cancer 2023; 23:303. [PMID: 37013511 PMCID: PMC10071745 DOI: 10.1186/s12885-023-10789-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Nonerythrocytic spectrin beta 1 (SPTBN1) is an important cytoskeletal protein that involves in normal cell growth and development via regulating TGFβ/Smad signaling pathway, and is aberrantly expressed in various cancer types. But, the exact role of SPTBN1 in pan-cancer is still unclear. This report aimed to display expression patterns and prognostic landscapes of SPTBN1 in human cancers, and further assess its prognostic/therapeutic value and immunological role in kidney renal carcinoma (KIRC) and uveal melanoma (UVM). METHODS We firstly analyzed expression patterns and prognostic landscapes of SPTBN1 in human cancers using various databases and web-based tools. The relationships between SPTBN1 expression and survival/tumor immunity in KIRC and UVM were further investigated via R packages and TIMER 2.0 platform. The therapeutic roles of SPTBN1 in KIRC and UVM were also explored via R software. Following this, the prognostic value and cancer immunological role of SPTBN1 in KIRC and UVM were validated in our cancer patients and GEO database. RESULTS Overall, cancer tissue had a lower expression level of SPTBN1 frequently in pan-cancer, compared with those in adjacent nontumor one. SPTBN1 expression often showed a different effect on survival in pan-cancer; upregulation of SPTBN1 was protective to the survival of KIRC individuals, which was contrary from what was found in UVM patients. In KIRC, there were significant negative associations between SPTBN1 expression and pro-tumor immune cell infiltration, including Treg cell, Th2 cell, monocyte and M2-macrophage, and expression of immune modulator genes, such as tumor necrosis factor superfamily member 9 (TNFSF9); while, in UVM, these correlations exhibited opposite patterns. The following survival and expression correlation analysis in our cancer cohorts and GEO database confirmed these previous findings. Moreover, we also found that SPTBN1 was potentially involved in the resistance of immunotherapy in KIRC, and the enhance of anti-cancer targeted treatment in UVM. CONCLUSIONS The current study presented compelling evidence that SPTBN1 might be a novel prognostic and therapy-related biomarker in KIRC and UVM, shedding new light on anti-cancer strategy.
Collapse
Affiliation(s)
- Wenting Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, 510060, Guangdong, China
- Department of Research and Molecular Diagnostics, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, 510060, Guangdong, China
| | - Qiong Shao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, 510060, Guangdong, China
- Department of Research and Molecular Diagnostics, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, 510060, Guangdong, China
| | - Zhanwen He
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Xu Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, 510060, Guangdong, China
- Department of Research and Molecular Diagnostics, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, 510060, Guangdong, China
| | - Xiaojuan Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Department of Research and Molecular Diagnostics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
| | - Ruohao Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
| |
Collapse
|
4
|
Guo W, Huai Q, Zhou B, Guo L, Sun L, Xue X, Tan F, Xue Q, Gao S, He J. Comprehensive analysis of the immunological implication and prognostic value of CXCR4 in non-small cell lung cancer. Cancer Immunol Immunother 2023; 72:1029-1045. [PMID: 36308553 PMCID: PMC10025233 DOI: 10.1007/s00262-022-03298-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/16/2022] [Indexed: 03/20/2023]
Abstract
CXCR4 (C-X-C chemokine receptor type 4) is the most commonly expressed of all chemokine receptors in malignant tumors. However, studies on CXCR4 in non-small cell lung cancer (NSCLC) tumor immune microenvironment, including those determining its immune efficacy and prognostic potential, are still scarce. Therefore, in this study, we determined the ability of CXCR4 to predict immunotherapy response and prognosis in NSCLC using immunohistochemical staining and RT-PCR, respectively, in two independent cohorts from the National Cancer Center of China. We analyzed transcriptome sequencing data and clinical information from multiple public databases to assess immune cell infiltration in NSCLC and constructed immune risk prognostic signatures based on CXCR4-related immunomodulators. We found that immune cell infiltration is significant differences in NSCLC tissues and is moderately correlated with CXCR4 expression. High CXCR4 expression was significantly associated with poor prognosis in NSCLC patients and a higher response rate to immunotherapy. The ROC curve showed that CXCR4 expression exhibited excellent performance in predicting the efficacy of immunotherapy in NSCLC. We identified 30 CXCR4-related immunomodulators in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) and constructed immune prognostic signatures based on CXCR4-related immunomodulators and CXCR4-related mutant genes. The signature-based prognostic risk score showed good performance in predicting patient prognosis in both LUAD and LUSC; high risk scores were significantly associated with poor prognosis (P < 0.0001) and was established as an independent prognostic factor by multivariate Cox regression. We postulate that CXCR4 is a potential predictive marker of immunotherapy efficacy in NSCLC and should be used in clinical settings. Moreover, the constructed signatures may be valuable in predicting patient prognosis in NSCLC.
Collapse
Affiliation(s)
- Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuannanli No 17, Chaoyang District, Beijing, 100021, China
- Key Laboratory of Minimally Invasive Therapy Research for Lung Cancer, Chinese Academy of Medical Sciences, Beijing, China
| | - Qilin Huai
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuannanli No 17, Chaoyang District, Beijing, 100021, China
| | - Bolun Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuannanli No 17, Chaoyang District, Beijing, 100021, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Sun
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuemin Xue
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuannanli No 17, Chaoyang District, Beijing, 100021, China
- Key Laboratory of Minimally Invasive Therapy Research for Lung Cancer, Chinese Academy of Medical Sciences, Beijing, China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuannanli No 17, Chaoyang District, Beijing, 100021, China
- Key Laboratory of Minimally Invasive Therapy Research for Lung Cancer, Chinese Academy of Medical Sciences, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuannanli No 17, Chaoyang District, Beijing, 100021, China.
- Key Laboratory of Minimally Invasive Therapy Research for Lung Cancer, Chinese Academy of Medical Sciences, Beijing, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Panjiayuannanli No 17, Chaoyang District, Beijing, 100021, China.
| |
Collapse
|
5
|
Zhu J, Cao K, Zhao M, Ma K, Jiang X, Bai Y, Ling X, Ma J. Improvement of ACK1-targeted therapy efficacy in lung adenocarcinoma using chloroquine or bafilomycin A1. Mol Med 2023; 29:6. [PMID: 36647009 PMCID: PMC9843944 DOI: 10.1186/s10020-023-00602-z] [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: 10/10/2022] [Accepted: 01/08/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Activated Cdc42-associated kinase 1 (ACK1) is a promising druggable target for cancer, but its inhibitors only showed moderate effects in clinical trials. The study aimed to investigate the underlying mechanisms and improve the antitumor efficacy of ACK1 inhibitors. METHODS RNA-seq was performed to determine the downstream pathways of ACK. Using Lasso Cox regression analysis, we built a risk signature with ACK1-related autophagy genes in the lung adenocarcinoma (LUAD) patients from The Cancer Genome Atlas (TCGA) project. The performance of the signature in predicting the tumor immune environment and response to immunotherapy and chemotherapy were assessed in LUAD. CCK8, mRFP-GFP-LC3 assay, western blot, colony formation, wound healing, and transwell migration assays were conducted to evaluate the effects of the ACK1 inhibitor on lung cancer cells. A subcutaneous NSCLC xenograft model was used for in vivo study. RESULTS RNA-seq revealed the regulatory role of ACK1 in autophagy. Furthermore, the risk signature separated LUAD patients into low- and high-risk groups with significantly different prognoses. The two groups displayed different tumor immune environments regarding 28 immune cell subsets. The low-risk groups showed high immune scores, high CTLA4 expression levels, high immunophenoscore, and low DNA mismatch repair capacity, suggesting a better response to immunotherapy. This signature also predicted sensitivity to commonly used chemotherapy and targeted drugs. In vitro, the ACK1 inhibitors (AIM-100 and Dasatinib) appeared to trigger adaptive autophagy-like response to protect lung cancer cells from apoptosis and activated the AMPK/mTOR signaling pathway, partially explaining its moderate antitumor efficacy. However, blocking lysosomal degradation with chloroquine/Bafilamycine A1 or inhibiting AMPK signaling with compound C/shPRKAA1 enhanced the ACK1 inhibitor's cytotoxic effects on lung cancer cells. The efficacy of the combined therapy was also verified using a mouse xenograft model. CONCLUSIONS The resulting signature from ACK1-related autophagy genes robustly predicted survival and drug sensitivity in LUAD. The lysosomal degradation inhibition improved the therapeutic effects of the ACK1 inhibitor, suggesting a potential role for autophagy in therapy evasion.
Collapse
Affiliation(s)
- Jinhong Zhu
- grid.412651.50000 0004 1808 3502Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040 Heilongjiang China
| | - Kui Cao
- grid.412651.50000 0004 1808 3502Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040 Heilongjiang China
| | - Meng Zhao
- grid.412651.50000 0004 1808 3502Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040 Heilongjiang China
| | - Keru Ma
- grid.412651.50000 0004 1808 3502Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040 Heilongjiang China
| | - Xiangyu Jiang
- grid.412651.50000 0004 1808 3502Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040 Heilongjiang China
| | - Yuwen Bai
- grid.412651.50000 0004 1808 3502Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040 Heilongjiang China
| | - Xiaodong Ling
- grid.412651.50000 0004 1808 3502Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040 Heilongjiang China
| | - Jianqun Ma
- grid.412651.50000 0004 1808 3502Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040 Heilongjiang China
| |
Collapse
|
6
|
Zhu J, Cao K, Zhang P, Ma J. LINC00669 promotes lung adenocarcinoma growth by stimulating the Wnt/β-catenin signaling pathway. Cancer Med 2023; 12:9005-9023. [PMID: 36621836 PMCID: PMC10134358 DOI: 10.1002/cam4.5604] [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: 09/26/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 01/10/2023] Open
Abstract
Lung cancer poses severe threats to human health. It is indispensable to discover more druggable molecular targets. We identified a novel dysregulated long non-coding RNA (lncRNA), LINC00669, in lung adenocarcinoma (LUAD) by analyzing the TCGA and GEO databases. Pan-cancer analysis indicated significantly upregulated LINC00669 across 33 cancer types. GSEA revealed a tight association of LINC00669 with the cell cycle. We next attempted to improve the prognostic accuracy of this lncRNA by establishing a risk signature in reliance on cell cycle genes associated with LINC00669. The resulting risk score combined with LINC00669 and stage showed an AUC of 0.746. The risk score significantly stratified LUAD patients into low- and high-risk subgroups, independently predicting prognosis. Its performance was verified by nomogram (C-index = 0.736) and decision curve analysis. Gene set variation analysis disclosed the two groups' molecular characteristics. We also evaluated the tumor immune microenvironment by dissecting 28 infiltrated immune cells, 47 immune checkpoint gene expressions, and immunophenoscore within the two subgroups. Furthermore, the risk signature could predict sensitivity to immune checkpoint inhibitors and other anticancer therapies. Eventually, in vitro and in vivo experiments were conducted to validate LINC00669's function using qRT-PCR, CCK8, flow cytometry, western blot, and immunofluorescence staining. The gain- and loss-of-function study substantiated LINC00669's oncogenic effects, which stimulated non-small cell lung cancer cell proliferation but reduced apoptosis via activating the Wnt/β-catenin pathway. Its oncogenic potentials were validated in the xenograft mouse model. Overall, we identified a novel oncogenic large intergenic non-coding RNA (lincRNA), LINC00669. The resulting signature may facilitate predicting prognosis and therapy responses in LUAD.
Collapse
Affiliation(s)
- Jinhong Zhu
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin, China
| | - Kui Cao
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ping Zhang
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jianqun Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| |
Collapse
|
7
|
Ma J, Cao K, Ling X, Zhang P, Zhu J. LncRNA HAR1A Suppresses the Development of Non-Small Cell Lung Cancer by Inactivating the STAT3 Pathway. Cancers (Basel) 2022; 14:cancers14122845. [PMID: 35740511 PMCID: PMC9221461 DOI: 10.3390/cancers14122845] [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: 04/25/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary We found that lncRNA Highly Accelerated Region 1A (HAR1A) was down regulated in NSCLC. Moreover, a 23-gene signature derived from HAR1A-related cancer cell survival genes could predict prognosis and chemotherapy response in LUAD. In vitro experiments indicated that HAR1A suppressed NSCLC growth by inhibiting the STAT3 signaling pathway, which was verified in the animal model. Overall, HAR1A acts as a tumor suppressor in NSCLC. The prognostic signature showed promise in predicting prognosis and chemotherapy sensitivity. Abstract It is imperative to advance the understanding of lung cancer biology. The Cancer Genome Atlas (TCGA) dataset was used for bioinformatics analysis. CCK-8 assay, flow cytometry, and western blot were performed in vitro, followed by in vivo study. We found that lncRNA Highly Accelerated Region 1A (HAR1A) is significantly downregulated in lung adenocarcinoma (LUAD) and negatively associated with prognosis. We improved the prognostic accuracy of HAR1A in LUAD by combining genes regulating cell apoptosis and cell cycle to generate a 23-gene signature. Nomogram and decision curve analysis (DCA) confirmed that the gene signature performed robustly in predicting overall survival. Gene set variation analysis (GSVA) demonstrated several significantly upregulated malignancy-related events in the high-risk group, including DNA replication, DNA repair, glycolysis, hypoxia, MYC targets v2, and mTORC1. The risk signature distinguished LUAD patients suitable for chemotherapies or targeted therapies. Additionally, the knockdown of HAR1A accelerated NSCLC cell proliferation but inhibited apoptosis and vice versa. HAR1A regulated cellular activities through the STAT3 signaling pathway. The tumor-suppressing role of HAR1A was verified in the mouse model. Overall, the gene signature was robustly predictive of prognosis and sensitivity to anti-tumor drugs. HAR1A functions as a tumor suppressor in NSCLC by regulating the STAT3 signaling pathway.
Collapse
Affiliation(s)
- Jianqun Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China; (J.M.); (X.L.)
| | - Kui Cao
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China; (K.C.); (P.Z.)
- Department of Clinical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China
| | - Xiaodong Ling
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China; (J.M.); (X.L.)
| | - Ping Zhang
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China; (K.C.); (P.Z.)
| | - Jinhong Zhu
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China; (K.C.); (P.Z.)
- Correspondence: ; Tel.: +86-451-86298398
| |
Collapse
|
8
|
Jing L, Zhang X, Liu D, Yang Y, Xiong H, Dong G. ACK1 Contributes to the Pathogenesis of Inflammation and Autoimmunity by Promoting the Activation of TLR Signaling Pathways. Front Immunol 2022; 13:864995. [PMID: 35669783 PMCID: PMC9164107 DOI: 10.3389/fimmu.2022.864995] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Toll-like receptors (TLRs) are the first line of defense in the immune system, whose activation plays a key role in the pathogenesis of inflammation and autoimmunity. TLRs can activate a variety of immune cells such as macrophages and dendritic cells, which produce proinflammatory cytokines, chemokines, and co-stimulatory molecules that lead to the development of inflammation and autoimmune diseases. As a nonreceptor tyrosine kinase, ACK1 is involved in multiple signaling pathways and physiological processes. However, the roles of ACK1 in the activation of TLR pathways and in the pathogenesis of inflammation and autoimmune diseases have not yet been reported. We found that the expression of ACK1 could be upregulated by TLR pathways in vivo and in vitro. Intriguingly, overexpression of ACK1 significantly promoted the activation of TLR4, TLR7, and TLR9 pathways, while knockdown of ACK1 or the use of the ACK1 inhibitor AIM-100 significantly inhibited the activation of TLR4, TLR7, and TLR9 pathways. In vivo studies showed that the inhibition of ACK1 activity by AIM-100 could significantly protect mice from the TLR4 agonist lipopolysaccharide (LPS)-mediated endotoxin shock and alleviate the condition of imiquimod-mediated lupus-prone mice and MRL/lpr mice. In summary, ACK1 participates in TLR-mediated inflammation and autoimmunity and has great potential in controlling inflammation and alleviating autoimmune diseases.
Collapse
Affiliation(s)
- Lina Jing
- Cheeloo College of Medicine, Shandong University, Jinan, China
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, China
| | - Xin Zhang
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, China
- School of Medical Laboratory, Weifang Medical University, Weifang, China
| | - Dong Liu
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining, China
| | - Yonghong Yang
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, China
| | - Huabao Xiong
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, China
- Jining Key Laboratory of Immunology, Jining Medical University, Jining, China
- *Correspondence: Guanjun Dong, ; Huabao Xiong,
| | - Guanjun Dong
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, China
- Jining Key Laboratory of Immunology, Jining Medical University, Jining, China
- *Correspondence: Guanjun Dong, ; Huabao Xiong,
| |
Collapse
|
9
|
Wang H, Zhang R, Li E, Yan R, Ma B, Ma Q. Pan-Cancer Transcriptome and Immune Infiltration Analyses Reveal the Oncogenic Role of Far Upstream Element-Binding Protein 1 (FUBP1). Front Mol Biosci 2022; 9:794715. [PMID: 35274005 PMCID: PMC8902172 DOI: 10.3389/fmolb.2022.794715] [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: 10/14/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Despite increasing evidence to support the relationship between FUBP1 and tumorigenesis in some types of cancers, there have been no analyses from a pan-cancer perspective. Here, we are the first to investigate the putative oncogenic role of FUBP1 in 33 cancer types based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Dysregulated FUBP1 expression was observed in most cancer types, and high FUBP1 expression suggests poor prognosis in cancers such as ACC, KICH, LIHC, LUAD, LUSC, SARC, CESC, and SKCM. Missense mutation is the most common type of FUBP1 mutation, and R430 in KH_4 is a predominant mutation site. Enhanced phosphorylation of FUBP1 at the S120 site has been observed in clear cell RCC, lung adenocarcinoma, and pediatric brain cancer specimens from African-American and Asian individuals. The expression of FUBP1 was found to be negatively correlated with the infiltration of CD8+ T lymphocytes in GBM, HNSC-HPV- and UCEC but positively correlated with that of tumor-associated fibroblasts in CESC, ESCA, HNSC, LIHC, LUAD, PAAD, and THYM. Furthermore, RNA splicing and spliceosome signaling were predominantly enriched in both GO and KEGG analyses of the functional mechanism of FUBP1. Briefly, this pan-cancer analysis comprehensively revealed the multifaceted characteristics and oncogenic role of FUBP1 in different human cancers.
Collapse
Affiliation(s)
| | | | | | | | - Baoan Ma
- *Correspondence: Qiong Ma, ; Baoan Ma,
| | - Qiong Ma
- *Correspondence: Qiong Ma, ; Baoan Ma,
| |
Collapse
|
10
|
Wang A, Pei J, Shuai W, Lin C, Feng L, Wang Y, Lin F, Ouyang L, Wang G. Small Molecules Targeting Activated Cdc42-Associated Kinase 1 (ACK1/TNK2) for the Treatment of Cancers. J Med Chem 2021; 64:16328-16348. [PMID: 34735773 DOI: 10.1021/acs.jmedchem.1c01030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activated Cdc42-associated kinase 1 (ACK1/TNK2) is a nonreceptor tyrosine kinase with a unique structure. It not only can act as an activated transmembrane effector of receptor tyrosine kinases (RTKs) to transmit various RTK signals but also can play a corresponding role in epigenetic regulation. A number of studies have shown that ACK1 is a carcinogenic factor. Blockage of ACK1 has been proven to be able to inhibit cancer cell survival, proliferation, migration, and radiation resistance. Thus, ACK1 is a promising potential antitumor target. To date, despite many efforts to develop ACK1 inhibitors, no specific small molecule inhibitors have entered clinical trials. This Perspective provides an overview of the structural features, biological functions, and association with diseases of ACK1 and in vitro and in vivo activities, selectivity, and therapeutic potential of small molecule ACK1 inhibitors with different chemotypes.
Collapse
Affiliation(s)
- Aoxue Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Junping Pei
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Congcong Lin
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yuxi Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Feng Lin
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| |
Collapse
|
11
|
Zhu J, Ao H, Liu M, Cao K, Ma J. UBE2T promotes autophagy via the p53/AMPK/mTOR signaling pathway in lung adenocarcinoma. J Transl Med 2021; 19:374. [PMID: 34461934 PMCID: PMC8407090 DOI: 10.1186/s12967-021-03056-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 08/24/2021] [Indexed: 12/25/2022] Open
Abstract
Background Ubiquitin-conjugating enzyme E2T (UBE2T) acts as an oncogene in various types of cancer. However, the mechanisms behind its oncogenic role remain unclear in lung cancer. This study aims to explore the function and clinical relevance of UBE2T in lung cancer. Methods Lentiviral vectors were used to mediate UBE2T depletion or overexpress UBE2T in lung cancer cells. CCK8 analysis and western blotting were performed to investigate the effects of UBE2T on proliferation, autophagy, and relevant signaling pathways. To exploit the clinical significance of UBE2T, we performed immunohistochemistry staining with an anti-UBE2T antibody on 131 NSCLC samples. Moreover, we downloaded the human lung adenocarcinoma (LUAD) dataset from The Cancer Atlas Project (TCGA). Lasso Cox regression model was adopted to establish a prognostic model with UBE2T-correlated autophagy genes. Results We found that UBE2T stimulated proliferation and autophagy, and silencing this gene abolished autophagy in lung cancer cells. As suggested by Gene set enrichment analysis, we observed that UBE2T downregulated p53 levels in A549 cells and vice versa. Blockade of p53 counteracted the inhibitory effects of UBE2T depletion on autophagy. Meanwhile, the AMPK/mTOR signaling pathway was activated during UBE2T-mediated autophagy, suggesting that UBE2T promotes autophagy via the p53/AMPK/mTOR pathway. Interestingly, UBE2T overexpression increased cisplatin-trigged autophagy and led to cisplatin resistance of A549 cells, whereas inhibiting autophagy reversed drug resistance. However, no association was observed between UEB2T and overall survival in a population of 131 resectable NSCLC patients. Therefore, we developed and validated a multiple gene signature by considering UBE2T and its relevance in autophagy in lung cancer. The risk score derived from the prognostic signature significantly stratified LUAD patients into low- and high-risk groups with different overall survival. The risk score might independently predict prognosis. Interestingly, nomogram and decision curve analysis demonstrated that the signature’s prognostic accuracy culminated while combined with clinical features. Finally, the risk score showed great potential in predicting clinical chemosensitivity. Conclusions We found that UBE2T upregulates autophagy in NSCLC cells by activating the p53/AMPK/mTOR signaling pathway. The clinical predicting ability of UBE2T in LUAD can be improved by considering the autophagy-regulatory role of UBE2T. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03056-1.
Collapse
Affiliation(s)
- Jinhong Zhu
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Haijiao Ao
- Department of Clinical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Mingdong Liu
- Department of Clinical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Kui Cao
- Department of Clinical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Jianqun Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China.
| |
Collapse
|
12
|
Ling S, He Y, Li X, Ma Y, Li Y, Kong B, Huang P. Significant Gene Biomarker Tyrosine Kinase Non-receptor 2 Mediated Cell Proliferation and Invasion in Colon Cancer. Front Genet 2021; 12:653657. [PMID: 34421982 PMCID: PMC8371684 DOI: 10.3389/fgene.2021.653657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/21/2021] [Indexed: 01/22/2023] Open
Abstract
Objective: This study aimed to investigate the expression and biological functions of TNK2 and miR-125a-3p in colon cancer. Materials and methods: The expression of TNK2 and miR-125a-3p in colon cancer tissues was analyzed using data deposited on public databases including UALCAN and ONCOMINE. We verified their expression in colon cancer cell lines by RT-qPCR and western blotting. By regulating the expression of TNK2 and miR-125a-3p in colon cancer cells, their functions and potential mechanisms were explored. Results:TNK2 was overexpressed in colon cancer cell lines, and it was found to directly bind to miR-125a-3p, which was downregulated in these cell lines. Their expression affected the proliferation and invasion of colon cancer cells. Additionally, colon cancer patients with lower TNK2 expression had better prognoses than those with higher TNK2 expression. Conclusion: Our results indicated that TNK2 and miR-125a-3p play critical roles in colon cancer, and could also serve as biomarkers for the diagnosis and prognosis of this malignant disease.
Collapse
Affiliation(s)
- Sunkai Ling
- Medical School of Southeast University, Nanjing, China
| | - Yanru He
- Department of Cardiology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
| | - Xiaoxue Li
- Medical School of Southeast University, Nanjing, China
| | - Yu Ma
- Medical School of Southeast University, Nanjing, China
| | - Yuan Li
- Medical School of Southeast University, Nanjing, China
| | - Bo Kong
- Department of Surgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany.,Department of General Surgery, University of Ulm, Ulm, Germany
| | - Peilin Huang
- Medical School of Southeast University, Nanjing, China
| |
Collapse
|
13
|
Meng T, Tong Z, Yang MY, Zhang Y, Liu Y, Wang ZZ, Zhu LX, Wu J. Immune implication of FAM83D gene in hepatocellular carcinoma. Bioengineered 2021; 12:3578-3592. [PMID: 34308751 PMCID: PMC8806426 DOI: 10.1080/21655979.2021.1950260] [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] [Indexed: 11/15/2022] Open
Abstract
FAM83D has been demonstrated to contribute to tumorigenesis. However, its immune effects in hepatocellular carcinoma (HCC) have not been reported. This study aimed to identify the immune role of FAM83D in HCC. FAM83D was over-expressed in HCC and contributed to poor prognosis according to the results of data analysis based on The Cancer Genome Atlas (TCGA). Afterward, the levels of immune cells infiltration were found to be correlated with the expression level of FAM83D in HCC. Through TISIDB and cBioPortal network tools, a total of 82 FAM83D-associated genes were screened out, including 12 immunoinhibitors, 20 immunostimulators and 50 tightly co-expressed genes. TCGA cohort was divided into train set and test set on the basis of the proportion of 7:3. According to FAM83D-associated immunomodulators, a four gene predicted model was established using train set via the Cox regression analysis. Survival analysis demonstrated that the overall survival (OS) of high-risk HCC patients was poor compared with the patients in low-risk group. The reliability and predicted power of the risk-score model were identified by a receiver operating characteristic (ROC) curve. A risk-score based nomogram as well as a calibration curve, which were created could be used to anticipate patient’s 1-year, 3-year and 5-year survival probabilities. The test set was used to validate these results. Our findings showed that the FAM83D gene was related with HCC immunity. The immune marker chosen could be a promising biomarker for HCC prognosis.
Collapse
Affiliation(s)
- Tao Meng
- Department of General Surgery and Centre Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhong Tong
- Department of General Surgery, Hefei City First People's Hospital, Hefei, China
| | - Ming-Ya Yang
- Department of General Surgery and Centre Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yan Zhang
- Department of General Surgery and Centre Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yu Liu
- Department of General Surgery and Centre Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhen-Zhen Wang
- Department of General Surgery and Centre Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li-Xin Zhu
- Department of General Surgery and Centre Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jin Wu
- Department of General Surgery and Centre Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| |
Collapse
|
14
|
Analyzing the characteristics of immune cell infiltration in lung adenocarcinoma via bioinformatics to predict the effect of immunotherapy. Immunogenetics 2021; 73:369-380. [PMID: 34302518 DOI: 10.1007/s00251-021-01223-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/14/2021] [Indexed: 02/05/2023]
Abstract
Recent studies have shown that tumor immune cell infiltration (ICI) is associated with immunotherapy sensitivity and the prognosis of lung adenocarcinoma (LUAD). However, the immunoinfiltrative landscape of LUAD has not been elucidated. We propose two computational algorithms to unravel the ICI landscape to evaluate the efficacy of immunotherapy in LUAD patients. The raw data of LUAD patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were analyzed. After merging these datasets and removing the batch differences, we used the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm to obtain the immune cell content of all the samples. The unsupervised consistency clustering algorithm was used to analyze the ICI subtypes, and three subgroups were obtained. In addition, the unsupervised consistency clustering algorithm was used to analyze the differentially expressed genes (DEGs) of the ICI subtypes and obtain three ICI gene clusters. Finally, the ICI score was determined by using principal component analysis (PCA) for the gene signature. The ICI score of LUAD patients ranged from - 32.26 to 12.89 and represents the prognosis and the response to immunotherapy. High ICI scores were characterized by the T cell receptor signaling pathway, B cell receptor signaling pathway, and natural killer cell-mediated cytotoxicity, suggesting that some immune cells were activated and had increased activity, which may be the cause of the better prognosis for patients with high ICI scores. Additionally, patients with higher ICI scores showed a significant immune therapeutic advantage and clinical benefit. This study shows that the ICI score may be a potent prognostic biomarker and predictor of therapy with immune checkpoint inhibitors.
Collapse
|
15
|
Wang X, Liu Y, Leng X, Cao K, Sun W, Zhu J, Ma J. UBE2T Contributes to the Prognosis of Esophageal Squamous Cell Carcinoma. Pathol Oncol Res 2021; 27:632531. [PMID: 34257599 PMCID: PMC8262217 DOI: 10.3389/pore.2021.632531] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
Background: The ubiquitin-conjugating enzyme E2 T (UBE2T) has been shown to contribute to several types of cancer. However, no publication has reported its implication in esophageal squamous cell cancer (ESCC). Methods: We explored several public databases, including The Cancer Genome Atlas (TCGA), Oncomine, and gene expression Omnibus (GEO). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene set enrichment analysis (GSEA) were adopted to explore involved signaling pathways. We used R software to develop prognostic gene signatures with the LASSO and stepwise Cox regression analysis, separately. Immunohistochemistry staining was performed to detect UBE2T in 90 ESCC patients, followed by survival analysis. We also used an R package pRRophetic to evaluate chemotherapy sensitivity for the TCGA–ESCC cohort. Results: We found significantly increased UBE2T transcript levels and DNA copy numbers in ESCC tissues. UBE2T was associated with the p53 signaling pathway, cell cycle, Fanconi anemia pathway, and DNA replication, as indicated by Go, KEGG pathway enrichment analysis. These pathways were also upregulated in ESCC. The prognostic signatures with UBE2T-associated genes could stratify ESCC patients into low- and high-risk groups with significantly different overall survival in the TCGA–ESCC cohort. We also validated the association of UBE2T with unfavorable survival in 90 ESCC patients recruited for this study. Moreover, we found that the low-risk group was significantly more sensitive to chemotherapy than the high-risk group. Conclusions: UBE2T is involved in the development of ESCC, and gene signatures derived from UBE2T-associated genes are predictive of prognosis in ESCC.
Collapse
Affiliation(s)
- Xiaoyuan Wang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yang Liu
- Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xue Leng
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Kui Cao
- Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wentao Sun
- Department of Radiology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinhong Zhu
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jianqun Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| |
Collapse
|
16
|
Zhou X, Zhang FY, Liu Y, Wei DX. A Risk Prediction Model for Breast Cancer Based on Immune Genes Related to Early Growth Response Proteins Family. Front Mol Biosci 2021; 7:616547. [PMID: 33614706 PMCID: PMC7887293 DOI: 10.3389/fmolb.2020.616547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022] Open
Abstract
Early growth response proteins (EGRs), a transcriptional regulatory family comprised of EGR1, EGR2, EGR3, and EGR 4, are reportedly involved in a vast array of functions. However, EGRs, as a whole, are rarely studied in breast cancer cases. This research was performed based on public datasets. The results demonstrated that, except EGR4, the other EGRs were differentially expressed genes in breast cancer. Subsequently, this study determined the prognosis significance of the EGR family, higher expression levels of EGRs indicating better overall survival (OS) and disease-free survival (DFS), except EGR4. So we attempted to explore the potential mechanism behind the prognostic value of EGRs. At the DNA level, however, neither DNA methylation status nor genetic alterations of EGRs contributed to the prognosis significance. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that EGRs were involved in several immune-related functions. Afterward, we assessed the correlation between EGRs and the immune system before establishing a risk prediction model with a 14-gene immune signature associated with EGRs, a prognostic nomogram predicting individuals’ 1-, 3-, and 5-year survival probabilities. The risk score was an independent prognosis predictor in the breast cancer cohorts. This study evidenced EGRs’ significance for tumor immunity, demonstrating that the EGR family may be a potential immunotherapeutic target for breast cancer. The 14-gene immune signature is a promising prognostic biomarker in breast cancer.
Collapse
Affiliation(s)
- Xin Zhou
- Department of Breast Surgery, Zibo Maternal and Child Health Hospital, Zibo, China
| | - Fang-Yuan Zhang
- Department of Breast Surgery, Zibo Maternal and Child Health Hospital, Zibo, China
| | - Yan Liu
- Department of Breast Surgery, Zibo Maternal and Child Health Hospital, Zibo, China
| | - Dong-Xin Wei
- Department of Breast Surgery, Zibo Maternal and Child Health Hospital, Zibo, China
| |
Collapse
|