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Choudhery MS, Arif T, Mahmood R, Harris DT. CAR-T-Cell-Based Cancer Immunotherapies: Potentials, Limitations, and Future Prospects. J Clin Med 2024; 13:3202. [PMID: 38892913 PMCID: PMC11172642 DOI: 10.3390/jcm13113202] [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: 03/14/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer encompasses various elements occurring at the cellular and genetic levels, necessitating an immunotherapy capable of efficiently addressing both aspects. T cells can combat cancer cells by specifically recognizing antigens on them. This innate capability of T cells has been used to develop cellular immunotherapies, but most of them can only target antigens through major histocompatibility complexes (MHCs). New gene-editing techniques such as clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (CRISPR-cas9) can precisely edit the DNA sequences. CRISPR-cas9 has made it possible to generate genetically engineered chimeric antigen receptors (CARs) that can overcome the problems associated with old immunotherapies. In chimeric antigen receptor T (CAR-T) cell therapy, the patient's T cells are isolated and genetically modified to exhibit synthetic CAR(s). CAR-T cell treatment has shown remarkably positive clinical outcomes in cancers of various types. Nevertheless, there are various challenges that reduce CAR-T effectiveness in solid tumors. It is required to address these challenges in order to make CAR-T cell therapy a better and safer option. Combining CAR-T treatment with other immunotherapies that target multiple antigens has shown positive outcomes. Moreover, recently generated Boolean logic-gated advanced CARs along with artificial intelligence has expanded its potential to treat solid tumors in addition to blood cancers. This review aims to describe the structure, types, and various methods used to develop CAR-T cells. The clinical applications of CAR-T cells in hematological malignancies and solid tumours have been described in detail. In addition, this discussion has addressed the limitations associated with CAR-T cells, explored potential strategies to mitigate CAR-T-related toxicities, and delved into future perspectives.
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Affiliation(s)
- Mahmood S. Choudhery
- Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore 54600, Pakistan;
| | - Taqdees Arif
- Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore 54600, Pakistan;
| | - Ruhma Mahmood
- Jinnah Hospital, Allama Iqbal Medical College, Lahore 54700, Pakistan;
| | - David T. Harris
- Department of Immunobiology, College of Medicine, University of Arizona Health Sciences Biorepository, The University of Arizona, Tucson, AZ 85724-5221, USA;
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Borikun T, Mushii O, Pavlova A, Burda T, Zadvornyi T. TUMOR MICROENVIRONMENT-ASSOCIATED miR-7-5p, miR-19a-3p, AND miR-23b-3p EXPRESSION IN PROSTATE CANCER WITH DIFFERENT PROGRESSION RISK. Exp Oncol 2024; 45:432-442. [PMID: 38328847 DOI: 10.15407/exp-oncology.2023.04.432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND The tumor microenvironment (TME) plays an important role in the occurrence and progression of prostate cancer (PCa). At the same time, the mechanisms and features of the interaction between tumor cells and individual components of the TME in PCa remain not fully elucidated. The aim was to study the expression levels of tumor-associated miR-7-5p, miR-19a-3p, and miR-23b-3p in the PCa tissue and to analyze their relationship with the features of TME. MATERIALS AND METHODS The work is based on the analysis of the results of the examination and treatment of 50 patients with PCa of stages II-IV. The expression of miRNA in the PCa tissue was analyzed by the real-time polymerase chain reaction. The expression of alpha-smooth muscle actin (α-SMA), vimentin (VIM), and CD68 in PCa tissue was determined by the immunohistochemical method. The identification of mast cells in the PCa tissue was assessed by the histochemical method. RESULTS The analysis of the expression levels of tumor-associated miRNAs demonstrated that the tumor tissue of patients with a high risk of PCa progression was characterized by 4.93 (p < 0.01) and 8.97 (p < 0.05) times higher levels of miR-19a-3p and miR-23b-3p, respectively, compared to similar indicators in the group of patients with a low risk of PCa progression. The levels of miR-7-5p and miR-19a-3p expression in the PCa tissue correlated with the expression level of α-SMA (r = 0.49 and r = 0.45, respectively; p < 0.05) and VIM (r = 0.45 and r = 0.46; respectively, p < 0.05). A direct relationship (r = 0.44; p < 0.05) was established between the level of miR-7-5p expression and the degree of infiltration of the prostate gland tissue by tumor-associated macrophages. CONCLUSIONS The features of the expression of tumor-associated miR-7-5p, miR-19a-3p, and miR-23b-3p indicated the prospect of their use as markers of the aggressiveness of the PCa course.
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Affiliation(s)
- T Borikun
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine
| | - O Mushii
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine
| | - A Pavlova
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine
| | - T Burda
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine
| | - T Zadvornyi
- R.E. Kavetsky Institute of Experimental Pathology, Oncology, and Radiobiology, NAS of Ukraine, Kyiv, Ukraine.
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Wu Z, Xu N, Li G, Yang W, Zhang C, Zhong H, Wu G, Chen F, Li D. Multi-omics analysis of the oncogenic role of optic atrophy 1 in human cancer. Aging (Albany NY) 2023; 15:12982-12997. [PMID: 37980164 DOI: 10.18632/aging.205214] [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: 08/03/2023] [Accepted: 10/15/2023] [Indexed: 11/20/2023]
Abstract
OBJECTIVE To investigate the prognostic significance of optic atrophy 1 (OPA1) in pan-cancer and analyze the relationship between OPA1 and immune infiltration in cancer. RESULTS OPA1 exhibited high expression levels or mutations in various types of tumor cells, and its expression levels were significantly correlated with the survival rate of tumor patients. In different tumor tissues, there was a notable positive correlation between OPA1 expression levels and the infiltration of cancer-associated fibroblasts in the immune microenvironment. Additionally, OPA1 and its related genes were found to be involved in several crucial biological processes, including protein phosphorylation, protein import into the nucleus, and protein binding. CONCLUSION OPA1 is highly expressed or mutated in numerous tumors and is strongly associated with protein phosphorylation, patient prognosis, and immune cell infiltration. OPA1 holds promise as a novel prognostic marker with potential clinical utility across various tumor types. METHODS We examined OPA1 expression in pan-cancer at both the gene and protein levels using various databases, including Tumor Immune Estimation Resource 2.0 (TIMER 2.0), Gene Expression Profiling Interactive Analysis (GEPIA2), UALCAN, and The Human Protein Atlas (HPA). We utilized the Kaplan-Meier plotter and GEPIA datasets to analyze the relationship between OPA1 expression levels and patient prognosis. Through the cBioPortal database, we detected OPA1 mutations in tumors and examined their relationship with patient prognosis. We employed the TIMER 2.0 database to explore the correlation between OPA1 expression levels in tumor tissue and the infiltration of cancer-associated fibroblasts in the immune microenvironment. Furthermore, we conducted a gene search associated with OPA1 and performed enrichment analysis to identify the main signaling pathways and biological processes linked to them.
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Affiliation(s)
- Ziyi Wu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Nuo Xu
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Guoqing Li
- Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Wen Yang
- The Department of Network Center, Hainan Normal University, Haikou, Hainan 571158, China
| | - Chen Zhang
- Department of Emergency, The Fourth People’s Hospital of Zigong, Zigong, Sichuan 643000, China
| | - Hua Zhong
- Department of Orthopedics, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong 510900, China
| | - Gen Wu
- Department of Orthopedics, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong 510900, China
| | - Fei Chen
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Dianqing Li
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
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Wang C, Jiang X, Zhao Q, Xie Z, Cai H. The diagnostic or prognostic values of FADD in cancers based on pan‑cancer analysis. Biomed Rep 2023; 19:77. [PMID: 37829257 PMCID: PMC10565789 DOI: 10.3892/br.2023.1659] [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: 04/11/2023] [Accepted: 08/10/2023] [Indexed: 10/14/2023] Open
Abstract
Previous studies have determined that aberrant expression of the fas-associated death domain (FADD) contributes to the development of cancer. However, no pan-cancer analysis has been reported to explore the relationship between FADD and various cancers. Multiple databases were screened to identify cancer datasets for the present study and to validate the expression of FADD in various tumors. The association of FADD alteration with cancer prognosis, clinical features and tumor immunity was also evaluated. Reverse transcription-quantitative PCR (RT-qPCR) was utilized to confirm the expression of FADD in breast, colon, liver and gastric cancer cells. Analysis of Gene Expression Omnibus database and The Cancer Genome Atlas database indicated that FADD was highly expressed in breast invasive carcinoma (BRCA), cervical squamous cell carcinoma and endocervical adenocarcinoma, cholangiocarcinoma, colon adenocarcinoma (COAD), esophageal carcinoma (ESCA), kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD) and prostate adenocarcinoma, whereas RT-qPCR results revealed that FADD was highly expressed in breast cancer and colon cancer. Further analyses demonstrated that FADD expression was significantly altered in ESCA, head and neck squamous cell carcinoma (HNSC), lung squamous cell carcinoma and BRCA. FADD expression was observed to be a risk factor of the overall survival in patients with HNSC, LIHC and LUAD as demonstrated by Kaplan-Meier and Cox regression analyses. The results of the present study demonstrated that FADD is highly expressed in numerous malignancies and can be utilized as a biomarker for the diagnosis of BRCA, COAD, LIHC and stomach adenocarcinoma. Moreover, FADD expression is a predictive risk factor for the development of HNSC, LIHC and LUAD and can potentially be used as a prognostic marker for these cancers.
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Affiliation(s)
- Chenyu Wang
- Clinical Medical College of Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, P.R. China
| | - Xianglai Jiang
- Clinical Medical College of Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, P.R. China
- Department of General Surgery, General Surgery Clinical Center, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Qiqi Zhao
- Clinical Medical College of Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, P.R. China
- Department of General Surgery, General Surgery Clinical Center, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Zhiyuan Xie
- Clinical Medical College of Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, P.R. China
| | - Hui Cai
- Department of General Surgery, General Surgery Clinical Center, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
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Ding N, Li M, Zhao X. PHF5A is a potential diagnostic, prognostic, and immunological biomarker in pan-cancer. Sci Rep 2023; 13:17521. [PMID: 37845358 PMCID: PMC10579340 DOI: 10.1038/s41598-023-44899-6] [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: 08/21/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023] Open
Abstract
Studying the molecular mechanisms and regulatory functions of genes is crucial for exploring new approaches and tactics in cancer therapy. Studies have shown that the aberrant expression of PHF5A in tumors is linked to the origin and advancement of multiple cancers. However, its role in diagnosis, prognosis, and immunological prediction has not been comprehensively investigated in a pan-cancer analysis. Using several bioinformatic tools, we conducted a systematic examination of the potential carcinogenesis of PHF5A in various tumors from multiple aspects. Our analysis indicated that PHF5A expression varied between normal and tumor tissues and was linked to clinical diagnosis and prognosis in various cancers. The results confirmed a notable variation in the levels of PHF5A promoter methylation among several types of primary tumor and normal tissues and methylation of the PHF5A promoter played a guiding role in prognosis in some cancers. According to our findings, PHF5A played a critical role in tumor immunity and it might be an excellent target for anticancer immunotherapy. To sum up, PHF5A can be used in pan-cancer diagnostics, prognostics, and immunotherapy.
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Affiliation(s)
- Na Ding
- Department of Pathology, Shaoxing Maternity and Child Health Care Hospital, Shaoxing, 312000, Zhejiang, People's Republic of China
| | - Meiping Li
- Department of Pathology, Shaoxing Maternity and Child Health Care Hospital, Shaoxing, 312000, Zhejiang, People's Republic of China
| | - Xiaokun Zhao
- School of Medicine, Shaoxing University, Shaoxing, 312000, Zhejiang, People's Republic of China.
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Adeuyan O, Gordon ER, Kenchappa D, Bracero Y, Singh A, Espinoza G, Geskin LJ, Saenger YM. An update on methods for detection of prognostic and predictive biomarkers in melanoma. Front Cell Dev Biol 2023; 11:1290696. [PMID: 37900283 PMCID: PMC10611507 DOI: 10.3389/fcell.2023.1290696] [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: 09/07/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
The approval of immunotherapy for stage II-IV melanoma has underscored the need for improved immune-based predictive and prognostic biomarkers. For resectable stage II-III patients, adjuvant immunotherapy has proven clinical benefit, yet many patients experience significant adverse events and may not require therapy. In the metastatic setting, single agent immunotherapy cures many patients but, in some cases, more intensive combination therapies against specific molecular targets are required. Therefore, the establishment of additional biomarkers to determine a patient's disease outcome (i.e., prognostic) or response to treatment (i.e., predictive) is of utmost importance. Multiple methods ranging from gene expression profiling of bulk tissue, to spatial transcriptomics of single cells and artificial intelligence-based image analysis have been utilized to better characterize the immune microenvironment in melanoma to provide novel predictive and prognostic biomarkers. In this review, we will highlight the different techniques currently under investigation for the detection of prognostic and predictive immune biomarkers in melanoma.
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Affiliation(s)
- Oluwaseyi Adeuyan
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Emily R. Gordon
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Divya Kenchappa
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Yadriel Bracero
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ajay Singh
- Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Larisa J. Geskin
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, United States
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7
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Huang Q, Lv Q, Tang W, Pan Y, Xing Y, He M, Wu H, Huang J, Huang C, Lan H, Chen J, Xiao G. A comprehensively prognostic and immunological analysis of chloride intracellular channel protein 5 (CLIC5) in pan-cancer and identification in ovarian cancer. J Cancer Res Clin Oncol 2023; 149:10561-10583. [PMID: 37286734 DOI: 10.1007/s00432-023-04927-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
CLIC5 encoded protein associates with actin-based cytoskeletal and is increasingly thought to play significant roles in human cancers. We use TCGA and GEO to explore CLIC5 expression differences, mutation and DNA methylation, TMB, MSI, and immune cell infiltration. We verified the mRNA expression of CLIC5 in human ovarian cancer cells by real-time PCR and detected the expression of CLIC5 as well as immune marker genes in ovarian cancer by immunohistochemistry. The pan-cancer analysis showed that CLIC5 is highly expressed in several malignant tumors. In some cancers, CLIC5 expression in tumor samples is associated with poorer overall survival. For example, patients with ovarian cancer with high expression of CLIC5 have a poor prognosis. CLIC5 mutation frequency increased in all tumor types. The CLIC5 promoter is hypomethylated in most tumors. CLIC5 was associated with tumor immunity and different immune cells of different tumor types, such as CD8 + T cells, tumor-associated fibroblasts, macrophages, etc. CLIC5 was positively correlated with various immune checkpoints, and TMB and MSI were correlated with dysregulation of CLIC5 in tumors. The expression of CLIC5 in ovarian cancer was detected by qPCR and IHC, and the results were consistent with the bioinformatics results. There were a strong positive correlation between CLIC5 expression and M2 macrophage (CD163) infiltration and a negative correlation with CD8 + T-cell infiltration. In conclusions, our first pan-cancer analysis offered a detailed grasp of the cancerogenic functions of CLIC5 in a variety of malignancies. CLIC5 participated in immunomodulation and performed a crucial function in the tumor microenvironment.
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Affiliation(s)
- Qiaoling Huang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
- Central Laboratory, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Quankun Lv
- Emergency Department, the Sixth Affiliated Hospital, South China University of Technology, Foshan, 528000, Guangdong, People's Republic of China
| | - Waner Tang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
- Central Laboratory, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Yuhua Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yue Xing
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Min He
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Huiyi Wu
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Jiamin Huang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Che Huang
- Hubei University of Medicine, Shiyan, 442000, China
| | - Haifeng Lan
- Department of Orthopaedic Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, People's Republic of China
| | - Jingqi Chen
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
- Oncology Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
| | - Guohong Xiao
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
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Ding J, Ji X, Liu L, Chen DZ, Luo N, Yu XT, Guo F. A prognostic and immunological analysis of 7B-containing Kelch structural domain (KLHDC7B) in pan-cancer: a potential target for immunotherapy and survival. J Cancer Res Clin Oncol 2023; 149:7857-7876. [PMID: 37039902 DOI: 10.1007/s00432-023-04738-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/01/2023] [Indexed: 04/12/2023]
Abstract
PURPOSE KLHDC7B is a member of Kelch family, with a Kelch domain in the C-terminal half, which plays a role in various cellular events, such as cytoskeletal arrangement, protein degradation, gene expression. Although there is increasing evidence supporting KLHDC7B's vital role in tumorigenesis, a systematic analysis of KLHDC7B in cancers remains lacking. Therefore, we intended to investigate the prognostic value for KLHDC7B across 33 cancer types and explore its potential immunological function. METHODS GEO (Gene Expression Omnibus database) and TCGA (The Cancer Genome Atla) database were used to explore the role of KLHDC7B in 33 cancers. TIMER2, GEPIA2 and Kaplan-Meier plotter were utilized to explore the KLHDC7B expression level and prognostic value in different cancers. The pan cancer genetic variation and DNA methylation of KLHDC7B were analyzed by cBioPortal and MEXPRESS. TIMER2 was employed to investigate the correlation between KLHDC7B expression and immune infiltration. The relationship of KLHDC7B expression with TMB (tumor mutational burden) and MSI (microsatellite instability) were evaluated using Spearman correlation analysis. Finally, by GO and KEGG enrichment analysis, the underlying mechanisms of KLHDC7B in tumor pathophysiology were further investigated. RESULTS KLHDC7B expression level was related to pathological stages, MSI, TMB, immune checkpoint and immune cell infiltration in most cancers. Especially, we found that the KLHDC7B expression was negatively correlated with the immune infiltration of Myeloid derived suppressor cells into TGCT and GBM. Additionally, survival analysis showed that the expression of KLHDC7B was connected with overall survival (OS) in 3 cancers and disease-free survival (DFS) in 5 cancers. Furthermore, the enrichment analysis revealed that the KLHDC7B collecting genes and binding proteins are related to the function of proteins and immune response. CONCLUSION KLHDC7B demonstrates strong clinical utility as markers of prognostic and immune response in pan-cancer.
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Affiliation(s)
- Jiatong Ding
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315000, China
- The First School of Clinical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Xunhui Ji
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315000, China
- The First School of Clinical Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Lanqi Liu
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315000, China
| | - De-Zhi Chen
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315000, China
| | - Nan Luo
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315000, China
| | - Xiao-Ting Yu
- Department of Breast Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, China
| | - Fei Guo
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315000, China.
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Chen G, Yan J, Fu Z. Comprehensive Analysis to Identify LINC00511-hsa-miR-625-5p-SEMA6A Pathway Fuels Progression of Skin Cutaneous Melanoma. Int J Genomics 2023; 2023:6422941. [PMID: 37434634 PMCID: PMC10332930 DOI: 10.1155/2023/6422941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/13/2023] Open
Abstract
Objective Skin cutaneous melanoma (SKCM) is a highly lethal malignancy that poses a significant threat to human health. Recent research has shown that competing endogenous RNA (ceRNA) regulatory networks play a critical role in the development and progression of various types of cancer, including SKCM. The objective of this study is to investigate the ceRNA regulatory network associated with the transmembrane protein semaphorin 6A (SEMA6A) and identify the underlying molecular mechanisms involved in SKCM. Methods Expression profiles of four RNAs, including pseudogenes, long non-coding RNAs, microRNAs, and mRNAs were obtained from The Cancer Genome Atlas database. The analysis was completed by bioinformatics methods, and the expression levels of the selected genes were verified by cell experiments. Results Bioinformatics analysis revealed that the LINC00511-hsa-miR-625-5p-SEMA6A ceRNA network was associated with SKCM prognosis. Furthermore, immune infiltration analysis indicated that the LINC00511-hsa-miR-625-5p-SEMA6A axis may have an impact on changes in the tumor immune microenvironment of SKCM. Conclusion The LINC00511-hsa-miR-625-5p-SEMA6A axis could be a promising therapeutic target and a prognostic biomarker for SKCM.
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Affiliation(s)
- Guanghua Chen
- Department of Dermatology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - Jia Yan
- Department of General Surgery, University-Town Hospital of Chongqing Medical University, Chongqing 401331, China
| | - Zhou Fu
- Department of Respiratory, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
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10
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Wang Y, Guo Y, Song Y, Zou W, Zhang J, Yi Q, Xiao Y, Peng J, Li Y, Yao L. A pan-cancer analysis of the expression and molecular mechanism of DHX9 in human cancers. Front Pharmacol 2023; 14:1153067. [PMID: 37214432 PMCID: PMC10192771 DOI: 10.3389/fphar.2023.1153067] [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: 01/28/2023] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Finding new targets is necessary for understanding tumorigenesis and developing cancer therapeutics. DExH-box helicase 9 (DHX9) plays a central role in many cellular processes but its expression pattern and prognostic value in most types of cancer remain unclear. In this study, we extracted pan-cancer data from TCGA and GEO databases to explore the prognostic and immunological role of DHX9. The expression levels of DHX9 were then verified in tumor specimens by western blot and immunohistochemistry (IHC). The oncogenic roles of DHX9 in cancers were further verified by in vitro experiments. We first verified that DHX9 is highly expressed in most tumors but significantly decreased in kidney and thyroid cancers, and it is prominently correlated with the prognosis of patients with different tumors. The phosphorylation level of DHX9 was also increased in cancers. Enrichment analysis revealed that DHX9 was involved in Spliceosome, RNA transport and mRNA surveillance pathway. Furthermore, DHX9 expression exhibited strong correlations with immune cell infiltration, immune checkpoint genes, and tumor mutational burden (TMB)/microsatellite instability (MSI). In liver, lung, breast and renal cancer cells, the knockdown or depletion of DHX9 significantly affected the proliferation, metastasis and EMT process of cancer cells. In summary, this pan-cancer investigation provides a comprehensive understanding of the prognostic and immunological role of DHX9 in human cancers, and experiments indicated that DHX9 was a potential target for cancer treatment.
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Affiliation(s)
- Yanfeng Wang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yongxin Guo
- Anesthesia and Operation Center, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanping Song
- Department of Anesthesiology, No. 922 Hospital of PLA, Hengyang, Hunan, China
| | - Wenbo Zou
- Department of General Surgery, No. 924 Hospital of PLA Joint Logistic Support Force, Guilin, Guangxi, China
| | - Junjie Zhang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiong Yi
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yujie Xiao
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Peng
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yingqi Li
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Yao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, China
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11
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Wang X, Zhang K, Fu C, Wu F, Zhang J, Han B, Pan H, Luan L. High expression of centromere protein N as novel biomarkers for gastric adenocarcinoma. Cancer Rep (Hoboken) 2023; 6:e1798. [PMID: 36916294 PMCID: PMC10075295 DOI: 10.1002/cnr2.1798] [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: 10/23/2022] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND The role and mechanism of centromeric protein N (CENP-N), which has been associated with the development of various cancer types, are yet unclear in stomach adenocarcinoma (STAD). METHODS Data from the Cancer Genome Atlas and Genotype-Tissue Expression were used to determine whether CENP-N expression was altered in STAD tumors compared to normal tissues. Xiantao was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analysis on CENP-N. The relationship between CENP-N expression and immune cell infiltration was assessed using TCGA database. The expression of CENP-N in STAD and surrounding tissues was confirmed using immunohistochemical staining and the correlation between CENP-N expression and clinicopathological characteristics was examined. The effects of CENP-N knockdown by siRNA on proliferation were measured by CCK-8 and EdU assays in AGS cells. Following siRNA transfection, flow cytometry was performed to evaluate cell cycle and apoptotic alterations in AGS cells. The effect of CENP-N knockdown on the expression level of related proteins was detected by Westren blot. RESULTS CENP-N was highly expressed in STAD tissues, which was confirmed by our immunohistochemistry results. The degree of invasion, TNM stage, and lymph node metastases were all strongly associated with CENP-N expression. CENP-N was essential for the cell cycle, DNA replication, chromosomal segregation, and nuclear division; there was a positive correlation between CENP-N expression and infiltrating Th2 and NK CD56dim cells and a negative correlation between CENP-N expression and mast, pDC, NK, and B cell infiltration. When CENP-N expression in AGS cells was knocked down, cell proliferation dramatically reduced (p < .05) and the percentage of cells in the S and G2-M phases decreased significantly (p < .05). Silencing CENP-N significantly promoted the apoptosis of AGS cells (p < .05). Mechanistic investigations showed that silencing CENP-N expression may inhibit STAD proliferation through the Cyclin E1 and promote STAD apoptosis through the Bcl-2/Bax. CONCLUSION According to our data, CENP-N acts as an oncogene in STAD and may be a viable therapeutic target.
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Affiliation(s)
- Xiaojie Wang
- Department of Pathology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China.,Basic Medical School, Shenyang Medical College, Shenyang, China
| | - Keyuan Zhang
- Department of Pathology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China.,Basic Medical School, Shenyang Medical College, Shenyang, China
| | - Cun Fu
- Department of Pathology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China.,Basic Medical School, Shenyang Medical College, Shenyang, China
| | - Fei Wu
- Department of Pathology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Junjie Zhang
- Department of Pathology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Bin Han
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hai Pan
- Central Laboratory, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Lan Luan
- Department of Pathology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
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12
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MYL5 as a Novel Prognostic Marker is Associated with Immune Infiltrating in Breast Cancer: A Preliminary Study. Breast J 2023; 2023:9508632. [PMID: 36846347 PMCID: PMC9957649 DOI: 10.1155/2023/9508632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/19/2023]
Abstract
Background Myosin light chain plays a vital regulatory function in a large-scale cellular physiological procedure, however, the role of myosin light chain 5 (MYL5) in breast cancer has not been reported. In this study, we aimed to elucidate the effects of MYL5 on clinical prognosis and immune cell infiltration, and further explore the potential mechanism in breast cancer patients. Methods In this study, we first explored the expression pattern and prognostic value of MYL5 in breast cancer across multiple databases, including Oncomine, TCGA, GTEx, GEPIA2, PrognoScan, and Kaplan-Meier Plotter. The correlations of MYL5 expression with immune cell infiltration and associational gene markers in breast cancer were analyzed by using the TIMER, TIMER2.0, and TISIDB databases. The enrichment and prognosis analysis of MYL5-related genes were implemented by using LinkOmics datasets. Results We found that there was a low expression of MYL5 in breast cancer than in corresponding normal tissue by analyzing the data from Oncomine and TCGA datasets. Furthermore, research showed the prognosis of the MYL5 high-expression group was better than the low-expression group in breast cancer patients. Furthermore, MYL5 expression is markedly related to the tumor-infiltrating immune cells (TIICs), including cancer-associated fibroblast, B cell, CD8+ T cell, CD4+ T cell, macrophage, neutrophil, and dendritic cell, and related to immune molecules as well as the associated gene markers of TIICs. Conclusion MYL5 can serve as a prognostic signature in breast cancer and is associated with immune infiltration. This study first offers a relatively comprehensive understanding of the oncogenic roles of MYL5 for breast cancer.
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Zhang J, Zhang J, Zhao W, Li Q, Cheng W. Low expression of NR1H3 correlates with macrophage infiltration and indicates worse survival in breast cancer. Front Genet 2023; 13:1067826. [PMID: 36699456 PMCID: PMC9868774 DOI: 10.3389/fgene.2022.1067826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/10/2022] [Indexed: 01/11/2023] Open
Abstract
Background: Nuclear receptor NR1H3 is a key regulator of macrophage function and lipid homeostasis. Here, we aimed to visualize the prognostic value and immunological characterization of NR1H3 in breast cancer. Methods: The expression pattern and prognostic value of NR1H3 were analyzed via multiple databases, including TIMER2, GEPIA2 and Kaplan-Meier Plotter. TISIDB, TIMER2 and immunohistochemical analysis were used to investigate the correlation between NR1H3 expression and immune infiltration. GO enrichment analysis, KEGG analysis, Reactome analysis, ConsensusPathDB and GeneMANIA were used to visualize the functional enrichment of NR1H3 and signaling pathways related to NR1H3. Results: We demonstrated that the expression of NR1H3 was significantly lower in breast cancer compared with adjacent normal tissues. Kaplan-Meier survival curves showed shorter overall survival in basal breast cancer patients with low NR1H3 expression, and poorer prognosis of relapse-free survival in breast cancer patients with low NR1H3 expression. NR1H3 was mainly expressed in immune cells, and its expression was closely related with infiltrating levels of tumor-infiltrating immune cells in breast cancer. Additionally, univariate and multivariate analysis indicated that the expression of NR1H3 and the level of macrophage infiltration were independent prognostic factors for breast cancer. Gene interaction network analysis showed the function of NR1H3 involved in regulating of innate immune response and macrophage activation. Moreover, NR1H3 may function as a predictor of chemoresponsiveness in breast cancer. Conclusion: These findings suggest that NR1H3 serves as a prognostic biomarker and contributes to the regulation of macrophage activation in breast cancer.
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Affiliation(s)
- Jing Zhang
- Department of Integrated Therapy, Shanghai Cancer Center, Fudan University, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiawen Zhang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiwei Zhao
- Department of Integrated Therapy, Shanghai Cancer Center, Fudan University, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qingxian Li
- The Center of Reproductive Medicine, Second Affiliated Hospital of Naval Medical University, Shanghai, China,*Correspondence: Qingxian Li, ; Wenwu Cheng,
| | - Wenwu Cheng
- Department of Integrated Therapy, Shanghai Cancer Center, Fudan University, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China,*Correspondence: Qingxian Li, ; Wenwu Cheng,
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14
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Zhang F, Wang Y, Li H, Li L, Yang X, You X, Tang L. Pan-cancer analysis identifies LIFR as a prognostic and immunological biomarker for uterine corpus endometrial carcinoma. Front Oncol 2023; 13:1118906. [PMID: 36925915 PMCID: PMC10011451 DOI: 10.3389/fonc.2023.1118906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Background Leukemia inhibitory factor (LIF) exhibits significant tumor-promoting function, while its cognate receptor (LIFR) is considered to act as either a tumor promoter or suppressor. Dysregulation of LIF and LIFR is associated with the initiation, progression and metastasis of multiple cancer entities. Although increasing numbers of studies are revealing an indispensable critical role of LIFR in tumorigenesis for various different cancers, no systematic analysis of LIFR has appeared thus far. Methods Here, we comprehensively analyzed the expression profile and prognostic value of LIFR, and correlations between LIFR and the infiltration of immune cells and clinicopathological parameters across different tumor types using several bioinformatic tools. The expression profile of LIFR in various tumor types and clinical stages was investigated using the TIMER2 and GEPIA2 databases. Genetic alternations of LIFR were extracted from cBioPortal. The prognostic value of LIFR was assessed using GEPIA2 and Sanger box databases, and correlations between LIFR expression and immune infiltration were analyzed using the CIBERSORT method and TIMER2 database. The correlations between LIFR expression and immune and stromal scores were assessed using ESTIMATE. We also analyzed correlations between LIFR and immunoregulators. Finally, we detected an effect of LIFR on Uterine Corpus Endometrial Carcinoma (UCEC) and evaluated the expression level of LIFR in clinical UCEC samples. Results Aberrant expression of LIFR in cancers and its prognosis ability, especially in UCEC was documented. Significantly lower levels of LIFR expression level correlated with better prognosis in multiple tumor types. LIFR expression was positively correlated with the abundance of cancer-associated fibroblasts (CAFs) and endothelial cells in the tumor microenvironment. Additionally, LIFR expression was strongly associated with the presence of immune modulators and checkpoint genes. Overexpression of LIFR suppressed the migration and invasion of UCEC cells in vitro. Conclusion Our pan-cancer detection data provided a novel understanding of the roles of LIFR in oncogenesis.
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Affiliation(s)
- Fang Zhang
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Yali Wang
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Hongjuan Li
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Li Li
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xiaofeng Yang
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xiaoyan You
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Lina Tang
- Metabolic Disease Research Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
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15
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Pan-Cancer Analysis of the Oncogenic and Prognostic Role of PKM2: A Potential Target for Survival and Immunotherapy. BIOMED RESEARCH INTERNATIONAL 2023; 2023:3375109. [PMID: 36865483 PMCID: PMC9974260 DOI: 10.1155/2023/3375109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 02/25/2023]
Abstract
Background No pan-cancer study has been conducted till date to explore the comprehensive oncogenic roles of pyruvate kinase M2 (PKM2). Methods TCGA, TIMER, GEPIA, UALCAN, STRING, and other databases were used to analyze the expression, prognostic roles, epigenetic variants, and possible oncogenic mechanisms of PKM2. Proteomic sequencing data and PRM were applied to validate. Results PKM2 showed higher expression in majority of cancers, the expression being significantly correlated with the clinical stage. Higher expression of PKM2 was associated with lower OS and DFS in several cancers, such as MESO and PAAD. In addition, the epigenetic variation of PKM2, including gene alteration, mutation type and sites, DNA methylation, and phosphorylation, showed diversity in different cancers. All four methods indicated that PKM2 is positively associated with the immune infiltration of tumor-associated fibroblasts, such as in THCA, GBM, and SARC. Further mechanistic exploration suggested that the ribosome pathway might play an essential role in the regulation of PKM2, and interestingly, four out of ten hub genes were found to be highly related to OS in several cancers. Finally, in thyroid cancer specimen, we validated the expression and potential mechanisms by proteomic sequencing and PRM validation. Conclusion In the majority of cancers, the higher expression of PKM2 was highly associated with poor prognosis. Further molecular mechanism exploration implied that PKM2 might serve as a potential target for cancer survival and immunotherapy by regulating the ribosome pathway.
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16
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Tan M, Lin X, Chen H, Ye W, Yi J, Li C, Liu J, Su J. Sterol regulatory element binding transcription factor 1 promotes proliferation and migration in head and neck squamous cell carcinoma. PeerJ 2023; 11:e15203. [PMID: 37090107 PMCID: PMC10117388 DOI: 10.7717/peerj.15203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/17/2023] [Indexed: 04/25/2023] Open
Abstract
Background Sterol-regulatory element-binding protein 1 (SREBP1) is a transcription factor involved in lipid metabolism that is encoded by sterol regulatory element binding transcription factor 1(SREBF1). SREBP1 overexpression is associated with the progression of several human tumors; however, the role of SREBP1 in head and neck squamous cell carcinoma (HNSC) remains unclear. Methods SREBF1 expression in pan-cancer was analyzed using the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) data, and the association between SREBF1 expression and clinical characteristics of HNSC patients was examined using the UALCAN database. Enrichment analysis of SREBF1-related genes was performed using the Cluster Profiler R package. TCGA database was used to investigate the relationship between immune cell infiltration and SREBF1 expression. CCK-8, flow cytometry, and wound healing assays were performed to investigate the effect of SREBF1 knockdown on the proliferation and migration of HNSC cells. Results SREBF1 was significantly upregulated in several tumor tissues, including HNSC, and SREBF1 overexpression was positively correlated with sample type, cancer stage, tumor grade, and lymph node stage in HNSC patients. Gene enrichment analysis revealed that SREBF1 is associated with DNA replication and homologous recombination. SREBF1 upregulation was positively correlated with the infiltration of cytotoxic cells, B cells, T cells, T helper cells, and NK CD56 bright cells in HNSC. Knockdown of SREBF1 inhibited the proliferation and migration of HNSC cells (Hep2 and TU212) and induced apoptosis by downregulating the expression of steroidogenic acute regulatory protein-related lipid transfer 4 (STARD4). Conclusions SREBF1 may promote HNSC proliferation, migration and inhibit apoptosis by upregulating STARD4 and affecting the level of immune cell infiltration.
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17
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Xu Q, Wang J, Wang J, Zhu Y, Chen B, Guo R, Qian Y, Yuan H, Liu F. A Pan-Cancer Analysis to Provide Insight into the Immunological Role and Prognostic Value of HTRA3. Crit Rev Eukaryot Gene Expr 2023; 33:57-75. [PMID: 37606164 DOI: 10.1615/critreveukaryotgeneexpr.2023048936] [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: 08/23/2023]
Abstract
High-temperature requirement factor A3 (HTRA3), a member of the HTRA protein family, is closely associated with apoptosis and plays a crucial role in controlling signal transmission and cancer development. However, the regulatory pathways of HTRA3 in tumors are not fully understood, necessitating a comprehensive analysis of HTRA3 in cancers. In this study, we conducted a multi-omics analysis of HTRA3 in pan-cancer using data from various databases including TCGA, cBioPortal, GeneMANIA, DAVID, TIMER2.0, SangerBox, and RNAactDrug. Our analysis included gene expression, survival prognosis, diagnostic value, mutation, gene-gene interaction, enrichment analysis, and drug sensitivity analysis. We found that HTRA3 is aberrantly expressed in a variety of cancers and significantly correlates with diagnosis, prognosis, TMB, MSI, immune checkpoint (ICP) genes, and drug sensitivity in various cancer types. HTRA3 is involved in a variety of cancer pathways, particularly extracellular matrix (ECM) alterations, and has a potential role in epithelial-mesenchymal transition (EMT). HTRA3 expression is positively correlated with the abundance of cancer-associated fibroblasts (CAFs) and endothelial cells in the tumor microenvironment, and is also positively correlated with immune scores, stromal scores, and ESTIMATE scores in multiple cancers. HTRA3 is often overexpressed in cancer and is associated with poor prognosis and regulation of the tumor's immune response. Therefore, it may serve as a novel biomarker for tumor diagnosis and treatment.
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Affiliation(s)
- Qi Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiale Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jing Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yukuan Zhu
- Department of Anesthesiology, Harbin Fifth Hospital, Harbin, China
| | - Baihui Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Runzhao Guo
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yao Qian
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Haiyu Yuan
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Feng Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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Ghosal S, Hadrava Vanova K, Uher O, Das S, Patel M, Meuter L, Huynh TT, Jha A, Talvacchio S, Knue M, Prodanov T, Zeiger MA, Nilubol N, Taieb D, Crona J, Shankavaram UT, Pacak K. Immune signature of pheochromocytoma and paraganglioma in context of neuroendocrine neoplasms associated with prognosis. Endocrine 2023; 79:171-179. [PMID: 36370152 PMCID: PMC10683554 DOI: 10.1007/s12020-022-03218-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022]
Abstract
PURPOSE To understand prognostic immune cell infiltration signatures in neuroendocrine neoplasms (NENs), particularly pheochromocytoma and paraganglioma (PCPG), we analyzed tumor transcriptomic data from The Cancer Genome Atlas (TCGA) and other published tumor transcriptomic data of NENs. METHODS We used CIBERSORT to infer immune cell infiltrations from bulk tumor transcriptomic data from PCPGs, in comparison to gastroenteropancreatic neuroendocrine tumors (GEPNETs) and small cell lung carcinomas (SCLCs). PCPG immune signature was validated with NanoString immune panel in an independent cohort. Unsupervised clustering of the immune infiltration scores from CIBERSORT was used to find immune clusters. A prognostic immune score model for PCPGs and the other NENs were calculated as a linear combination of the estimated infiltration of activated CD8+/CD4+ T cells, activated NK cells, and M0 and M2 macrophages. RESULTS In PCPGs, we found five dominant immune clusters, associated with M2 macrophages, monocytes, activated NK cells, M0 macrophages and regulatory T cells, and CD8+/CD4+ T cells respectively. Non-metastatic tumors were associated with activated NK cells and metastatic tumors were associated with M0 macrophages and regulatory T cells. In GEPNETs and SCLCs, M0 macrophages and regulatory T cells were associated with unfavorable outcomes and features, such as metastasis and high-grade tumors. The prognostic immune score model for PCPGs and the NENs could predict non-aggressive and non-metastatic diseases. In PCPGs, the immune score was also an independent predictor of metastasis-free survival in a multivariate Cox regression analysis. CONCLUSION The transcriptomic immune signature in PCPG correlates with clinical features like metastasis and prognosis.
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Affiliation(s)
- Suman Ghosal
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Katerina Hadrava Vanova
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ondrej Uher
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Medical Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice, 37005, Czech Republic
| | - Shaoli Das
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mayank Patel
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Leah Meuter
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thanh-Truc Huynh
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Abhishek Jha
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sara Talvacchio
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marianne Knue
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tamara Prodanov
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Martha A Zeiger
- Office of Surgeon Scientists Programs, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Naris Nilubol
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Taieb
- Department of Nuclear Medicine, La Timone University Hospital, Aix-Marseille University, Marseille, France
- European Center for Research in Medical Imaging, Aix-Marseille University, Marseille, France
| | - Joakim Crona
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Medical Sciences, Uppsala University, Akademiska Sjukhuset ing 78, 75185, Uppsala, Sweden
| | - Uma T Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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FAM3D as a Prognostic Indicator of Head and Neck Squamous Cell Carcinoma Is Associated with Immune Infiltration. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5851755. [PMID: 36510584 PMCID: PMC9741545 DOI: 10.1155/2022/5851755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/09/2022] [Accepted: 10/27/2022] [Indexed: 12/04/2022]
Abstract
Background Globally, head and neck squamous cell carcinoma (HNSCC) is a common malignant tumor with high morbidity and mortality. Hence, it is important to find effective biomarkers for the diagnosis and prediction of the prognosis of patients with HNSCC. FAM3D had been proven to be vital in other cancers. However, its predictive and therapeutic value in HNSCC is unclear. Therefore, it is valuable to explore the association between the expression level of FAM3D and its impacts on the prognosis and tumor microenvironment in HNSCC. Methods The Cancer Genome Atlas (TCGA) dataset, Genotype-Tissue Expression (GTEx) dataset, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset, and The Human Protein Atlas (THPA) website were used to assess HNSCC expressions in tumor and nontumor tissues. Then, we further conducted immunohistochemistry experiment as internal cohort to validate the same results. The Cox regression analysis, Kaplan-Meier analysis, and nomograms were performed to find the predictive prognostic value of FAM3D in HNSCC patients and its relationship with the clinicopathological features in HNSCC. The Gene Expression Omnibus (GEO) dataset was utilized to externally verify the prognosis value of FAM3D in HNSCC. Gene Set Enrichment Analysis (GESA) was applied to search the molecular and biological functions of FAM3D. The association between FAM3D and immune cell infiltration was investigated with the Tumor Immune Estimating Resource, version 2 (TIMER2). The relationships between FAM3D expression and tumor microenvironment (TME) scores, immune checkpoints, and antitumor compound half-maximal inhibitory concentration predictions were also explored. Results In different datasets, FAM3D mRNA and protein levels were all significantly lower in HNSCC tissues than in normal tissues, and they were strongly inversely associated with tumor grade, stage, lymph node metastasis, and T stage. Patients with high-FAM3D-expression displayed better prognosis than those with low-FAM3D-expression. FAM3D was also determined to be a suitable biomarker for predicting the prognosis of patients with HNSCC. This was externally validated in the GEO dataset. As for gene and protein level, the functional and pathway research results of FAM3D indicated that it was enriched in alteration of immune-related pathways in HNSCC. The low-expression group had higher stromal and ESTIMATE scores by convention than the high-expression group. FAM3D expression were found to be positively correlated with immune infiltrating cells, such as cancer-associated fibroblasts, myeloid-derived suppressor cells, macrophage cells, T cell CD8+ cells, regulatory T cells, and T cell follicular helper cells. FAM3D's relationships with immune checkpoints and sensitivity to antitumor drugs were also investigated. Conclusion Our study explored the impact of FAM3D as a favorable prognostic marker for HNSCC on the tumor immune microenvironment from multiple perspectives. The results may provide new insights into HNSCC-targeted immunotherapy.
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Huang T, Liu Y, Li J, Shi B, Shan Z, Shi Z, Yang Z. Insights into prognosis and immune infiltration of cuproptosis-related genes in breast cancer. Front Immunol 2022; 13:1054305. [PMID: 36518756 PMCID: PMC9742524 DOI: 10.3389/fimmu.2022.1054305] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Breast cancer (BC) has been ranking first in incidence and the leading cause of death among female cancers worldwide based on the latest report. Regulated cell death (RCD) plays a significant role in tumor initiation and provides an important target of cancer treatment. Cuproptosis, a novel form of RCD, is ignited by mitochondrial stress, particularly the lipoylated mitochondrial enzymes aggregation. However, the role of cuproptosis-related genes (CRGs) in tumor generation and progression remains unclear. Methods In this study, the mRNA expression data of CRGs in BC and normal breast tissue were extracted from TCGA database, and protein expression patterns of these CRGs were analyzed using UALCAN. The prognostic values of CRGs in BC were explored by using KaplanMeier plotter and Cox regression analysis. Genetic mutations profiles were evaluated using the cBioPortal database. Meanwhile, we utilized CIBERSORT and TIMER 2.0 database to perform the correlation analysis between CRGs and immune cell infiltration. Results Our results indicated that CRGs expression is significantly different in BC and normal breast tissues. Then we found that upregulated PDHA1 expression was associated with worse endpoint of BC. Moreover, we also performed immune infiltration analysis of CRGs, and demonstrated that PDHA1 expression was closely related to the infiltration levels of CD4+ memory T cell, macrophage M0 and M1 cell and mast cell in BC. Conclusions Our results demonstrated the prognostic and immunogenetic values of PDHA1 in BC. Therefore, PDHA1 can be an independent prognostic biomarker and potential target for immunotherapy of BC.
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Affiliation(s)
| | - Yankuo Liu
- School of Medicine, Xiamen University, Xiamen, China
| | - Jiwei Li
- School of Medicine, Xiamen University, Xiamen, China
| | - Bingbing Shi
- Department of Critical Care Medicine, The Affiliated Hospital of Putian University, Putian, China
| | - Zhengda Shan
- School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Zhiyuan Shi
- School of Medicine, Xiamen University, Xiamen, China,*Correspondence: Zhiyuan Shi, ; Zhangru Yang,
| | - Zhangru Yang
- Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Zhiyuan Shi, ; Zhangru Yang,
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Hu A, Wang Y, Tian J, Chen Z, Chen R, Han X, Chen Y, Liu T, Chen Q. Pan-cancer analysis reveals DDX21 as a potential biomarker for the prognosis of multiple tumor types. Front Oncol 2022; 12:947054. [PMID: 36505822 PMCID: PMC9730287 DOI: 10.3389/fonc.2022.947054] [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: 05/18/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
Background DExD-box helicase 21 (DDX21) is an essential member of the RNA helicase family. DDX21 is involved in the carcinogenesis of various malignancies, but there has been no comprehensive research on its involvement in different types of cancer. Method This study used TCGA, CPTAC, GTEx, GEO, FANTOM5, BioGRID, TIMER2, GEPIA2, cBioPortal, STRING, and Metascape databases and Survival ROC software to evaluate DDX21 gene expression, protein expression, immunohistochemistry, gene mutation, immune infiltration, and protein phosphorylation in 33 TCGA tumor types, as well as the prognostic relationship between DDX21 and different tumors, by survival analysis and similar gene enrichment analysis. Furthermore, Cell Counting Kit-8 (CCK-8) and Transwell studies were employed to assess the effect of DDX21 expression on lung adenocarcinoma (LUAD) cell proliferation and migration. Result The DDX21 gene was highly expressed in most cancers, and overexpression was associated with poor overall survival (OS) and disease-free survival (DFS). DDX21 mutations were most common in uterine corpus endometrial carcinoma (UCEC; >5%), and DDX21 expression was positively correlated with the degree of infiltration of CAF and CD8+ cells in several tumor types. Numerous genes were co-expressed with DDX21. Gene enrichment analysis revealed close links between DDX21, RNA metabolism, and ribosomal protein production. In vitro analysis of LUAD cells showed that DDX21 expression was positively correlated with cell proliferation and migration capacity, consistent with prior bioinformatics studies. Conclusions DDX21 is overexpressed in a variety of cancers, and overexpression in some cancers is associated with poor prognosis. Immune infiltration and DDX21-related gene enrichment analyses indicated that DDX21 may affect cancer development through mechanisms that regulate tumor immunity, RNA metabolism, and ribosomal protein synthesis. This pan-cancer study revealed the prognostic value and the oncogenic role of DDX21.
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Affiliation(s)
- Ankang Hu
- Laboratory Animal Center, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yonghui Wang
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiahao Tian
- Clinical Medicine Science, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zihan Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Renjin Chen
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xufeng Han
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yang Chen
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Tingjun Liu
- Laboratory Animal Center, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Quangang Chen
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, China,*Correspondence: Quangang Chen,
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Pan-Cancer Analysis of TLE3 Revealed Its Value in Tumor Microenvironment and Prognosis. JOURNAL OF ONCOLOGY 2022; 2022:4085770. [DOI: 10.1155/2022/4085770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/23/2022]
Abstract
Background. Transducin-like enhancer of split 3 (TLE3), a member of the TLE gene family, is related to tumor genesis and progression. However, whether TLE3 played a crucial role in the whole pan-cancer remained unknown. Methods. Comprehensive analysis of TCGA, GEO, and GTEx data with an online tool, and R language was performed to explore the relationship of TLE3 expression between prognosis, gene mutation, protein phosphorylation, DNA methylation, tumor microenvironment, and related pathways in 33 tumors. Results. TLE3 was high-expressed in most tumors, and TLE3 expression and the prognosis of some tumor types were significantly correlated. The level of TLE3 expression in 33 cancer types was closely associated with DNA methylation. High-level phosphorylation sites of Tle3, such as S267 and S217, may promote cancers. In terms of the tumor microenvironment, TLE3 affected a wide variety of cancers, especially PRAD and LIHC, and TLE3 may act on them via immune-related pathways. Conclusions. The current work provided the first comprehensive investigation of TLE3 in a pan-cancer study, highlighting the role of TLE3 in the tumor immune microenvironment, and also determined the potential of TLE3 as a prognostic, immunotherapy response, and diagnostic biomarker in many cancers. However, the present results were preliminary and required further validation as this study was based on bioinformatics analyses.
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Liu A, Li Y, Shen L, Li N, Zhao Y, Shen L, Li Z. Molecular subtypes based on cuproptosis regulators and immune infiltration in kidney renal clear cell carcinoma. Front Genet 2022; 13:983445. [PMID: 36338990 PMCID: PMC9635053 DOI: 10.3389/fgene.2022.983445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Copper toxicity involves the destruction of mitochondrial metabolic enzymes, triggering an unusual mechanism of cell death called cuproptosis, which proposes a novel approach using copper toxicity to treat cancer. However, the biological function of cuproptosis has not been fully elucidated in kidney renal clear cell carcinoma (KIRC). Using the expression profile of 13 cuproptosis regulators, we first identified two molecular subtypes related to cuproptosis defined as “hot tumor” and “cold tumor”, having different levels of biological function, clinical prognosis, and immune cell infiltration. We obtained three gene clusters using the differentially expressed genes between the two cuproptosis-related subtypes, which were associated with different molecular activities and clinical characteristics. Next, we developed and validated a cuproptosis prognostic model that included two genes (FDX1 and DBT). The calculated risk score could divide patients into high- and low-risk groups. The high-risk group had a poorer prognosis, lower level of immune infiltration, higher frequency of gene alterations, and greater levels of FDX1 methylation and limited DBT methylation. The risk score was also an independent predictive factor for overall survival in KIRC. The established nomogram calculating the risk score achieved a high predictive ability for the prognosis of individual patients (area under the curve: 0.860). We then identified small molecular inhibitors as potential treatments and analyzed the sensitivity to chemotherapy of the signature genes. Tumor immune dysfunction and exclusion (TIDE) showed that the high-risk group had a higher level of TIDE, exclusion and dysfunction that was lower than the low-risk group, while the microsatellite instability of the high-risk group was significantly lower. The results of two independent immunotherapy datasets indicated that cuproptosis regulators could influence the response and efficacy of immunotherapy in KIRC. Our study provides new insights for individualized and comprehensive therapy of KIRC.
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Affiliation(s)
- Aibin Liu
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yanyan Li
- Department of Nursing, Xiangya Hospital, Central South University, Changsha, China
| | - Lin Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Na Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Yajie Zhao
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Liangfang Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Zhanzhan Li,
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Zhou B, Ying X, Chen Y, Cai X. A Comprehensive Pan-Cancer Analysis of the Tumorigenic Effect of Leucine-Zipper-Like Transcription Regulator (LZTR1) in Human Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2663748. [PMID: 36304963 PMCID: PMC9593223 DOI: 10.1155/2022/2663748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022]
Abstract
The elucidation of the action site, mechanism of Leucine-Zipper-like Transcription Regulator-1 (LZTR1) and its relationship with RAS-MAPK signaling pathway attracts more and more scholars to focus on the researches of LZTR1 and its role in tumorigenesis. However, there was no pan-cancer analysis between LZTR1 and human tumors reported before. Therefore, we are the first to investigate the potential oncogenic roles of LZTR1 across all tumor types based on the datasets of TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus). LZTR1 plays a double-edged role in tumor development and prognosis. We found that the high expression of LZTR1 brings better outcomes in esophageal carcinoma (ESCA) and head and neck squamous cell carcinoma (HNSC) but brings worth outcomes in uveal melanoma (UVM), adrenocortical carcinoma (ACC), liver hepatocellular carcinoma (LIHC), and prostate adenocarcinoma (PRAD). Moreover, the expression of LZTR1 also strongly associated with pathological in ACC and bladder urothelial carcinoma (BLCA). We also found that the LZTR1 expression was associated with some immune cell infiltration including endothelial cells, regulatory T cells (Tregs), T cell CD8+, natural killer cells (NK cell), macrophages, neutrophil granulocyte, and cancer-associated fibroblasts in different cancers. Missense mutation in LZTR1 was detected in most cancers from TCGA datasets. Finally, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Body (GO) method was used to explain the pathogenesis of LZTR1. Our pan-cancer study provides a relatively comprehensive understanding of the carcinogenic role of LZTR1 in human tumors.
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Affiliation(s)
- Bo Zhou
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo 315040, China
| | - Xinyu Ying
- Department of Clinical Laboratory, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo 315040, China
| | - Yingcong Chen
- Department of Clinical Laboratory, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo 315040, China
| | - Xingchen Cai
- Medical School, Ningbo University, Ningbo 315211, China
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Wang J, Huang D, Wang Y, Yuan Q, Chen X, Cheng Y. Pretreatment plasma fibrinogen and serum albumin levels predict therapeutic efficacy of concurrent radiochemotherapy for esophageal squamous cell cancer. Front Oncol 2022; 12:1021214. [PMCID: PMC9610838 DOI: 10.3389/fonc.2022.1021214] [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: 08/17/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
PurposeEvidence implies that plasma fibrinogen and serum albumin level (FA score) based on plasma fibrinogen and serum albumin is related to cancer prognosis. However, the association between the FA score and therapeutic efficacy of concurrent radiochemotherapy in esophageal squamous cell carcinoma (ESCC) has not yet been evaluated. This study aimed to assess the role of pretreatment FA score in predicting the therapeutic efficacy of concurrent radiochemotherapy for patients with esophageal squamous cell cancer.MethodsThis retrospective study evaluated 154 patients with ESCC who underwent concurrent radiochemotherapy. Receiver operating characteristic curve (ROC) analysis was used to determine the appropriate cut-off values, and multivariate analysis and Kaplan-Meier curve were used to evaluate prognosis.ResultsFA score was significantly associated with the N stage and M stage (P = 0.015 and 0.042, respectively). Chi-square analysis/Fisher’s exact tests revealed a correlation between the FA score and curative effect (P < 0.001), and higher FA score was associated with poorer treatment effect. Multivariate analysis indicated that FA score (P < 0.001) was predictor of overall survival (OS). Kaplan-Meier curve demonstrated that pretreatment FA score was significantly associated with the OS of ESCC: Patient with higher FA score has lower median OS.ConclusionsThe FA score is a reliable prognostic predictor that could assess the curative effect and OS benefit of concurrent radiochemotherapy in patients with ESCC.
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Affiliation(s)
- Jijin Wang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Di Huang
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, China
| | - Yuanyuan Wang
- Department of Oncology, Linyi People’s Hospital, Dezhou, China
| | - Qianqian Yuan
- Department of Oncology, Tengzhou Central People’s Hospital, Zaozhuang, China
| | - Xue Chen
- Department of Minimally Invasion Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Yufeng Cheng, ; Xue Chen,
| | - Yufeng Cheng
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Yufeng Cheng, ; Xue Chen,
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The Oncogenic and Immunological Roles of Apoptosis Antagonistic Transcription Factors in Human Tumors: A Pan-Cancer Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3355365. [PMID: 36275893 PMCID: PMC9581705 DOI: 10.1155/2022/3355365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/23/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022]
Abstract
Background Apoptosis-antagonizing transcription factor (AATF) participates in tumor progression in multiple cancer types. However, its role across cancers is not well understood. Methods Data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Human Protein Atlas (HPA) were used to analyze the multiomic roles of AATF in 33 tumor types, including gene and protein expression, survival prognosis, gene mutation, DNA methylation, protein phosphorylation, AATF coexpressed genes and their enrichment analysis, and immunological analysis. Results In TCGA and GTEx databases, 31 tumors and their corresponding normal tissues had AATF expression data, and it was differentially expressed in 29 of them. AATF was elevated in 27 tumors, decreased in 2 tumors, and was a risk factor for overall survival (OS) in 8 tumors and a risk factor for disease-free survival (DFS) in 4 tumors. AATF expression levels in various cancer types were significantly correlated with the infiltration levels of cancer-associated fibroblasts, endothelial cells, CD4+ T cells, B cells, myeloid dendritic cells, eosinophils, and macrophages. The immune checkpoints PD-1, PD-L1, and CTLA4 were positively correlated with AATF expression in bladder urothelial carcinoma (BLCA), kidney chromophobe (KICH), and prostate adenocarcinoma (PRAD). Conclusion In cancer, AATF expression is generally higher than that in normal tissue, and it is also associated with immunomodulation-related genes. AATF may be a risk factor for poor prognosis across cancers.
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Li S, Feng J, Weng H, Zhao F, Cui G, Fu W, Lin X, Hu H. Identification of Key Genes and FUNCTIONAL Pathway in Radioresistance of Non-Small Cell Lung Cancer. Cancer Manag Res 2022; 14:2871-2884. [PMID: 36171861 PMCID: PMC9512540 DOI: 10.2147/cmar.s382079] [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: 07/15/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose For better understanding of radiotherapy resistance and its potential mechanism. Methods We established radioresistance cell lines of non-small cell lung cancer (NSCLC) followed by microarray analysis. 529 differentially expressed genes (DEGs) were then screened between radiation resistant cell lines compared with the sensitive cell lines. The biological functions and enrichment pathways of the above DEGs were identified using Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses. Gene Set Enrichment Analysis (GSEA) revealed that the radiation resistance group had the most gene sets enriched in altered immune response, such as TNF signaling pathway, when compared to the radiation sensitive group. Protein-protein interaction (PPI) network was carried out through the STRING database, and then five hub genes (CXCL10, IFIH1, DDX58, CXCL11, RSAD2) were screened by Cytoscape software. RT-PCR confirmed the expression of the above hub genes. ChIP-X Enrichment Analysis showed that STAT1 might be the transcription factor of the above hub genes. Considering that PD-L1 could be activated by STAT1 in a variety of tumors and ultimately lead to immune exhaustion, RT-PCR and Western blot verified the expression level of PD-L1. Results Five hub genes (CXCL10, IFIH1, DDX58, CXCL11, RSAD2) were screened and verified to be highly expressed in radioresistance group, STAT1 might be the transcription factor of the above hub genes. Our study found that the expression level of PD-L1 was increased after radiotherapy resistance. Conclusion Although immune system activation occurs followed by radiation resistance, we hypothesized that the upregulation of PD-L1 expression caused by STAT1 activation might be one of the mechanisms of radiotherapy resistance.
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Affiliation(s)
- Shouying Li
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jiaxin Feng
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Haiyan Weng
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Feng Zhao
- Research and Development Department, Guangzhou BioBlue Technology Co. Ltd, Guangzhou, People's Republic of China
| | - Guohui Cui
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wenkui Fu
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaorong Lin
- Diagnosis and Treatment Center of Breast Diseases, Shantou Central Hospital, Shantou, People's Republic of China
| | - Hai Hu
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
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Qiu X, Shen C, Zhao W, Zhang X, Zhao D, Wu X, Yang L. A pan-cancer analysis of the oncogenic role of dual-specificity tyrosine (Y)-phosphorylation- regulated kinase 2 (DYRK2) in human tumors. Sci Rep 2022; 12:15419. [PMID: 36104345 PMCID: PMC9474874 DOI: 10.1038/s41598-022-19087-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 08/24/2022] [Indexed: 11/15/2022] Open
Abstract
Although there have been studies correlating DYRK2 with a number of human cancers, there has been no pan-cancer analysis. Therefore, through the TCGA database, we conducted a related study on the expression of DYRK2 in cancers.The expression of DYRK2 is obviously increased in some cancers, while the opposite is true in others, and there is a clear association between its expression and the prognosis of cancer patients.The mutation of DYRK2 is also significantly correlated with patients’ prognosis in certain human tumors. In addition, phosphorylation and methylation levels of DYRK2 are different between tumor tissues and adjacent normal tissues in various tumors. In the tumour microenvironment, the expression of DYRK2 correlates with cancer-associated fibroblast infiltration, such as BLCA or HNSC. In order to fully understand the role of DYRK2 in different tumors, we conducted a pan-cancer analysis.
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Systematic Pan-Cancer Analysis Identifies CDK1 as an Immunological and Prognostic Biomarker. JOURNAL OF ONCOLOGY 2022; 2022:8115474. [PMID: 36090896 PMCID: PMC9452984 DOI: 10.1155/2022/8115474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/07/2022] [Accepted: 06/23/2022] [Indexed: 11/21/2022]
Abstract
Cyclin-dependent kinase 1 (CDK1) plays an important role in cancer development, progression, and the overall process of tumorigenesis. However, no pan-cancer analysis has been reported for CDK1, and the predictive role of CDK1 in immune checkpoint inhibitors (ICIs) therapy response remains unexplored. Thus, in this study, we first investigated the potential oncogenic role of CDK1 in 33 tumors by multidimensional bioinformatics analysis based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Bioinformatic analysis and immunohistochemical experiments confirmed that CDK1 is significantly upregulated in most common cancers and is strongly associated with prognosis. Further analysis indicated that CDK1 may influence tumor immunity mainly by mediating the degree of tumor infiltration of immune-associated cells, and the effect of CDK1 on immunity is diverse across tumor types in tumor microenvironment. CDK1 was also positively correlated with tumor mutational burden (TMB) and microsatellite instability (MSI) in certain cancer types, linking its expression to the assessment of possible treatment response. The results of the pan-cancer analysis study showed that the CDK1 gene was positively associated with the expression of three classes of RNA methylation regulatory proteins, and affects RNA function through multiple mechanisms of action and plays an important role in the posttranscriptional regulation of the tumor microenvironment. These findings shed light on the role of the CDK1 gene in cancer progression and provide information to further study the CDK1 gene as a potential target for pan-cancer.
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Pan-Cancer Analysis Reveals the Relation between TRMT112 and Tumor Microenvironment. JOURNAL OF ONCOLOGY 2022; 2022:1445932. [PMID: 36081672 PMCID: PMC9448524 DOI: 10.1155/2022/1445932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022]
Abstract
Dysregulated epigenetic modifications play a critical role in cancer development where TRMT112 is a member of the transfer RNA (tRNA) methyltransferase family. Till now, no studies have revealed the linkage between TRMT112 expression and diverse types of tumors. Based on TCGA data, we first probed into the relation between TRMT112 and prognosis and the potential role of TRMT112 in tumor microenvironment across 33 types of tumor. TRMT112 presented with increased expression in most cancers, which was significantly prognostic. Furthermore, TRMT112 was associated with tumor-associated fibroblasts in a variety of cancers. Additionally, a positive relationship was identified between TRMT112 expression and multiple tumor-related immune infiltrations, such as dendritic cells, CD8+ T cells, macrophages, CD4+ T cells, neutrophils, and B cells in lung adenocarcinoma and breast invasive carcinoma. In summary, our results suggest that TRMT112 might be a potential prognostic predictor of cancers and involved in regulating multiple cancer-related immune responses to some extent.
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Feng M, Cui H, Tu W, Li L, Gao Y, Chen L, Li D, Chen X, Xu F, Zhou C, Cao Y. An integrated pan-cancer analysis of PSAT1: A potential biomarker for survival and immunotherapy. Front Genet 2022; 13:975381. [PMID: 36105075 PMCID: PMC9465327 DOI: 10.3389/fgene.2022.975381] [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] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Phosphoserine aminotransferase 1 (PSAT1) may be an oncogene that plays an important role in various cancer types. However, there are still many gaps in the expression of PSAT1 gene and its biological impact in different types of tumors. Here, we performed an integrated pan-cancer analysis to explore the potential molecular mechanisms of PSAT1 in cancers. We found that most human tumors express higher levels of PSAT1 than normal tissues, and that higher PSAT1 expression is associated with worse prognosis in Lung adenocarcinoma (LUAD), Pan-kidney cohort (KIPAN) and breast invasive carcinoma (BRCA), etc. In BRCA cases, the prognosis of patients with altered PSAT1 was worse than that of patients without alteration. In addition, PSAT1 hypermethylation is associated with T cell dysfunction and shortened survival time in BRCA. The Gene Set Enrichment Analysis (GSEA) analysis showed that PSAT1 can be enriched into the classic signaling pathways of cancer such as mTORC1 signaling, MYC targets and JAK STAT3. Further analysis demonstrated that PSAT1 was enriched in immune related signaling pathways in LUAD and BRCA. The results of immunoassay showed that PSAT1 was associated with immune cell infiltration in multiple cancer species. Furthermore, expression of PSAT1 was correlated with both tumor mutational burden (TMB) and microsatellite instability (MSI) in BRCA. Additionally, a remarkable correlation was found between PSAT1 expression and TMB in LUAD, and the expression of PSAT1 was negatively correlated with the Tumor Immune Dysfunction and Exclusion (TIDE) value, suggesting a good effect of immunotherapy. Together, these data suggest that PSAT1 expression is associated with the clinical prognosis, DNA methylation, gene mutations, and immune cell infiltration, contributing to clarify the role of PSAT1 in tumorigenesis from a variety of perspectives. What’s more, PSAT1 may be a new biomarker for survival and predicting the efficacy of immunotherapy for LUAD and BRCA.
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Affiliation(s)
- Mingtao Feng
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Huanhuan Cui
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wenjing Tu
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Liangdong Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yang Gao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lei Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Deheng Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xin Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Fengfeng Xu
- Department of Neurosurgery, Naval Medical Center of PLA, Shanghai, China
- *Correspondence: Fengfeng Xu, ; Changshuai Zhou, ; Yiqun Cao,
| | - Changshuai Zhou
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
- *Correspondence: Fengfeng Xu, ; Changshuai Zhou, ; Yiqun Cao,
| | - Yiqun Cao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, China
- *Correspondence: Fengfeng Xu, ; Changshuai Zhou, ; Yiqun Cao,
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Zheng X, Wang X, He Y, Ge H. Systematic analysis of expression profiles of HMGB family members for prognostic application in non-small cell lung cancer. Front Mol Biosci 2022; 9:844618. [PMID: 35923467 PMCID: PMC9340210 DOI: 10.3389/fmolb.2022.844618] [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: 12/28/2021] [Accepted: 06/27/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Lung cancer is a significant challenge to human health. Members of the high mobility group (HMG) superfamily (HMGB proteins) are implicated in a wide variety of physiological and pathophysiological processes, but the expression and prognostic value of HMGB family members in non-small cell lung cancer (NSCLC) have not been elucidated. Methods: In this study, ONCOMINE, UALCAN, GEPIA, Kaplan–Meier Plotter, starBase, OncomiR databases, and GeneMANIA were utilized to evaluate the prognostic significance of HMGB family members in NSCLC. Results: HMGB2/3 expression levels were higher in NSCLC patients. HMGB1 expression was higher in lung squamous cell carcinoma (LUSC) and was lower in lung adenocarcinoma (LUAD) tissue than in normal lung tissue. HMGB2 expression was related to cancer stage. Increased HMGB1 mRNA expression levels were associated with improved lung cancer prognosis, including overall survival (OS), first-progression survival (FP), and post-progression survival (PPS). There was no significant association between HMGB2 levels and prognostic indicators. HMGB3 expression was associated with poorer OS. GeneMANIA and GO/KEGG pathway analysis showed that HMGB family members mainly associated with chromosome condensation, regulation of chromatin organization, and nucleosome binding in NSCLC. HMGBs expression were closely correlated with infiltrating levels of specific types of immune cells in NSCLC, especially Th2 cells, Th17 cells, and mast cells. hsa-miR-25-3p, hsa-miR-374a-3p, and hsa-miR-93-5p were significantly positively correlated with HMGB1, HMGB2, and HMGB3, respectively. However, hsa-miR-30a-5p was predicted to significantly negatively regulate HMGB3 expression. Conclusion: Our study revealed that HMGB1 is positively related to the improved prognosis in NSCLC, and demonstrate that HMGB3 might be a risk factor for poorer survival of NSCLC patients.
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Yue T, Li J, Liang M, Yang J, Ou Z, Wang S, Ma W, Fan D. Identification of the KCNQ1OT1/ miR-378a-3p/ RBMS1 Axis as a Novel Prognostic Biomarker Associated With Immune Cell Infiltration in Gastric Cancer. Front Genet 2022; 13:928754. [PMID: 35910231 PMCID: PMC9330051 DOI: 10.3389/fgene.2022.928754] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Gastric cancer (GC) is the second leading cause of cancer-related mortality and the fifth most common cancer worldwide. However, the underlying mechanisms of competitive endogenous RNAs (ceRNAs) in GC are unclear. This study aimed to construct a ceRNA regulation network in correlation with prognosis and explore a prognostic model associated with GC. Methods: In this study, 1,040 cases of GC were obtained from TCGA and GEO datasets. To identify potential prognostic signature associated with GC, Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) regression were employed. The prognostic value of the signature was validated in the GEO84437 training set, GEO84437 test set, GEO15459 set, and TCGA-STAD. Based on the public databases, TargetScan and starBase, an mRNA-miRNA-lncRNA regulatory network was constructed, and hub genes were identified using the CytoHubba plugin. Furthermore, the clinical outcomes, immune cell infiltration, genetic variants, methylation, and somatic copy number alteration (sCNA) associated with the ceRNA network were derived using bioinformatics methods. Results: A total of 234 prognostic genes were identified. GO and GSEA revealed that the biological pathways and modules related to immune response and fibroblasts were considerably enriched in GC. A nomogram was generated to provide accurate prognostic outcomes and individualized risk estimates, which were validated in the training, test dataset, and two independent validation datasets. Thereafter, an mRNA-miRNA-lncRNA regulatory network containing 4 mRNAs, 22 miRNAs, 201 lncRNAs was constructed. The KCNQ1OT1/hsa-miR-378a-3p/RBMS1 ceRNA network associated with the prognosis was obtained by hub gene analysis and correlation analysis. Importantly, we found that the KCNQ1OT1/miR-378a-3p/RBMS1 axis may play a vital role in the diagnosis and prognosis of GC patients based on Cox regression analyses. Furthermore, our findings demonstrated that mutations and sCNA of the KCNQ1OT1/miR-378a-3p/RBMS1 axis were associated with increased immune infiltration, while the abnormal upregulation of the axis was primarily a result of hypomethylation. Conclusion: Our findings suggest that the KCNQ1OT1/miR-378a-3p/RBMS1 axis may be a potential prognostic biomarker and therapeutic target for GC. Moreover, such findings provide insights into the molecular mechanisms of GC pathogenesis.
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Affiliation(s)
- Ting Yue
- The Fifth Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Oncology Rehabilitation, Jincheng People’s Hospital, Jincheng, China
| | - Jingjing Li
- Department of Anesthesiology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Anesthesiology, Jincheng People’s Hospital, Jincheng, China
| | - Manguang Liang
- The Fifth Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiaman Yang
- The Fifth Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhiwen Ou
- The Fifth Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuchen Wang
- Department of Anesthesiology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wuhua Ma
- Department of Anesthesiology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Wuhua Ma, ; Dehui Fan,
| | - Dehui Fan
- The Fifth Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Rehabilitation, GuangDong Second Traditional Chinese Medicine Hospital, Guangzhou, China
- *Correspondence: Wuhua Ma, ; Dehui Fan,
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Sahin Y. LncRNA H19 is a potential biomarker and correlated with immune infiltration in thyroid carcinoma. Clin Exp Med 2022:10.1007/s10238-022-00853-w. [PMID: 35810257 DOI: 10.1007/s10238-022-00853-w] [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: 01/13/2022] [Accepted: 06/15/2022] [Indexed: 11/03/2022]
Abstract
The bulk of evidence has revealed that dysregulated expression of long non-coding RNAs (lncRNAs) plays a crucial functional role in cancer biology. However, the mechanistic role of lncRNAs in the initiation, progression and immune landscape of thyroid carcinoma (THCA) still remains largely unknown. This study aimed to explore the significance of H19 in the diagnostic and immune related roles in THCA. The expression level of H19 was analyzed using the TNMplot, GSCA, UALCAN, GEPIA, Wanderer, UCSC Xena and GEO databases. Enrichment analyses were performed to investigate the possible underlying biological pathways by LinkedOmics. Moreover, cBioPortal web tool was used to analyze genetic alterations of H19. Finally, we used TIMER and GEPIA databases to explore the correlations between H19 and tumor-infiltrated immune cells and immune markers. LncRNA H19 was differentially expressed in various cancers and also remarkably downregulated in the THCA tissues compared to the normal ones. Genetic alteration analysis revealed that there was a significant correlation between alterations in H19 and overall survival of THCA patients. Furthermore, enrichment analysis indicated the functional relationship between co-expression network of H19 and extracellular structure organization, and immune microenvironment. In addition, H19 expression was positively correlated with infiltration level of diverse immune cells including CD4+T cells, CD8+T cells, B cells, dendritic cells, neutrophils and macrophages and was closely associated with multiple immune markers in THCA. Conclusively, this comprehensive study indicates the lncRNA H19 might have a significant role in the initiation and progression of THCA. Hence, our findings might provide ideas on the selection of novel diagnostic biomarkers and assist in the designing of the effective pharmaceutical targets for THCA.
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Affiliation(s)
- Yunus Sahin
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey.
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Cao Y, Duan H, Su A, Xu L, Lai B. A pan-cancer analysis confirms PTPN11's potential as a prognostic and immunological biomarker. Aging (Albany NY) 2022; 14:5590-5610. [PMID: 35802774 PMCID: PMC9320542 DOI: 10.18632/aging.204171] [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: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022]
Abstract
Protein tyrosine phosphatase, non-receptor type 11 (PTPN11) is a multifunctional tyrosine phosphatase and has a significant part in many types of tumors. As of yet, neither the expression profile of PTPN11 nor its significance in pan-cancer diagnosis has been clarified. With the assistance of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we have comprehensively mapped the expression profiles, prognostic significance, genetic alteration, phosphorylation status, infiltration of immune cells, and functional properties of PTPN11 in 33 human tumors. There was an inconsistent expression of PTPN11 in different tumors, and the alteration of PTPN11 expression predicted the survival outcomes of cancer patients. A significant association was found between the genetic alteration levels of PTPN11 and some tumor predictions. Besides, the reduced PTPN11 phosphorylation levels were observed in breast cancer, clear cell RCC, head and neck carcinoma, and lung adenocarcinoma (LUAD). Furthermore, there was a significant association between PTPN11 expression and infiltration of cancer-associated fibroblasts and endothelial cells, along with tumor mutation burden, microsatellite instability, mismatch repair genes, and immunoregulators. Finally, pathway enrichment analysis demonstrated that PTPN11-associated terms and pathways were involved in malignancy. Taken together, PTPN11 may become a new biomarker and target for cancer therapy.
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Affiliation(s)
- Yapeng Cao
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Haixia Duan
- Department of Reproduction Gynecology, Northwest Women and Children's Hospital, Xi'an, Shaanxi 710061, China
| | - Ailing Su
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Liran Xu
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Baochang Lai
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
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Zhao F, Chang J, Zhao P, Wang W, Sun X, Ma X, Yin M, Wang Y, Yang Y. Oncogenetic Function and Prognostic Value of DNA Topoisomerase II Alpha in Human Malignances: A Pan-Cancer Analysis. Front Genet 2022; 13:856692. [PMID: 35873470 PMCID: PMC9301266 DOI: 10.3389/fgene.2022.856692] [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: 01/24/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing studies have revealed significant associations between TOP2A with oncogenesis and prognosis of human cancers; however, pan-cancer analysis has not been reported. Here, we explored the potential carcinogenic function and the association with clinical outcomes of TOP2A in 33 different human cancers. The results showed that TOP2A was amplified in 31 investigated cancers; TOP2A expression was significantly associated with metastasis of six different cancers and significantly associated with the survival of patients in ten different cancers; TOP2A-encoded protein was obviously upregulated in five available cancers; phosphorylated TOP2A protein at S1106 was significantly upregulated in all six available cancers. Moreover, TOP2A expression was found to be associated with the cancer-associated immune cell infiltration, including fibroblasts, Tregs, and macrophages. In addition, the Kyoto encyclopedia of genes and genomes (KEGG) pathway and Gene Ontology (GO) enrichment analyses revealed a most significant association between TOP2A with the Wnt signaling pathway and DNA conformation change. This work provides a comprehensive knowledge of TOP2A in different cancers, including carcinogenic function, prognostic values for metastasis, and clinical outcomes.
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Affiliation(s)
- Fulai Zhao
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Junli Chang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Peng Zhao
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Wenyi Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Xingyuan Sun
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Xiaoping Ma
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Mengchen Yin
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yongjun Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Yanping Yang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
- *Correspondence: Yanping Yang,
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Yu S, Qian L, Ma J. Genetic alterations, RNA expression profiling and DNA methylation of HMGB1 in malignancies. J Cell Mol Med 2022; 26:4322-4332. [PMID: 35765707 PMCID: PMC9344825 DOI: 10.1111/jcmm.17454] [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: 04/19/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 11/27/2022] Open
Abstract
The high mobility group box 1 (HMGB1) is a potential biomarker and therapeutic target in various human diseases. However, a systematic, comprehensive pan‐cancer analysis of HMGB1 in human cancers remains to be reported. This study analysed the genetic alteration, RNA expression profiling and DNA methylation of HMGB1 in more than 30 types of tumours. It is worth noting that HMGB1 is overexpressed in malignant tissues, including lymphoid neoplasm diffuse large B‐cell lymphoma (DLBC), pancreatic adenocarcinoma (PAAD) and thymoma (THYM). Interestingly, there is a positive correlation between the high expression of HMGB1 and the high survival prognosis of THYM. Finally, this study comprehensively evaluates the genetic variation of HMGB1 in human malignant tumours. As a prospective biomarker of COVID‐19, the role that HMGB1 plays in THYM is highlighted.
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Affiliation(s)
- Shoukai Yu
- Hongqiao International Institue of Medicine & Clinical Research Center, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingmei Qian
- Hongqiao International Institue of Medicine & Clinical Research Center, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Ma
- Hongqiao International Institue of Medicine & Clinical Research Center, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Ding JT, Yu XT, He JH, Chen DZ, Guo F. A Pan-Cancer Analysis Revealing the Dual Roles of Lysine (K)-Specific Demethylase 6B in Tumorigenesis and Immunity. Front Genet 2022; 13:912003. [PMID: 35783266 PMCID: PMC9246050 DOI: 10.3389/fgene.2022.912003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Epigenetic-targeted therapy has been increasingly applied in the treatment of cancers. Lysine (K)-specific demethylase 6B (KDM6B) is an epigenetic enzyme involved in the coordinated control between cellular intrinsic regulators and the tissue microenvironment whereas the pan-cancer analysis of KDM6B remains unavailable. Methods: The dual role of KDM6B in 33 cancers was investigated based on the GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas) databases. TIMER2 and GEPIA2 were applied to investigate the KDM6B levels in different subtypes or stages of tumors. Besides, the Human Protein Atlas database allowed us to conduct a pan-cancer study of the KDM6B protein levels. GEPIA2 and Kaplan–Meier plotter were used for the prognosis analysis in different cancers. Characterization of genetic modifications of the KDM6B gene was analyzed by the cBioPortal. DNA methylation levels of different KDM6B probes in different TCGA tumors were analyzed by MEXPRESS. TIMER2 was applied to determine the association of the KDM6B expression and immune infiltration and DNA methyltransferases. Spearman correlation analysis was used to assess the association of the KDM6B expression with TMB (tumor mutation burden) and MSI (microsatellite instability). The KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis and GO (Gene ontology) enrichment analysis were used to further investigate the potential mechanism of KDM6B in tumor pathophysiology. Results: KDM6B was downregulated in 11 cancer types and upregulated across five types. In KIRC (kidney renal clear cell carcinoma) and OV (ovarian serous cystadenocarcinoma), the KDM6B level was significantly associated with the pathological stage. A high level of KDM6B was related to poor OS (overall survival) outcomes for THCA (thyroid carcinoma), while a low level was correlated with poor OS and DFS (disease-free survival) prognosis of KIRC. The KDM6B expression level was associated with TMB, MSI, and immune cell infiltration, particularly cancer-associated fibroblasts, across various cancer types with different correlations. Furthermore, the enrichment analysis revealed the relationship between H3K4 and H3K27 methylation and KDM6B function. Conclusion: Dysregulation of the DNA methyltransferase activity and methylation levels of H3K4 and H3K27 may involve in the dual role of KDM6B in tumorigenesis and development. Our study offered a relatively comprehensive understanding of KDM6B’s dual role in cancer development and response to immunotherapy.
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Affiliation(s)
- Jia-Tong Ding
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, China
- The Second Clinical Medical College of Nanchang University, Nanchang, China
| | - Xiao-Ting Yu
- Burn Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jin-Hao He
- Burn Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - De-Zhi Chen
- Burn Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fei Guo
- Ningbo Institute for Medicine & Biomedical Engineering Combined Innovation, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, China
- Burn Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Fei Guo,
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Ding J, Meng Y, Han Z, Luo X, Guo X, Li Y, Liu S, Zhuang K. Pan-Cancer Analysis of the Oncogenic and Immunological Role of RCN3: A Potential Biomarker for Prognosis and Immunotherapy. Front Oncol 2022; 12:811567. [PMID: 35651805 PMCID: PMC9149440 DOI: 10.3389/fonc.2022.811567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/25/2022] [Indexed: 12/30/2022] Open
Abstract
Despite emerging publications have elucidated a functional association between RCN3 and tumors, no evidence about a pan-cancer analysis of RCN3 is available. Our study first conducted a comprehensive assessment of its expression profiles, prognosis value, immune infiltration, and relevant cellular pathways via bioinformatics techniques based on the public database of TCGA (The Cancer Genome Atlas). RCN3 is highly expressed in most tumors, and it is associated with poor prognosis. Kaplan-Meier analysis and Cox regression analysis suggested that the high expression of RCN3 was associated with poor overall survival (OS) in pan-cancer, Cox regression analysis also indicated high RCN3 expression was correlated with disease-specific survival (DSS) and progression-free interval (PFI) in most tumors. We observed a regulation function of RCN3 at genetic and epigenetic levels through CNA and DNA methylation using cBioPortal database. Based on Gene Set Enrichment Analysis, we first identified related pathways of RCN3 and its potential biological functions in pan-cancer, RCN3 was implicated in oncogenic pathways, and was related to extracellular matrix and immune regulation. We found that RCN3 positively correlated with the levels of infiltrating cells such as TAMs and CAFs, but negatively correlated with CD8+ T-cells by analyzing immune cell infiltration data we downloaded from published work and online databases, further investigation of the correlation between immunosuppressive genes, chemokines, chemokines receptors, and high RCN3 expression showed a significant positive association in the vast majority of TCGA cancer types. These results indicated its role as an immune regulatory in cancers and suggested that RCN3 is a potential biomarker for immunotherapy. Also, we found that expression of RCN3 was much higher in CRC tissues than in normal tissues with a higher expression level of RCN3 closely correlating to advanced American Joint Committee on Cancer (AJCC) stage, poor differentiation, increased tumor size, and poor prognosis of CRC. Biological function experiments showed that RCN3 regulated CRC cells’ proliferation and metastasis ability. Upregulation of RCN3 in CRC cells increased the expression of immune related factor, including TGFβ1, IL-10, and IL-6. Thus, our pan-cancer analysis offers a deep understanding of potential oncogenic roles of RCN3 in different cancers.
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Affiliation(s)
- Jian Ding
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan Meng
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zelong Han
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaobei Luo
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuxue Guo
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yiwen Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Side Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Pazhou Lab, Guangzhou, China
| | - Kangmin Zhuang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Yang J, Lu F, Ma G, Pang Y, Zhao Y, Sun T, Ma D, Ye J, Ji C. Role of CDH23 as a prognostic biomarker and its relationship with immune infiltration in acute myeloid leukemia. BMC Cancer 2022; 22:568. [PMID: 35597916 PMCID: PMC9123811 DOI: 10.1186/s12885-022-09532-1] [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: 10/15/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cadherin-23 (CDH23) plays an important role in intercellular adhesion and is involved in the progression of several types of cancer. However, the biological functions and effect of CDH23 expression on the prognosis of patients with acute myeloid leukemia (AML) are unexplored. Herein, we aim to characterize the role and molecular functions of CDH23 in AML. Methods We downloaded the transcriptomic profiles and clinical data from the Cancer Genome Atlas and Beat AML trial. The expression level of CDH23 was assessed using Gene Expression Profiling Interactive Analysis (GEPIA). Kaplan-Meier survival analysis was used to assess prognostic value of CDH23. Correlation and biological function analyses were performed using LinkedOmics and GeneMANIA. Relationship of CDH23 with immune infiltration level was determined using Tumor Immune Estimation Resource (TIMER). Results We found that the CDH23 expression was aberrantly upregulated in patients with AML and could be used as an independent risk factor of overall survival using Cox multivariate analysis. Notably, we observed a negative correlation between CDH23 expression and immune cell infiltration abundance by calculating the immune and stromal scores. In addition, functional enrichment analysis established that CDH23 plays a crucial role in tumor immunity. Conclusions Our findings indicate that upregulated CDH23 expression corresponds to decreased overall survival of patients with AML. CDH23 may be involved in mediating tumor immune environment, and this highlights the potential of CDH23 as a therapeutic target in AML. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09532-1.
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Affiliation(s)
- Jiao Yang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Fei Lu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Guangxin Ma
- Hematology and Oncology Unit, Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Yihua Pang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yanan Zhao
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Tao Sun
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jingjing Ye
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
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Wu X, Song P, Wang S, Qian Z, Ying J, Gao S, Li W. A Pan-Cancer Analysis of the Oncogenic Role of WD Repeat Domain 74 in Multiple Tumors. Front Genet 2022; 13:860940. [PMID: 35559034 PMCID: PMC9086290 DOI: 10.3389/fgene.2022.860940] [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: 01/27/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022] Open
Abstract
Although emerging patient-derived samples and cellular-based evidence support the relationship between WDR74 (WD Repeat Domain 74) and carcinogenesis in multiple cancers, no systematic pan-cancer analysis is available. Our preliminary research demonstrated that WDR74 is over-expressed in lung squamous cell carcinoma (LUSC) and related with worse survival. We thus investigated the potential oncogenic roles of WDR74 across 33 tumors based on the database of TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus). WDR74 is highly expressed in most cancers and correlated with poor prognosis in several cancers (all p < 0.05). Mutation analysis demonstrated that WDR74 is frequently mutated in promoter regions of lung cancer. Moreover, we found that CD8+ T-cells and the fibroblast infiltration level increased in WDR74 over-expressed cancer cells. The GO (Gene Ontology) enrichment analysis of the WDR74 pathway revealed its participation in cellular biogenesis of the RNA metabolism and its critical role in cancer initiation and progression through the tumor cell energy metabolism. Our first pan-cancer study inferred a relatively comprehensive understanding of the oncogenic roles of WDR74 across various cancers.
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Affiliation(s)
- Xiaoxuan Wu
- 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
| | - Peng Song
- Department of Thoracic Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shun Wang
- Beidou Academic and Research Center, Beidou Life Science, Guangzhou, China
| | - Zhirong Qian
- Beidou Academic and Research Center, Beidou Life Science, Guangzhou, China.,Guangdong Provincial Key Laboratory of Digestive Cancer Research, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Department of Radiation Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jianming Ying
- 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
| | - Shugeng Gao
- Department of Thoracic Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenbin Li
- 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
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Zhao H, Chen Y, Shen P, Gong L. Prognostic value and immune characteristics of RUNX gene family in human cancers: a pan-cancer analysis. Aging (Albany NY) 2022; 14:4014-4035. [PMID: 35522574 PMCID: PMC9134966 DOI: 10.18632/aging.204065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/23/2022] [Indexed: 11/25/2022]
Abstract
Background: Runt-related transcription factors (RUNX) are involved in numerous fundamental biological processes and play crucial parts in tumorigenesis and metastasis both directly and indirectly. However, the pan-cancer evidence of the RUNX gene family is not available. Methods: In this study, we analyzed the potential association between RUNX gene family expression and patient’s prognosis, immune cell infiltration, drug response, and genetic mutation data across different types of tumors using based on The Cancer Genome Atlas, Gene Expression Omnibus, and Oncomine database. Results: The results showed that the expression of the RUNX gene family varied among different cancer types, revealing its heterogeneity in cancers and that expression of RUNX2 was lower than that of RUNX1 and RUNX3 across all cancer types. RUNX gene family gene expression was related to prognosis in several cancers. Furthermore, our study revealed a clear association between RUNX gene family expression and ESTIMATE score, RNA stemness, and DNA stemness scores. Compared with RUNX1 and RUNX2, RUNX3 showed relatively low levels of genetic alterations. RUNX gene family genes had clear associations with immune infiltrate subtypes, and their expression was positively related to immune checkpoint genes and drug sensitivity in most cases. Two immunotherapy cohorts confirm that the expression of RUNX was correlated with the clinical response of immunotherapy. Conclusions: These findings will help to elucidate the potential oncogenic roles of RUNX gene family genes in different types of cancer and it can function as a prognostic marker in various malignant tumors.
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Affiliation(s)
- Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, Shanghai, China.,Laboratory of Myopia, NHC Key Laboratory of Myopia, Fudan University, Chinese Academy of Medical Sciences, Shanghai 200000, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, Shanghai, China
| | - Yun Chen
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Peijun Shen
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, Henan, China
| | - Lan Gong
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, Shanghai, China.,Laboratory of Myopia, NHC Key Laboratory of Myopia, Fudan University, Chinese Academy of Medical Sciences, Shanghai 200000, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, Shanghai, China
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43
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Li Y, Huang Y, Ren S, Xiao X, Cao H, He J. A Pan-Cancer Analysis of the Oncogenic Role of Nuclear Transport Factor 2 in Human Cancers. Front Oncol 2022; 12:829389. [PMID: 35155261 PMCID: PMC8831323 DOI: 10.3389/fonc.2022.829389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/04/2022] [Indexed: 12/24/2022] Open
Abstract
Nuclear transport factor 2 (NUTF2) is a GDP-binding protein that participates in the nucleocytoplasmic transport process. The role of NUTF2 in cancer development is largely unknown and lacks systemic assessment across human cancers. In this study, we performed a pan-cancer analysis of NUTF2 in human cancers. Out of 33 types of cancers, 19 types had significantly different expression of NUTF2 between tumor and normal tissues. Meanwhile, survival analysis showed that NUTF2 could be an independent prognostic factor in several tumor types. Further analysis suggested that the expression of NUTF2 expression was correlated with the infiltration of immune cells, such as CD8+ T cells, effector memory CD4+ T cells, and cancer-associated fibroblasts in kidney renal clear cell carcinoma. Moreover, co-expression analysis showed the positive association between NUTF2 and cell proliferation biomarkers (MKI67and PCNA) and epithelial–mesenchymal transition markers (VIM, TWIST1, SNAI1, SNAI2, FN1, and CDH2), suggesting that NUTF2 plays important roles in regulating cancer proliferation and metastasis. This pan-cancer analysis of NUTF2 provides a systemic understanding of its oncogenic role across different types of cancers.
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Affiliation(s)
- Yu Li
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yongsheng Huang
- Cellular & Molecular Diagnostics Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shuwei Ren
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sun Yat-Sen University Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xing Xiao
- Department of Dermatology, Shenzhen Children's Hospital, Shenzhen, China
| | - Haotian Cao
- Department of Oral and Maxillofacial Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Juan He
- Department of Rheumatology and Immunology, Peking University Shenzhen Hospital, Shenzhen, China.,Shenzhen Key Laboratory of Immunity and Inflammatory Diseases, Shenzhen, China
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Li C, Teng Y, Wu J, Yan F, Deng R, Zhu Y, Li X. A pan-cancer analysis of the oncogenic role of Keratin 17 ( KRT17) in human tumors. Transl Cancer Res 2022; 10:4489-4501. [PMID: 35116305 PMCID: PMC8797707 DOI: 10.21037/tcr-21-2118] [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: 08/13/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022]
Abstract
Background Although new evidence from cells or animals suggests a relationship between Keratin 17 (KRT17) and cancer, no pan-cancer analysis is currently available. Methods The expression level of KRT17 in generalized carcinoma was detected by the Tumor Immune Estimation Resource, version 2 (TIMER2) database, and then verified the protein expression of KRT17 in different cancer species in UALCAN database, and analyzed the relationship between the expression level of KRT17 and the clinical stage and survival of different cancers. We further explored the genetic variation of KRT17 in different tumor types included in The Cancer Genome Atlas (TCGA) and the specific mutations in each domain. The changes of KRT17 protein phosphorylation levels and protein expression levels at different phosphorylation sites in different tumors were explored. TIMER2 database was used to explore the potential relationship between the infiltration level of different immune cells and KRT17 gene expression in different TCGA cancer types. Finally, the protein binding to KRT17 and genes related to KRT17 expression were explored by STRING database and TCGA database. Results KRT17 is overexpressed in most malignancies, and we observed a distinct relationship between KRT17 expression and tumor patient prognosis. Enhanced phosphorylation levels of S13, S24, S32, and S39 were observed in several tumors, such as lung adenocarcinoma (LUAD), colon and ovarian cancers, and uterine corpus endometrial carcinoma (UCEC). Intermediate filament cytoskeleton and keratinization may be simultaneously acting with KRT17 on tumor pathogenesis. Conclusions Our pan-cancer analysis provides relatively complete information on the oncogenic functions of KRT17 in various cancers.
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Affiliation(s)
- Chenchen Li
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Teng
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jiacheng Wu
- Department of Urology, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Fei Yan
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Deng
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Ying Zhu
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoyou Li
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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Zhang C, Yang W, Zhang S, Zhang Y, Liu P, Li X, Zhi W, Yang D, Li M, Lu Y. Pan-cancer analysis of osteogenesis imperfecta causing gene SERPINF1. Intractable Rare Dis Res 2022; 11:15-24. [PMID: 35261846 PMCID: PMC8898391 DOI: 10.5582/irdr.2021.01138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/23/2022] [Accepted: 01/31/2022] [Indexed: 11/05/2022] Open
Abstract
Osteogenesis imperfecta (OI) type VI causative gene SERPINF1, encodes a member of the serpin family that does not display the serine protease inhibitory activity shown by many of the other serpin proteins. The encoded protein (pigment epithelium-derived factor, PEDF) has anti-tumor, anti-angiogenesis, anti-inflammation, nutrition and nerve protection functions, and participates in fat metabolism. In this paper, a series of bioinformatics analyses were conducted based on the regulation of SERPINF1 in the human. Pan-cancer analysis of SERPINF1 revealed it to play a role in the prognosis of tumors, especially in KIRC, and that high expression of SERPINF1 leads to a poor prognosis of the disease, the occurrence of which is largely related to the high expression of SERPINF1 leading to immune infiltration of cancer associated fibroblasts. Mutation analysis found that SERPINF1 had eight identical amino acids alterations sites with different in both cancer and OI patients. which hints the possible relationship between genotype and phenotype.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yanqin Lu
- Address correspondence to:Yanqin Lu, Shandong First Medical University & Shandong Academy of Medical Sciences, #6699 Qingdao Road, Ji'nan 250117, China. E-mail: (YL)
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Systematic pan-cancer landscape identifies CARM1 as a potential prognostic and immunological biomarker. BMC Genom Data 2022; 23:7. [PMID: 35033016 PMCID: PMC8761291 DOI: 10.1186/s12863-021-01022-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/23/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Belonging to the protein arginine methyltransferase (PRMT) family, the enzyme encoded by coactivator associated arginine methyltransferase 1 (CARM1) catalyzes the methylation of protein arginine residues, especially acts on histones and other chromatin related proteins, which is essential in regulating gene expression. Beyond its well-established involvement in the regulation of transcription, recent studies have revealed a novel role of CARM1 in tumorigenesis and development, but there is still a lack of systematic understanding of CARM1 in human cancers. An integrated analysis of CARM1 in pan-cancer may contribute to further explore its prognostic value and potential immunological function in tumor therapy. RESULTS Based on systematic analysis of data in multiple databases, we firstly verified that CARM1 is highly expressed in most tumors compared with corresponding normal tissues, and is bound up with poor prognosis in some tumors. Subsequently, relevance between CARM1 expression level and tumor immune microenvironment is analyzed from the perspectives of tumor mutation burden, microsatellite instability, mismatch repair genes, methyltransferases genes, immune checkpoint genes and immune cells infiltration, indicating a potential relationship between CARM1 expression and tumor microenvironment. A gene enrichment analysis followed shortly, which implied that the role of CARM1 in tumor pathogenesis may be related to transcriptional imbalance and viral carcinogenesis. CONCLUSIONS Our first comprehensive bioinformatics analysis provides a broad molecular perspective on the role of CARM1 in various tumors, highlights its value in clinical prognosis and potential association with tumor immune microenvironment, which may furnish an immune based antitumor strategy to provide a reference for more accurate and personalized immunotherapy in the future.
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Whiteside TL. Tumor-Infiltrating Lymphocytes and Their Role in Solid Tumor Progression. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 113:89-106. [PMID: 35165861 PMCID: PMC9113058 DOI: 10.1007/978-3-030-91311-3_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tumor-infiltrating lymphocytes (TIL) are an important component of the tumor environment. Their role in tumor growth and progression has been debated for decades. Today, emphasis has shifted to beneficial effects of TIL for the host and to therapies optimizing the benefits by reducing immune suppression in the tumor microenvironment. Evidence indicates that when TILs are present in the tumor as dense aggregates of activated immune cells, tumor prognosis and responses to therapy are favorable. Gene signatures and protein profiling of TIL at the population and single-cell levels provide clues not only about their phenotype and numbers but also about TIL potential functions in the tumor. Correlations of the TIL data with clinicopathological tumor characteristics, clinical outcome, and patients' survival indicate that TILs exert influence on the disease progression, especially in colorectal carcinomas and breast cancer. At the same time, the recognition that TIL signatures vary with time and cancer progression has initiated investigations of TIL as potential prognostic biomarkers. Multiple mechanisms are utilized by tumors to subvert the host immune system. The balance between pro- and antitumor responses of TIL largely depends on the tumor microenvironment, which is unique in each cancer patient. This balance is orchestrated by the tumor and thus is shifted toward the promotion of tumor growth. Changes occurring in TIL during tumor progression appear to serve as a measure of tumor aggressiveness and potentially provide a key to selecting therapeutic strategies and inform about prognosis.
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Affiliation(s)
- Theresa L Whiteside
- Departments of Pathology and Immunology, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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Li L, Huang Z, Du K, Liu X, Li C, Wang D, Zhang Y, Wang C, Li J. Integrative Pan-Cancer Analysis Confirmed that FCGR3A is a Candidate Biomarker Associated With Tumor Immunity. Front Pharmacol 2022; 13:900699. [PMID: 35668930 PMCID: PMC9163829 DOI: 10.3389/fphar.2022.900699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/18/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Fc gamma receptor 3A (FCGR3A) encodes a receptor for the Fc portion of immunoglobulin G, which plays a significant role in the immune response. However, the role of FCGR3A in cancers remains unclear. This study aimed to visualize the prognostic landscape of FCGR3A in pan-cancer and investigate the relationship between FCGR3A expression and tumor microenvironment. Method: Based on the TCGA database, GTEx database, and GDSC database, we analyzed the expression of FCGR3A in pan-cancers and adjacent normal tissues and its relationship with prognosis, immune cells infiltration, immune-related genes, DNA mismatch repair (MMR) genes, DNA methylation, and drugs sensitivity. The gene alteration frequency of FCGR3A was acquired on the cBioportal website. Moreover, we constructed PPI networks, performed GO and KEGG analysis to illustrate the function, and signaling pathways of FCGR3A-related genes, and conducted gene set enrichment analysis (GSEA) of FCGR3A to further explore its potential biological functions. Result: The differential analysis results of the publicly available databases showed that FCGR3A was generally highly expressed in pan-cancer. Survival analysis revealed that FCGR3A predominated as a risk prognostic factor in most cancers. Additionally, the expression of FCGR3A was confirmed to be associated with several immune cells infiltration, multiple immune checkpoint genes, and DNA mismatch repair genes expression in generalized carcinoma. We also identified a negative correlation between FCGR3A and DNA methylation levels. Through GO/KEGG and GESA, we found that FCGR3A was involved in many pathologic and physiological processes, and was most closely related to tumor immune-related pathways. Drug sensitivity analysis showed that higher FCGR3A expression predicts a low IC50 value for the vast majority of drugs. Conclusions: FCGR3A may be an immune-oncogenic molecule that correlates with tumor immune infiltration levels and affects drug sensitivity, thus it can be served as a promising biomarker for cancer detection, prognosis, therapeutic design, and follow-up.
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Affiliation(s)
- Lilin Li
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Zijian Huang
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Kunpeng Du
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiang Liu
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Chunhui Li
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Duanyu Wang
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Yangfeng Zhang
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Changqian Wang
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Jiqiang Li
- Department of Radiation Oncology, Oncology Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- *Correspondence: Jiqiang Li, , orcid.org/0000-0002-585-5911
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Huang W, Fan L, Tang Y, Chi Y, Li J. A Pan-Cancer Analysis of the Oncogenic Role of Integrin Beta4 (ITGB4) in Human Tumors. Int J Gen Med 2021; 14:9629-9645. [PMID: 34924769 PMCID: PMC8674675 DOI: 10.2147/ijgm.s341076] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
Background Integrin beta4 (ITGB4) is a transmembrane receptor that plays a key role in tumorigenesis and tumor development. However, there are no pan-cancer analyses of ITGB4. Methods This study demonstrates the first potential oncogenic roles of ITGB4 across 33 tumors based on the dataset of the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Results ITGB4 is highly expressed in many cancers, and distinct correlations exist between ITGB4 expression and the prognosis of tumor patients. We also found that the methylation and genetic alteration level of ITGB4 was associated with some cancer prognosis. Furthermore, we found a reduced phosphorylation of ITGB4 at S1457 in several tumors, such as breast and ovarian cancers. Finally, ITGB4 expression was correlated with cancer-associated fibroblasts in liver hepatocellular carcinoma and prostate adenocarcinoma, and the infiltration level of NK cells and neutrophils was observed in other cancers, such as breast invasive carcinoma and lung adenocarcinoma. Moreover, RNA metabolism and protein processing-associated functions are involved in the functional mechanism of ITGB4. Conclusion Our first pan-cancer study may offer a relatively comprehensive understanding of the oncogenic roles of ITGB4 across different tumors.
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Affiliation(s)
- Wenjie Huang
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Affiliated Women and Children's Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi, 545001, People's Republic of China
| | - Li Fan
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Affiliated Women and Children's Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi, 545001, People's Republic of China
| | - Yongmei Tang
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Affiliated Women and Children's Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi, 545001, People's Republic of China
| | - Yinxiu Chi
- School of Basic Medicine, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Jingjing Li
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Affiliated Women and Children's Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi, 545001, People's Republic of China
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Landscape of the oncogenic role of fatty acid synthase in human tumors. Aging (Albany NY) 2021; 13:25106-25137. [PMID: 34879004 PMCID: PMC8714155 DOI: 10.18632/aging.203730] [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: 09/07/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022]
Abstract
Background: Identifying a unique and common regulatory pathway that drives tumorigenesis in cancers is crucial to foster the development of effective treatments. However, a systematic analysis of fatty acid synthase across pan-cancers has not been carried out. Methods: We investigated the oncogenic roles of fatty acid synthase in 33 cancers based on the cancer genome atlas and gene expression omnibus. Results: Fatty acid synthase is profoundly expressed in most cancers and is an important factor in predicting the outcome of cancer patients. Further, the level of S207 phosphorylation was found to be improved in several neoplasms (e.g., colon cancer). Fatty acid synthase expression is related to tumor-infiltrating immune cells in tumors (e.g., CD8+ T-cell infiltration level in cervical squamous cell carcinoma). Moreover, hormone receptor binding- and fatty acid metabolic process-associated pathways are involved in the functional mechanisms of fatty acid synthase. Conclusions: This study provides a complete understanding of the oncogenic role of fatty acid synthase in human tumors.
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