1
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Coffey NJ, Simon MC. Metabolic alterations in hereditary and sporadic renal cell carcinoma. Nat Rev Nephrol 2024; 20:233-250. [PMID: 38253811 PMCID: PMC11165401 DOI: 10.1038/s41581-023-00800-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2023] [Indexed: 01/24/2024]
Abstract
Kidney cancer is the seventh leading cause of cancer in the world, and its incidence is on the rise. Renal cell carcinoma (RCC) is the most common form and is a heterogeneous disease comprising three major subtypes that vary in their histology, clinical course and driver mutations. These subtypes include clear cell RCC, papillary RCC and chromophobe RCC. Molecular analyses of hereditary and sporadic forms of RCC have revealed that this complex and deadly disease is characterized by metabolic pathway alterations in cancer cells that lead to deregulated oxygen and nutrient sensing, as well as impaired tricarboxylic acid cycle activity. These metabolic changes facilitate tumour growth and survival. Specifically, studies of the metabolic features of RCC have led to the discovery of oncometabolites - fumarate and succinate - that can promote tumorigenesis, moonlighting functions of enzymes, and substrate auxotrophy owing to the disruption of pathways that enable the production of arginine and cholesterol. These metabolic alterations within RCC can be exploited to identify new therapeutic targets and interventions, in combination with novel approaches that minimize the systemic toxicity of metabolic inhibitors and reduce the risk of drug resistance owing to metabolic plasticity.
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Affiliation(s)
- Nathan J Coffey
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Han A, Liu T, Du P, Wang M, Liu J, Chen L. The FOXO1/G6PC axis promotes gastric cancer progression and mediates 5-fluorouracil resistance by targeting the PI3K/AKT/mTOR signaling pathway. Mol Carcinog 2024; 63:688-700. [PMID: 38224261 DOI: 10.1002/mc.23681] [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: 11/08/2023] [Revised: 12/20/2023] [Accepted: 12/31/2023] [Indexed: 01/16/2024]
Abstract
Gastric cancer (GC) is a prevalent malignancy of the digestive system. Distant metastasis and chemotherapy resistance are the crucial obstacles to prognosis in GC. Recent research has discovered that the glucose-6-phosphatase catalytic subunit (G6PC) plays an important role in tumor malignant development. However, little evidence has highlighted its role in GC. Herein, through a comprehensive analysis including profiling of tissue samples and functional validation in vivo and in vitro, we identify G6PC as a crucial factor in GC tumorigenesis. Importantly, we found that the FOXO1/G6PC axis could accelerate GC cell proliferation, metastasis, and 5-Fluorouracil (5-FU) resistance by targeting the PI3K/AKT/mTOR signaling pathway, implicating that as a prospective therapeutic approach in GC.
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Affiliation(s)
- Anna Han
- Key Laboratory Pathobiology (Yanbian University), State Ethnic Affairs Commission, Yanji, China
| | - Taorui Liu
- Key Laboratory Pathobiology (Yanbian University), State Ethnic Affairs Commission, Yanji, China
- Center for Joint Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Pan Du
- Key Laboratory Pathobiology (Yanbian University), State Ethnic Affairs Commission, Yanji, China
| | - Mengying Wang
- Key Laboratory Pathobiology (Yanbian University), State Ethnic Affairs Commission, Yanji, China
| | - Jiajing Liu
- Key Laboratory Pathobiology (Yanbian University), State Ethnic Affairs Commission, Yanji, China
| | - Liyan Chen
- Key Laboratory Pathobiology (Yanbian University), State Ethnic Affairs Commission, Yanji, China
- Cancer Research Center, Yanbian University Medical College, Yanji, China
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3
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Iacobas DA, Obiomon EA, Iacobas S. Genomic Fabrics of the Excretory System's Functional Pathways Remodeled in Clear Cell Renal Cell Carcinoma. Curr Issues Mol Biol 2023; 45:9471-9499. [PMID: 38132440 PMCID: PMC10742519 DOI: 10.3390/cimb45120594] [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: 10/19/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most frequent form of kidney cancer. Metastatic stages of ccRCC reduce the five-year survival rate to 15%. In this report, we analyze the ccRCC-induced remodeling of the five KEGG-constructed excretory functional pathways in a surgically removed right kidney and its metastasis in the chest wall from the perspective of the Genomic Fabric Paradigm (GFP). The GFP characterizes every single gene in each region by these independent variables: the average expression level (AVE), relative expression variability (REV), and expression correlation (COR) with each other gene. While the traditional approach is limited to only AVE analysis, the novel REV analysis identifies the genes whose correct expression level is critical for cell survival and proliferation. The COR analysis determines the real gene networks responsible for functional pathways. The analyses covered the pathways for aldosterone-regulated sodium reabsorption, collecting duct acid secretion, endocrine and other factor-regulated sodium reabsorption, proximal tubule bicarbonate reclamation, and vasopressin-regulated water reabsorption. The present study confirms the conclusion of our previously published articles on prostate and kidney cancers that even equally graded cancer nodules from the same tumor have different transcriptomic topologies. Therefore, the personalization of anti-cancer therapy should go beyond the individual, to his/her major cancer nodules.
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Affiliation(s)
- Dumitru Andrei Iacobas
- Personalized Genomics Laboratory, Undergraduate Medical Academy, Prairie View A&M University, Prairie View, TX 77446, USA;
| | - Ehiguese Alade Obiomon
- Personalized Genomics Laboratory, Undergraduate Medical Academy, Prairie View A&M University, Prairie View, TX 77446, USA;
| | - Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA;
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4
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Shen C, Zhang DL, Cheng XL, Zhang WC, Zhao JJ. Urological Tumor: A Narrative Review of Tertiary Lymphatic Structures. Urol Int 2023; 107:841-847. [PMID: 37769625 PMCID: PMC10623398 DOI: 10.1159/000532127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/17/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Tertiary lymphoid structures (TLSs), as ectopic lymphoid-like tissues, are highly similar to secondary lymphoid organs and are not only involved in chronic inflammation and autoimmune responses but are also closely associated with tumor immunotherapy and prognosis. The complex composition of the urological tumor microenvironment not only varies greatly in response to immunotherapy, but the prognostic value of TLSs in different urological tumors remains controversial. SUMMARY We searched PubMed, Web of Science, and other full-text database systems. TLSs, kidney cancer, uroepithelial cancer, bladder cancer, and prostate cancer as keywords, relevant literature was searched from the time the library was built to 2023. Systematically explore the role and mechanism of TLSs in urological tumors. It includes the characteristics of TLSs, the role and mechanism of TLSs in urological tumors, and the clinical significance of TLSs in urological tumors. KEY MESSAGES The prognostic role of TLSs in different urological tumors was significantly different. It is not only related to its enrichment in the tumor but also highly correlated with the location of the tumor. In addition, autoimmune toxicity may be a potential barrier to its role in the formation of TLSs through induction. Therefore, studying the mechanisms of TLSs in autoimmune diseases may help in the development of antitumor target drugs.
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Affiliation(s)
- Chong Shen
- College of Clinical Medicine, Hebei University of Engineering, Handan, China
| | - Dong-Li Zhang
- College of Clinical Medicine, Hebei University of Engineering, Handan, China
| | - Xiao-Long Cheng
- Department of Urology II, Affiliated Hospital of Hebei Engineering University, Handan, China
| | - Wei-Chuan Zhang
- Department of Urology II, Affiliated Hospital of Hebei Engineering University, Handan, China
| | - Jian-Jun Zhao
- Department of Urology II, Affiliated Hospital of Hebei Engineering University, Handan, China
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5
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Mahé M, Rios-Fuller TJ, Karolin A, Schneider RJ. Genetics of enzymatic dysfunctions in metabolic disorders and cancer. Front Oncol 2023; 13:1230934. [PMID: 37601653 PMCID: PMC10433910 DOI: 10.3389/fonc.2023.1230934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Inherited metabolic disorders arise from mutations in genes involved in the biogenesis, assembly, or activity of metabolic enzymes, leading to enzymatic deficiency and severe metabolic impairments. Metabolic enzymes are essential for the normal functioning of cells and are involved in the production of amino acids, fatty acids and nucleotides, which are essential for cell growth, division and survival. When the activity of metabolic enzymes is disrupted due to mutations or changes in expression levels, it can result in various metabolic disorders that have also been linked to cancer development. However, there remains much to learn regarding the relationship between the dysregulation of metabolic enzymes and metabolic adaptations in cancer cells. In this review, we explore how dysregulated metabolism due to the alteration or change of metabolic enzymes in cancer cells plays a crucial role in tumor development, progression, metastasis and drug resistance. In addition, these changes in metabolism provide cancer cells with a number of advantages, including increased proliferation, resistance to apoptosis and the ability to evade the immune system. The tumor microenvironment, genetic context, and different signaling pathways further influence this interplay between cancer and metabolism. This review aims to explore how the dysregulation of metabolic enzymes in specific pathways, including the urea cycle, glycogen storage, lysosome storage, fatty acid oxidation, and mitochondrial respiration, contributes to the development of metabolic disorders and cancer. Additionally, the review seeks to shed light on why these enzymes represent crucial potential therapeutic targets and biomarkers in various cancer types.
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Affiliation(s)
| | | | | | - Robert J. Schneider
- Department of Microbiology, Grossman NYU School of Medicine, New York, NY, United States
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6
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Bergamini C, Leoni I, Rizzardi N, Melli M, Galvani G, Coada CA, Giovannini C, Monti E, Liparulo I, Valenti F, Ferracin M, Ravaioli M, Cescon M, Vasuri F, Piscaglia F, Negrini M, Stefanelli C, Fato R, Gramantieri L, Fornari F. MiR-494 induces metabolic changes through G6pc targeting and modulates sorafenib response in hepatocellular carcinoma. J Exp Clin Cancer Res 2023; 42:145. [PMID: 37301960 DOI: 10.1186/s13046-023-02718-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Metabolic reprogramming is a well-known marker of cancer, and it represents an early event during hepatocellular carcinoma (HCC) development. The recent approval of several molecular targeted agents has revolutionized the management of advanced HCC patients. Nevertheless, the lack of circulating biomarkers still affects patient stratification to tailored treatments. In this context, there is an urgent need for biomarkers to aid treatment choice and for novel and more effective therapeutic combinations to avoid the development of drug-resistant phenotypes. This study aims to prove the involvement of miR-494 in metabolic reprogramming of HCC, to identify novel miRNA-based therapeutic combinations and to evaluate miR-494 potential as a circulating biomarker. METHODS Bioinformatics analysis identified miR-494 metabolic targets. QPCR analysis of glucose 6-phosphatase catalytic subunit (G6pc) was performed in HCC patients and preclinical models. Functional analysis and metabolic assays assessed G6pc targeting and miR-494 involvement in metabolic changes, mitochondrial dysfunction, and ROS production in HCC cells. Live-imaging analysis evaluated the effects of miR-494/G6pc axis in cell growth of HCC cells under stressful conditions. Circulating miR-494 levels were assayed in sorafenib-treated HCC patients and DEN-HCC rats. RESULTS MiR-494 induced the metabolic shift of HCC cells toward a glycolytic phenotype through G6pc targeting and HIF-1A pathway activation. MiR-494/G6pc axis played an active role in metabolic plasticity of cancer cells, leading to glycogen and lipid droplets accumulation that favored cell survival under harsh environmental conditions. High miR-494 serum levels associated with sorafenib resistance in preclinical models and in a preliminary cohort of HCC patients. An enhanced anticancer effect was observed for treatment combinations between antagomiR-494 and sorafenib or 2-deoxy-glucose in HCC cells. CONCLUSIONS MiR-494/G6pc axis is critical for the metabolic rewiring of cancer cells and associates with poor prognosis. MiR-494 deserves attention as a candidate biomarker of likelihood of response to sorafenib to be tested in future validation studies. MiR-494 represents a promising therapeutic target for combination strategies with sorafenib or metabolic interference molecules for the treatment of HCC patients who are ineligible for immunotherapy.
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Affiliation(s)
- Christian Bergamini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Ilaria Leoni
- Centre for Applied Biomedical Research - CRBA, University of Bologna, Policlinico di Sant'Orsola, 40138, Bologna, Italy
- Department for Life Quality Studies, University of Bologna, 47921, Rimini, Italy
| | - Nicola Rizzardi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Mattia Melli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Giuseppe Galvani
- Centre for Applied Biomedical Research - CRBA, University of Bologna, Policlinico di Sant'Orsola, 40138, Bologna, Italy
- Department for Life Quality Studies, University of Bologna, 47921, Rimini, Italy
| | | | - Catia Giovannini
- Centre for Applied Biomedical Research - CRBA, University of Bologna, Policlinico di Sant'Orsola, 40138, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138, Bologna, Italy
| | - Elisa Monti
- Centre for Applied Biomedical Research - CRBA, University of Bologna, Policlinico di Sant'Orsola, 40138, Bologna, Italy
- Department for Life Quality Studies, University of Bologna, 47921, Rimini, Italy
| | - Irene Liparulo
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Francesca Valenti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences, University of Bologna, 40138, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Matteo Ravaioli
- Department of Medical and Surgical Sciences, University of Bologna, 40138, Bologna, Italy
- Hepato-biliary Surgery and Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Matteo Cescon
- Department of Medical and Surgical Sciences, University of Bologna, 40138, Bologna, Italy
- Hepato-biliary Surgery and Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Francesco Vasuri
- Department of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Fabio Piscaglia
- Department of Medical and Surgical Sciences, University of Bologna, 40138, Bologna, Italy
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Massarenti, 9, 40138, Bologna, Italy
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44100, Ferrara, Italy
| | - Claudio Stefanelli
- Department for Life Quality Studies, University of Bologna, 47921, Rimini, Italy
| | - Romana Fato
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Laura Gramantieri
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Massarenti, 9, 40138, Bologna, Italy.
| | - Francesca Fornari
- Centre for Applied Biomedical Research - CRBA, University of Bologna, Policlinico di Sant'Orsola, 40138, Bologna, Italy.
- Department for Life Quality Studies, University of Bologna, 47921, Rimini, Italy.
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7
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Wang L, Shen J, Wang Y, Bi J. Identification of fatty acid metabolism-based molecular subtypes and prognostic signature to predict immune landscape and guide clinical drug treatment in renal clear cell carcinoma. Int Immunopharmacol 2023; 116:109735. [PMID: 36716517 DOI: 10.1016/j.intimp.2023.109735] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/29/2023]
Abstract
Three subtypes of samples were generated based on genes involved in fatty acid metabolism in The Cancer Genome Atlas (TCGA)-RCC patients using a non-negative matrix factorization (NMF) algorithm. 32 co-expressed modules were identified using WCGNA. We constructed a four-gene signature in our training set using least absolute shrinkage selection operator regression analysis and verified it in our testing and overall sets. A relevant study analysis in clinical trials was conducted, which showed the model had good stability and potential application value for predicting outcomes. We analyzed the immune microenvironment using MCPcounter, CIBERSORT, quanTIseq, TIMER and ESTIMATE algorithms, and the result indicated risk was positively related to T cells, B-lineage, and fibroblasts and negatively correlated with monocytic lineage, myeloid dendritic cells, neutrophils, and endothelial cells, and CPT1B was positively related to T cells, CD8 + T cells, Cytotoxic lymphocytes and NK cells, and negatively correlated with myeloid dendritic cells, fibroblasts, endothelial cells. Tumor mutation burden was positively related to risk score and the expression of CPT1B using the R packages corrplot, circlize. Through the R package pRRophetic, drug sensitivity tests showed that the low-risk score group would benefit more from sunitinib and less from pazopanib, sorafenib, temsirolimus, gemcitabine and doxorubicin than the high-risk score group. We performed the relevant basic assay validation for CPT1B, and the proliferation ability of RCC cells was inhibited after the knockdown of protein expression of CPT1B. In conclusion, we established a four-gene model that can predict outcomes of RCC with potential applications in diagnosis and treatment.
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Affiliation(s)
- Linhui Wang
- Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Junlin Shen
- Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yutao Wang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianbin Bi
- Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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Shen J, Wang L, Bi J. Bioinformatics analysis and experimental validation of cuproptosis-related lncRNA LINC02154 in clear cell renal cell carcinoma. BMC Cancer 2023; 23:160. [PMID: 36797708 PMCID: PMC9936708 DOI: 10.1186/s12885-023-10639-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is common in urinary system tumors. Cuproptosis is a non-apoptotic cell death pathway. Copper binds to fatty acylated mitochondrial proteins and activates various forms of cell death. LncRNA LINC02154 is significantly highly expressed in cells and tissues of many types of tumors, and the risk signature of LINC02154 in some tumors has been validated for effectiveness. METHODS We constructed a risk prognostic signature by obtaining differentially expressed long noncoding RNAs (lncRNAs) associated with ccRCC outcomes and cuproptosis from The Cancer Genome Atlas (TCGA). We used TCGA to construct training and testing sets to analyze the risk signature and the impact of LINC02154, and we performed relevant survival analyses. Tumor mutational burdens were analyzed in different LINC02154 expression groups and risk score groups. We next analyzed the immune microenvironment of LINC20154. We performed LINC20154-related drug sensitivity analyses. We also investigated the cellular function of LINC02154 in the ACHN cell line and performed CCK-8 assay, EdU, wound-healing assay, and Transwell assay. The essential genes FDX1 and DLST of cuproptosis were detected by western blot. RESULTS We demonstrated that LINC02154's impact on outcomes was statistically significant. We also demonstrated the association of different ages, genders, stages, and grades with LINC02154 and risk models. The results showed a significant difference in tumor mutation burden between the groups, which was closely related to clinical prognosis. We found differences in immune cells among groups with different levels of LINC02154 expression and significant differences in immune function, immunotherapeutic positive markers, and critical steps of the immune cycle. The sensitivity analysis showed that differential expression of LINC02154 discriminated between sensitivity to axitinib, doxorubicin, gemcitabine, pazopanib, sorafenib, sunitinib, and temsirolimus. This difference was also present in the high-risk group and low-risk group. We demonstrated that the proliferation and migration of t ACHN cells in the LINC02154 knockdown group were inhibited. The western blot results showed that the knockdown of LINC02154 significantly affected the expression of FDX1 and DLST, critical genes of cuproptosis. CONCLUSION Finally, we demonstrated that LINC02154 and our constructed risk signature could predict outcomes and have potential clinical value.
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Affiliation(s)
- Junlin Shen
- grid.412449.e0000 0000 9678 1884Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning China
| | - Linhui Wang
- grid.412449.e0000 0000 9678 1884Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning China
| | - Jianbin Bi
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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He H, Jin Z, Dai J, Wang H, Sun J, Xu D. Computed tomography‐based radiomics prediction of
CTLA4
expression and prognosis in clear cell renal cell carcinoma. Cancer Med 2022; 12:7627-7638. [PMID: 36397666 PMCID: PMC10067074 DOI: 10.1002/cam4.5449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES To predict CTLA4 expression levels and prognosis of clear cell renal cell carcinoma (ccRCC) by constructing a computed tomography-based radiomics model and establishing a nomogram using clinicopathologic factors. METHODS The clinicopathologic parameters and genomic data were extracted from 493 ccRCC cases of the Cancer Genome Atlas (TCGA)-KIRC database. Univariate and multivariate Cox regression and Kaplan-Meier analysis were performed for prognosis analysis. Cibersortx was applied to evaluate the immune cell composition. Radiomic features were extracted from the TCGA/the Cancer Imaging Archive (TCIA) (n = 102) datasets. The support vector machine (SVM) was employed to establish the radiomics signature for predicting CTLA4 expression. Receiver operating characteristic curve (ROC), decision curve analysis (DCA), and precision-recall curve were utilized to assess the predictive performance of the radiomics signature. Correlations between radiomics score (RS) and selected features were also evaluated. An RS-based nomogram was constructed to predict prognosis. RESULTS CTLA4 was significantly overexpressed in ccRCC tissues and was related to lower overall survival. A higher CTLA4 expression was independently linked to the poor prognosis (HR = 1.458, 95% CI 1.13-1.881, p = 0.004). The radiomics model for the prediction of CTLA4 expression levels (AUC = 0.769 in the training set, AUC = 0.724 in the validation set) was established using seven radiomic features. A significant elevation in infiltrating M2 macrophages was observed in the RS high group (p < 0.001). The predictive efficiencies of the RS-based nomogram measured by AUC were 0.826 at 12 months, 0.805 at 36 months, and 0.76 at 60 months. CONCLUSIONS CTLA4 mRNA expression status in ccRCC could be predicted noninvasively using a radiomics model based on nephrographic phase contrast-enhanced CT images. The nomogram established by combining RS and clinicopathologic factors could predict overall survival for ccRCC patients. Our findings may help stratify prognosis of ccRCC patients and identify those who may respond best to ICI-based treatments.
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Affiliation(s)
- Hongchao He
- Department of Urology Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai China
| | - Zhijia Jin
- Department of Radiology Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai China
| | - Jun Dai
- Department of Urology Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai China
| | - Haofei Wang
- Department of Urology Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai China
| | - Jianqi Sun
- School of Biomedical Engineering Shanghai Jiaotong University Shanghai China
| | - Danfeng Xu
- Department of Urology Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai China
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10
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Tian L, Liao Y. Identification of G6PC as a potential prognostic biomarker in hepatocellular carcinoma based on bioinformatics analysis. Medicine (Baltimore) 2022; 101:e29548. [PMID: 35984176 PMCID: PMC9388022 DOI: 10.1097/md.0000000000029548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has high mortality and incidence rates around the world with limited therapeutic options. There is an urgent need for identification of novel therapeutic targets and biomarkers for early diagnosis and predicting patient survival with HCC. Several studies (GSE102083, GSE29722, GSE101685, and GSE112790) from the GEO database in HCC were screened and analyzed by GEO2R, gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were conducted with the Database for Annotation, Visualization and Integrated Discovery. The protein-protein interaction network was plotted and the module analysis was performed using Search Tool for the Retrieval of Inter-acting Genes/Proteins database and Cytoscape. The expression and survival of key genes were identified using UALCAN, Kaplan-Meier Plotter and ONCOMINE online databases, and the immune infiltration level of key genes was analyzed via the Tumor Immune Estimation Resource (TIMER) database. Through database analysis, eight key genes were finally screened out, and the expressions of cyclin-dependent kinase regulatory subunit 2 and glucose-6-phosphatase catalytic (G6PC), which were closely related to the survival of HCC patients, was detected by using UALCAN. Further analysis on the differential expression of G6PC in multiple cancerous tumors and normal tissues revealed low expression in many solid tumors by Oncomine and TIMER. In addition, Kaplan-Meier plotter and UALCAN database analysis to access diseases prognosis suggested that low expression of G6PC was significantly associated with poor overall survival in HCC patients. Finally, TIMER database analysis showed a significant negative correlation between G6PC and infiltration levels of six kinds of immune cells. The somatic copy number alterations of G6PC were associated with B cells, CD8+ T cells, CD4+ T cells, macrophages, dentritic cells and neutrophils. These bioinformatic data identified G6PC as a potential key gene in the diagnosis and prognosis of HCC.
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Affiliation(s)
- Li Tian
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China
- Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China
- Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yong Liao
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China
- Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China
- Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Yong Liao, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China. Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China. Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China (e-mail: )
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11
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Prognostic value, DNA variation and immunologic features of a tertiary lymphoid structure-related chemokine signature in clear cell renal cell carcinoma. Cancer Immunol Immunother 2022; 71:1923-1935. [PMID: 35043231 DOI: 10.1007/s00262-021-03123-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/24/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND The tumor microenvironment (TME) and tertiary lymphoid structures (TLS) affect the occurrence and development of cancers. How the immune contexture interacts with the phenotype of clear cell renal cell carcinoma (ccRCC) remains unclear. METHODS We identified and evaluated TLS clusters in ccRCC using machine learning algorithms and the 12-chemokine gene signature for TLS. Analyses for functional enrichment, DNA variation, immune cell distribution, association with independent clinicopathological features and predictive value of CXCL13 in ccRCC were performed. RESULTS We found a prominently enrichment of the 12-chemokine gene signature for TLS in patients with ccRCC compared with other types of renal cell carcinoma. We identified a prognostic value of CCL4, CCL5, CCL8, CCL19 and CXCL13 expression in ccRCC. DNA deletion of the TLS gene signature significantly predicted poor outcome in ccRCC compared with amplification and wild-type gene signature. We established TLS clusters (C1-4) and observed distinct differences in survival, stem cell-like characteristics, immune cell distribution, response to immunotherapies and VEGF-targeted therapies among the clusters. We found that elevated CXCL13 expression significantly predicted aggressive progression and poor prognosis in 232 patients with ccRCC in a real-world validation cohort. CONCLUSION This study described a 12-chemokine gene signature for TLS in ccRCC and established TLS clusters that reflected different TME immune status and corresponded to prognosis of ccRCC. We confirmed the dense presence of TILs aggregation and TLS in ccRCC and demonstrated an oncogenic role of CXCL13 expression of ccRCC, which help develop immunotherapies and provide novel insights on the long-term management of ccRCC.
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Zhang W, Chen K, Tian W, Zhang Q, Sun L, Wang Y, Liu M, Zhang Q. A Novel and Robust Prognostic Model for Hepatocellular Carcinoma Based on Enhancer RNAs-Regulated Genes. Front Oncol 2022; 12:849242. [PMID: 35646665 PMCID: PMC9133429 DOI: 10.3389/fonc.2022.849242] [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: 01/08/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Evidence has demonstrated that enhancer RNAs (eRNAs) play a vital role in the progression and prognosis of cancers, but few studies have focused on the prognostic ability of eRNA-regulated genes (eRGs) for hepatocellular carcinoma (HCC). Using gene expression profiles of HCC patients from the TCGA-LIHC and eRNA expression profiles from the enhancer RNA in cancers (eRic) data portal, we developed a novel and robust prognostic signature composed of 10 eRGs based on Lasso-penalized Cox regression analysis. According to the signature, HCC patients were stratified into high- and low-risk groups, which have been shown to have significant differences in tumor immune microenvironment, immune checkpoints, HLA-related genes, DNA damage repair-related genes, Gene-set variation analysis (GSVA), and the lower half-maximal inhibitory concentration (IC50) of Sorafenib. The prognostic nomogram combining the signature, age, and TNM stage had good predictive ability in the training set (TCGA-LIHC) with the concordance index (C-index) of 0.73 and the AUCs for 1-, 3-, and 5-year OS of 0.82, 0.77, 0.74, respectively. In external validation set (GSE14520), the nomogram also performed well with the C-index of 0.71 and the AUCs for 1-, 3-, and 5-year OS of 0.74, 0.77, 0.74, respectively. In addition, an important eRG (AKR1C3) was validated using two HCC cell lines (Huh7 and MHCC-LM3) in vitro, and the results demonstrated the overexpression of AKR1C3 is related to cell proliferation, migration, and invasion in HCC. Altogether, our eRGs signature and nomogram can predict prognosis accurately and conveniently, facilitate individualized treatment, and improve prognosis for HCC patients.
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Affiliation(s)
- Wei Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Kegong Chen
- Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Ultrasound, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Tian
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Qi Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Lin Sun
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Yupeng Wang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Meina Liu
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Qiuju Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
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13
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Wang J, Liu W, Xu W, Yang B, Cui M, Li Z, Zhang H, Jin C, Xue H, Zhang J. Comprehensive Analysis of the Oncogenic, Genomic Alteration, and Immunological Landscape of Cation-Chloride Cotransporters in Pan-Cancer. Front Oncol 2022; 12:819688. [PMID: 35372048 PMCID: PMC8968682 DOI: 10.3389/fonc.2022.819688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background Assessing the phenotypic diversity underlying tumor progression requires the identification of variations in the respective molecular interaction in the tumor microenvironment (TME). Despite emerging studies focusing on the association between cation-chloride cotransporters (CCCs) and carcinogenesis, direct evidence that CCCs (KCC2 and NKCC1) mediate tumor progression in pan-cancer remains unclear. Methods We conducted a comprehensive assessment of the expression, DNA variation profiles, and prognostic and immunologic implications of CCCs based on a large-scale pan-cancer population, including 10,967 cancer patients from the Cancer Genome Atlas, 9,162 cancer patients from Genomics Expression Omnibus, 48,834 cancer patients from 188 independent studies, and 356 cancer patients from three real-world cohorts. Results In this study, we first found that CCCs were highly expressed in most tumors, and prominently associated with prognosis. Kaplan–Meier analysis and Cox regression analysis revealed that KCC2 and NKCC1 significantly predicted survival for patients with pan-cancer, suggesting that CCCs have inconsistent tumorigenesis regulatory mechanisms in cancers. Next, we examined the DNA variation landscape of KCC2 and NKCC1 and their prognostic implications in pan-cancer. The results demonstrated that UCEC patients with somatic copy number variation (CNV) of NKCC1 received significantly better outcomes (p < 0.05). Besides emphasizing the clinical implications of CNV of CCCs for cancer patients, we found that NKCC1MUT could prominently prolong progression-free survival (p = 2.59e-04), disease-specific survival (p = 0.019), and overall survival (p = 0.034) compared with NKCC1WT cancer patients possibly via regulation of cell proliferation and oncogenic stress pathways. Additionally, KCC2 positively correlated with the levels of tumor-infiltrating macrophages and CD4+ T cells, but NKCC1 showed a significantly widely negative association with tumor-infiltrated lymphocytes, suggesting an immune-excluded TME in cancers. Similarly, expression of KCC2, rather than NKCC1, was positively correlated with the immune checkpoint molecules, indicating its role as an immune regulator in a wide variety of cancers. Finally, to verify our hypothesis and altered expression of CCCs, we performed IHC analysis and revealed the staining distribution in tumor and adjacent normal tissues of glioma, clear cell renal cell carcinoma, papillary cell renal cell carcinoma, and hepatocellular and breast cancer from three real-world cohorts, and validated prominently prognostic implications of CCCs in patients with clear cell renal cell carcinoma. Conclusion This study first comprehensively investigated the molecular and clinical role of CCCs, and illustrated the significant association among KCC2/NKCC1 expression, DNA variation profiles prognosis, and TME of pan-cancer. The pan-cancer findings provided an in-depth understanding of potential oncogenic and immunologic of differential expression and DNA alteration of KCC2/NKCC1 cancers.
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Affiliation(s)
- Jie Wang
- Department of Anesthesiology and Perioperative Medicine, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Baofeng Yang
- Department of Anesthesiology and Perioperative Medicine, Affiliate Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Mingzhu Cui
- Department of Anesthesiology and Perioperative Medicine, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Zhen Li
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chuntao Jin
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Jiaqiang Zhang, ; Huanzhou Xue, ; Chuntao Jin,
| | - Huanzhou Xue
- Department of Hepatobiliary Surgery, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
- *Correspondence: Jiaqiang Zhang, ; Huanzhou Xue, ; Chuntao Jin,
| | - Jiaqiang Zhang
- Department of Anesthesiology and Perioperative Medicine, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
- *Correspondence: Jiaqiang Zhang, ; Huanzhou Xue, ; Chuntao Jin,
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14
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Zhu K, Deng C, Du P, Liu T, Piao J, Piao Y, Yang M, Chen L. G6PC indicated poor prognosis in cervical cancer and promoted cervical carcinogenesis in vitro and in vivo. Reprod Biol Endocrinol 2022; 20:50. [PMID: 35277194 PMCID: PMC8915493 DOI: 10.1186/s12958-022-00921-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/27/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The glucose-6-phosphatase catalytic subunit (G6PC) is a key enzyme that is involved in gluconeogenesis and glycogen decomposition during glycometabolism. Studies have shown that G6PC is abnormally expressed in various cancers and participates in the proliferation and metastasis of tumors. However, the role of G6PC in cervical cancer remains poorly established. METHODS To analyze the expression of G6PC in cervical cancer tissues in patients by immunohistochemistry. Effects of G6PC deregulation on cervical cancer phenotype were determined using MTT, colony formation, transwell, and wound-healing assays. And constructed a nude mouse xenograft tumor model and CAM assay in vivo. The effect of G6PC on glycolysis in cervical cancer was also evaluated. Effect of G6PC on PI3K/AKT/mTOR pathway was detected by Western blot assay. RESULTS In this study, G6PC expression was found to be upregulated in cervical cancer tissues, and this upregulated expression was associated with LN metastasis, clinical stage, recurrence, and disease-free survival and overall survival rates, indicating that G6PC could serve as a novel marker of early diagnosis in cervical cancer. G6PC promoted proliferation, invasion, epithelial mesenchymal transition (EMT) progression, and angiogenesis of cervical cancer cells. Mechanistically, G6PC activated PI3K/AKT/mTOR pathways. The PI3K/AKT pathway inhibitor, LY294002 could partially attenuate the effect. CONCLUSIONS G6PC plays a key role in the progression of cervical cancer, and overexpressed G6PC is closely related to patient LN metastasis, clinical stage, recurrence and shortened survival. G6PC promoted cervical cancer proliferation, invasion, migration, EMT progression, and angiogenesis, partially through activating the PI3K/AKT pathway. G6PC, as a metabolic gene, not only plays a role in metabolism, but also participates in the development of cervical cancer. Its complex metabolic and non metabolic effects may be a potential therapeutic target and worthy of further study.
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Affiliation(s)
- Kun Zhu
- Cancer Research Center, Yanbian University Medical College, Gong Yuan Road No.977, Yanji, 133002, China
| | - Chunling Deng
- Cancer Research Center, Yanbian University Medical College, Gong Yuan Road No.977, Yanji, 133002, China
| | - Pan Du
- Cancer Research Center, Yanbian University Medical College, Gong Yuan Road No.977, Yanji, 133002, China
| | - Taorui Liu
- Cancer Research Center, Yanbian University Medical College, Gong Yuan Road No.977, Yanji, 133002, China
| | - Junjie Piao
- Cancer Research Center, Yanbian University Medical College, Gong Yuan Road No.977, Yanji, 133002, China
- Key Laboratory of the Science and Technology Department of Jilin Province, Yanji, China
| | - Yingshi Piao
- Cancer Research Center, Yanbian University Medical College, Gong Yuan Road No.977, Yanji, 133002, China
- Key Laboratory of the Science and Technology Department of Jilin Province, Yanji, China
| | - Meng Yang
- Department of Physiology, Medicine College, Jingchu University of Technology, Jingmen, 448000, China.
| | - Liyan Chen
- Cancer Research Center, Yanbian University Medical College, Gong Yuan Road No.977, Yanji, 133002, China.
- Key Laboratory of the Science and Technology Department of Jilin Province, Yanji, China.
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15
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Kumar V, Kumar A, Mir KUI, Yadav V, Chauhan SS. Pleiotropic role of PARP1: an overview. 3 Biotech 2022; 12:3. [PMID: 34926116 PMCID: PMC8643375 DOI: 10.1007/s13205-021-03038-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/20/2021] [Indexed: 01/03/2023] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) protein is encoded by the PARP1 gene located on chromosome 1 (1q42.12) in human cells. It plays a crucial role in post-translational modification by adding poly (ADP-ribose) (PAR) groups to various proteins and PARP1 itself by utilizing nicotinamide adenine dinucleotide (NAD +) as a substrate. Since the discovery of PARP1, its role in DNA repair and cell death has been its identity. This is evident from an overwhelmingly high number of scientific reports in this regard. However, PARP1 also plays critical roles in inflammation, metabolism, tumor development and progression, chromatin modification and transcription, mRNA stability, and alternative splicing. In the present study, we attempted to compile all the scattered scientific information about this molecule, including the structure and multifunctional role of PARP1 in cancer and non-cancer diseases, along with PARP1 inhibitors (PARPis). Furthermore, for the first time, we have classified PARP1-mediated cell death for ease of understanding its role in cell death pathways.
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Affiliation(s)
- Vikas Kumar
- grid.413618.90000 0004 1767 6103Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Anurag Kumar
- grid.413618.90000 0004 1767 6103Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Khursheed Ul Islam Mir
- grid.413618.90000 0004 1767 6103Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Vandana Yadav
- grid.413618.90000 0004 1767 6103Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Shyam Singh Chauhan
- grid.413618.90000 0004 1767 6103Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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16
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Wu X, Tang H, Xu WH, Tang H, Wei S, Anwaier A, Huang H, Qu YY, Zhang H, Zhao S, Li H, Liu W, Chen H, Ding C, Ye D. Protumorigenic Role of Elevated Levels of DNA Polymerase Epsilon Predicts an Immune-Suppressive Microenvironment in Clear Cell Renal Cell Carcinoma. Front Genet 2021; 12:751977. [PMID: 34950188 PMCID: PMC8689073 DOI: 10.3389/fgene.2021.751977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/29/2021] [Indexed: 11/21/2022] Open
Abstract
Increasing evidence indicates that DNA polymerase epsilon (POLE), which mediates DNA damage repair, is significantly associated with tumor prognosis. This study aimed to analyze POLE expression in tumor samples and its prognostic value for patients with clear cell renal cell carcinoma (ccRCC). We found significantly elevated POLE expression in ccRCC tissues compared with normal tissues of multiple independent cohorts. The POLE expression levels of 523 patients with ccRCC (The Cancer Genome Atlas RNA-seq data) and 179 patients with ccRCC with immunohistochemical data (Fudan University Shanghai Cancer Center) were analyzed to investigate the prognostic implications of POLE expression. Cox regression analyses were implemented to explore the effect of POLE expression on the prognosis of pan-cancer. These findings revealed that elevated POLE expression levels significantly correlated with shorter overall survival (p < 0.001, n = 701) of patients with ccRCC. These data indicate that POLE expression may serve as a prognostic biomarker for cancers. Although POLE mutations were not significantly associated with survival benefits conferred upon patients with ccRCC, a CD4+ T cell-regulated immune microenvironment was significantly activated. Moreover, we found that POLE expression in cancers significantly correlated with an immunosuppressive tumor microenvironment, higher intratumoral heterogeneity, and expression of immune checkpoint genes PDCD1, CTLA4, and CD86, possibly mediated via the JAK/STAT and Notch signaling pathways. In conclusion, the present study is the first to our knowledge to indicate that elevated POLE expression is significantly associated with poor survival and an immune-suppressive tumor microenvironment in ccRCC. These findings suggest that POLE can serve as a biomarker for guiding molecular diagnosis and facilitating the development of novel individual therapeutic strategies for patients with advanced ccRCC.
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Affiliation(s)
- Xiaohui Wu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Haijia Tang
- Department of Integrated Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Haidan Tang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
| | - Shiyin Wei
- Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
| | - Aihetaimujiang Anwaier
- Department of Integrated Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haineng Huang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Shuai Zhao
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Li
- Department of Endocrinology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Wangrui Liu
- Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China.,Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongjing Chen
- Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, China
| | - Chen Ding
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
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17
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Zhao S, Wei C, Tang H, Ding H, Han B, Chen S, Song X, Gu Q, Zhang Y, Liu W, Wang J. Elevated DNA Polymerase Delta 1 Expression Correlates With Tumor Progression and Immunosuppressive Tumor Microenvironment in Hepatocellular Carcinoma. Front Oncol 2021; 11:736363. [PMID: 34868924 PMCID: PMC8632622 DOI: 10.3389/fonc.2021.736363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/26/2021] [Indexed: 12/31/2022] Open
Abstract
Background and Objective Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and the DNA polymerase delta (POLD) family is significantly related to cancer prognosis. This study aimed to explore the significance of the POLD family in HCC via the DNA damage repair (DDR) pathway. Methods Data mining was conducted using bioinformatics methods. RNA sequencing and clinicopathological data were collected from The Cancer Genome Atlas, GTEx database and the Gumz Renal cohort. Statistical analyses were also performed in cancer samples (n>12,000) and the Affiliated Hospital of Youjiang Medical University for Nationalities (AHYMUN, n=107) cohort. Results The POLD family (POLD1-4) was identified as the most important functional component of the DDR pathway. Based on the analysis of independent cohorts, we found significantly elevated POLD expression in HCC compared with normal tissues. Second, we investigated the prognostic implication of elevated POLD1 expression in HCC and pan-cancers, revealing that increased POLD1 levels were correlated to worse prognoses for HCC patients. Additionally, we identified 11 hub proteins interacting closely with POLD proteins in base excision repair, protein-DNA complex and mismatch repair signaling pathways. Moreover, POLD1 mutation functioned as an independent biomarker to predict the benefit of targeted treatment. Importantly, POLD1 expression was associated with immune checkpoint molecules, including CD274, CD80, CD86, CTLA4, PDCD1 and TCGIT, and facilitated an immune-excluded tumor microenvironment. Additionally, we confirmed that elevated POLD1 expression was closely correlated with the aggressive progression and poor prognosis of HCC in the real-world AHYMUN cohort. Conclusion We identified a significant association between elevated POLD1 expression and poor patient survival and immune-excluded tumor microenvironment of HCC. Together, these findings indicate that POLD1 provides a valuable biomarker to guide the molecular diagnosis and development of novel targeted therapeutic strategies for HCC patients.
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Affiliation(s)
- Shuai Zhao
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cuicui Wei
- Department of Outpatient, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Haijia Tang
- Department of Integrated Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Han Ding
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Han
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuxian Chen
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoling Song
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiang Gu
- Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, China
| | - Yichi Zhang
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wangrui Liu
- Department of Outpatient, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.,Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Xu W, Anwaier A, Ma C, Liu W, Tian X, Palihati M, Hu X, Qu Y, Zhang H, Ye D. Multi-omics reveals novel prognostic implication of SRC protein expression in bladder cancer and its correlation with immunotherapy response. Ann Med 2021; 53:596-610. [PMID: 33830879 PMCID: PMC8043611 DOI: 10.1080/07853890.2021.1908588] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/21/2021] [Indexed: 12/14/2022] Open
Abstract
PURPOSE This study aims to identify potential prognostic biomarkers of bladder cancer (BCa) based on large-scale multi-omics data and investigate the role of SRC in improving predictive outcomes for BCa patients and those receiving immune checkpoint therapies (ICTs). METHODS Large-scale multi-comic data were enrolled from the Cancer Proteome Atlas, the Cancer Genome Atlas and gene expression omnibus based on machining-learning methods. Immune infiltration, survival and other statistical analyses were implemented using R software in cancers (n = 12,452). The predictive value of SRC was performed in 81 BCa patients receiving ICT from aa validation cohort (n = 81). RESULTS Landscape of novel candidate prognostic protein signatures of BCa patients was identified. Differential BECLIN, EGFR, PKCALPHA, ANNEXIN1, AXL and SRC expression significantly correlated with the outcomes for BCa patients from multiply cohorts (n = 906). Notably, risk score of the integrated prognosis-related proteins (IPRPs) model exhibited high diagnostic accuracy and consistent predictive ability (AUC = 0.714). Besides, we tested the clinical relevance of baseline SRC protein and mRNA expression in two independent confirmatory cohorts (n = 566) and the prognostic value in pan-cancers. Then, we found that elevated SRC expression contributed to immunosuppressive microenvironment mediated by immune checkpoint molecules of BCa and other cancers. Next, we validated SRC expression as a potential biomarker in predicting response to ICT in 81 BCa patient from FUSCC cohort, and found that expression of SRC in the baseline tumour tissues correlated with improved survival benefits, but predicts worse ICT response. CONCLUSION This study first performed the large-scale multi-omics analysis, distinguished the IPRPs (BECLIN, EGFR, PKCALPHA, SRC, ANNEXIN1 and AXL) and revealed novel prediction model, outperforming the currently traditional prognostic indicators for anticipating BCa progression and better clinical strategies. Additionally, this study provided insight into the importance of biomarker SRC for better prognosis, which may inversely improve predictive outcomes for patients receiving ICT and enable patient selection for future clinical treatment.
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Chunguang Ma
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Wangrui Liu
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Maierdan Palihati
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Xiaoxin Hu
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
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19
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Xu W, Tao J, Zhu W, Liu W, Anwaier A, Tian X, Su J, Shi G, Huang H, Wei G, Li C, Qu Y, Zhang H, Ye D. Comprehensive Multi-Omics Identification of Interferon-γ Response Characteristics Reveals That RBCK1 Regulates the Immunosuppressive Microenvironment of Renal Cell Carcinoma. Front Immunol 2021; 12:734646. [PMID: 34795663 PMCID: PMC8593147 DOI: 10.3389/fimmu.2021.734646] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/11/2021] [Indexed: 12/09/2022] Open
Abstract
Interferon-gamma (IFN-γ) has a complex role in modulating the tumor microenvironment (TME) during renal cell carcinoma (RCC) development. To define the role of IFN-γ response genes in RCC progression, we characterized the differential gene expression, prognostic implications, and DNA variation profiles of selected IFN-γ response signatures, which exhibited a significant hazard ratio for the overall survival (OS) and progression-free survival (PFS) of papillary, chromophobia, and clear cell RCC (ccRCC) patients (n = 944). Prognostic nomograms were constructed to predict the outcomes for ccRCC patients, highlighting the prognostic implications of RANBP2-type and C3HC4-type zinc finger containing 1 (RBCK1). Interestingly, large-scale pan-cancer samples (n = 12,521) and three single-cell RNA datasets revealed that RBCK1 showed markedly differential expression between cancer and normal tissues and significantly correlated with tumor-infiltrating immune cells, tumor purity, and immune checkpoint molecules, such as PD-L1, CTLA-4, LAG-3, and TIGIT in pan-cancer samples. Notably, the TIDE score was significantly higher in the RBCK1high group compared with the RBCK1low group in both ccRCC and RCC cohorts. Besides, immunohistochemistry staining showed significantly elevated RBCK1 expression in tumors (n = 50) compared with kidney samples (n = 40) from a real-world cohort, Fudan University Shanghai Cancer Center (FUSCC, Shanghai). After RBCK1 expression was confirmed in ccRCC, we found a significantly decreased number of infiltrating CD4+ T cells, CD4+ FOXP3+ Treg cells, M1 macrophages, and CD56bight/dim NK cells in the immune-cold RBCK1high group. In addition to the distinct heterogeneous immune microenvironment, the increased expression of RBCK1 predicted a prominently worse prognosis than the RBCK1low group for 232 ccRCC patients in the FUSCC proteomic cohort. Furthermore, after transfected with siRNA in human ccRCC cells, extraordinarily decreased cell proliferation, migration capacities, and prominently elevated apoptosis tumor cell proportion were found in the siRNA groups compared with the negative control group. In conclusion, this study identified IFN-γ response clusters, which might be used to improve the prognostic accuracy of immune contexture in the ccRCC microenvironment. Immune-cold RBCK1high patients have pro-tumorigenic immune infiltration and significantly worse outcomes than RBCK1low patients based on results from multi-omics to real-world data. Our discovery of novel independent prognostic indicators for RCC highlights the association between tumor alterations and immune phenotype.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/enzymology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/therapy
- Cell Line, Tumor
- Databases, Genetic
- Decision Support Techniques
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Genomics
- Humans
- Interferon-gamma/genetics
- Interferon-gamma/metabolism
- Kidney Neoplasms/enzymology
- Kidney Neoplasms/genetics
- Kidney Neoplasms/immunology
- Kidney Neoplasms/therapy
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Nomograms
- Phenotype
- Progression-Free Survival
- Protein Interaction Maps
- Proteome
- Proteomics
- RNA-Seq
- Signal Transduction
- Single-Cell Analysis
- Time Factors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptome
- Tumor Microenvironment
- Tumor-Associated Macrophages/immunology
- Tumor-Associated Macrophages/metabolism
- Ubiquitin-Protein Ligases/genetics
- Ubiquitin-Protein Ligases/metabolism
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Juli Tao
- Department of Hematology and Rheumatology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wenkai Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | | | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Haineng Huang
- Department of Hematology and Rheumatology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Gaomeng Wei
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Chuanyu Li
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
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20
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Traditional Chinese medicine Bu-Shen-Jian-Pi-Fang attenuates glycolysis and immune escape in clear cell renal cell carcinoma: results based on network pharmacology. Biosci Rep 2021; 41:228654. [PMID: 34002799 PMCID: PMC8202066 DOI: 10.1042/bsr20204421] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common malignant type of kidney cancer. The present study aims to explore the underlying mechanism and potential targets of the traditional Chinese medicine Bu-Shen-Jian-Pi-Fang (BSJPF) in the treatment of ccRCC based on network pharmacology. After obtaining the complete composition information for BSJPF from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, we analyzed its chemical composition and molecular targets and then established a pharmacological interaction network. Twenty-four significantly differentially expressed genes and nine pathways mainly related to tumor proliferation were identified and screened. Functional enrichment analysis indicated that the potential targets might be significantly involved in glycolysis and the HIF-1 signaling pathway. To further confirm the effect of BSJPF on ccRCC cell proliferation, a BALB/c xenograft mouse model was constructed. Potential targets involved in regulating glycolysis and the tumor immune microenvironment were evaluated using RT-qPCR. VEGF-A expression levels were markedly decreased, and heparin binding-EGF expression was increased in the BSJPF group. BSJPF also inhibited tumor proliferation by enhancing GLUT1- and LDHA-related glycolysis and the expression of the immune checkpoint molecules PD-L1 and CTLA-4, thereby altering the immune-rejection status of the tumor microenvironment. In summary, the present study demonstrated that the mechanism of BSJPF involves multiple targets and signaling pathways related to tumorigenesis and glycolysis metabolism in ccRCC. Our research provides a novel theoretical basis for the treatment of tumors with traditional Chinese medicine and new strategies for immunotherapy in ccRCC patients.
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21
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Xu W, Liu WR, Xu Y, Tian X, Anwaier A, Su JQ, Zhu WK, Shi GH, Wei GM, Huang YP, Qu YY, Zhang HL, Ye DW. Hexokinase 3 dysfunction promotes tumorigenesis and immune escape by upregulating monocyte/macrophage infiltration into the clear cell renal cell carcinoma microenvironment. Int J Biol Sci 2021; 17:2205-2222. [PMID: 34239350 PMCID: PMC8241725 DOI: 10.7150/ijbs.58295] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Purpose: This study aimed to identify the potential prognostic role of HK3 and provide clues about glycolysis and the microenvironmental characteristics of ccRCC. Methods: Based on the Cancer Genome Atlas (TCGA, n = 533) and Gene expression omnibus (GEO) (n = 127) databases, real-world (n = 377) ccRCC cohorts, and approximately 15,000 cancer samples, the prognostic value and immune implications of HK3 were identified. The functional effects of HK3 in ccRCC were analyzed in silico and in vitro. Results: The large-scale findings suggested a significantly higher HK3 expression in ccRCC tissues and the predictive efficacy of HK3 for tumor progression and a poor prognosis. Next, the subgroup survival and Cox regression analyses showed that HK3 serves as a promising and independent predictive marker for the prognosis and survival of patients with ccRCC from bioinformatic databases and real-world cohorts. Subsequently, we found that HK3 could be used to modulate glycolysis and the malignant behaviors of ccRCC cells. The comprehensive results suggested that HK3 is highly correlated with the abundance of immune cells, and specifically stimulates the infiltration of monocytes/macrophages presenting surface markers, regulates the immune checkpoint molecules PD-1 and CTLA-4 of exhaustive T cells, restrains the immune escape of tumor cells, and prompts the immune-rejection microenvironment of ccRCC. Conclusion: In conclusion, the large-scale data first revealed that HK3 could affect glycolysis, promote malignant biologic processes, and predict the aggressive progression of ccRCC. HK3 may stimulate the abundance of infiltrating monocytes/macrophages presenting surface markers and regulate the key molecular subgroups of immune checkpoint molecules of exhaustive T cells, thus inducing the microenvironmental characteristics of active anti-tumor immune responses.
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Wang-Rui Liu
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, P.R. China
| | - Yue Xu
- Department of Ophthalmology, Dushuhu Public Hospital Affiliated to Soochow University, Suzhou, 215000, P.R. China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Jia-Qi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Wen-Kai Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Gao-Meng Wei
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, P.R. China
| | - Yong-Ping Huang
- Department of Urology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, P.R. China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
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22
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Xiao H, Xu Y. Overexpression of Apolipoprotein C1 (APOC1) in Clear Cell Renal Cell Carcinoma and Its Prognostic Significance. Med Sci Monit 2021; 27:e929347. [PMID: 33591959 PMCID: PMC7896428 DOI: 10.12659/msm.929347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background The aims of this study included 3 aspects: 1) assessing the expression of Apolipoprotein C1 (APOC1) in clear cell renal cell carcinoma (ccRCC) and normal groups; 2) evaluating the prognostic significance of APOC1 expression in the overall survival (OS) of ccRCC patients; and 3) exploring APOC1-related signaling pathways. Material/Methods The APOC1 expression value and clinical data of ccRCC patients were obtained from the cBioPortal database. We then evaluated the association of APOC1 expression with clinical characteristics of ccRCC patients. We also assessed the correlation between APOC1 expression and clinical outcome using Kaplan-Meier method. Our work then verified the independent prognostic factors of ccRCC by Cox regression analysis. Finally, the potential role of genes co-expressed with APOC1 was revealed via functional enrichment analysis. Results Bioinformatic data revealed that APOC1 was expressed at higher levels in ccRCC tissue than in the normal group (all P<0.05). The high expression of APOC1 was associated with unfavorable prognosis of female patients (P<0.01), but not of male patients. APOC1 high expression also shortened the survival time of ccRCC patients age ≥60 years old (P<0.05). Cox regression analysis further indicated that APOC1 expression was an independent prognostic factor for OS of ccRCC patients. Additionally, we found that APOC1 expression was significantly associated with sex, grade, clinical stage, and T stage. Finally, enrichment analysis suggested that APOC1-associated pathways were involved in tumor growth and metastasis. Conclusions The current study indicated that APOC1 was highly expressed in ccRCC and was significantly associated with key clinical features. APOC1 appears to be an independent prognostic factor in patients with ccRCC. Importantly, APOC1 might be a potential therapeutic target for ccRCC via regulating pathways involved in cell growth and metastasis.
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Affiliation(s)
- Huaying Xiao
- Department of Nephrology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Yifang Xu
- Department of Nephrology, Dongyang People's Hospital, Dongyang, Zhejiang, China (mainland)
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23
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Xu W, Hu X, Anwaier A, Wang J, Liu W, Tian X, Zhu W, Ma C, Wan F, Shi G, Qu YY, Zhang H, Ye D. Fatty Acid Synthase Correlates With Prognosis-Related Abdominal Adipose Distribution and Metabolic Disorders of Clear Cell Renal Cell Carcinoma. Front Mol Biosci 2021; 7:610229. [PMID: 33569391 PMCID: PMC7868388 DOI: 10.3389/fmolb.2020.610229] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/04/2020] [Indexed: 12/22/2022] Open
Abstract
Purpose: Lipid metabolism reprogramming is a major pathway in tumor evolution. This study investigated fatty acid synthase (FASN) mRNA expression in anthropometric adipose tissue and elucidated the prognostic value and potential mechanism of clear cell renal cell carcinoma (ccRCC). Materials and Methods: Transcription profiles were obtained from 533 ccRCC samples in The Cancer Genome Atlas (TCGA) cohorts. Real-time quantitative PCR (RT-qPCR) and immunohistochemistry were performed to detect FASN expression in 380 paired ccRCC and normal tissues from the Fudan University Shanghai Cancer Center (FUSCC). Visceral adipose tissue (VAT) and subcutaneous adipose tissue were at the level of the umbilicus as measured by magnetic resonance imaging (MRI). Non-targeted metabolomics and in vitro experiments were used to reveal the biological functions of FASN. Results: Increased FASN expression was significantly relevant to advanced T, N, and American Joint Committee on Cancer (AJCC) stages (p < 0.01) and significantly correlated to poor progression-free survival (PFS) and overall survival (OS) of 913 ccRCC patients in FUSCC and TCGA cohorts. Pearson's correlation coefficient indicated that FASN amplification was positively correlated to VAT% (r = 0.772, p < 0.001), which significantly correlated to poor PFS (HR = 2.066, p = 0.028) and OS (HR = 2.773, p = 0.023) in the FUSCC cohort. Transient inhibition or overexpression of FASN significantly regulated A498 and 786O cell proliferation and migration by regulating epithelial–mesenchymal transition. Inhibition of FASN led to a higher apoptotic rate and decreased lipid droplet formation compared with normal control in ccRCC cells. Non-targeted metabolomics showed that decreased de novo lipogenesis might be required to sustain an elevation of glycolytic activity in 786O cells by regulating galactinol, dl-lactate, N-acetylaspartylglutamate, and sucrose, thereby participating in carcinogenesis and progression of ccRCC. Conclusion: This study demonstrated that FASN expression is positively related to aggressive cell proliferation, migration, apoptosis, and lipid droplet formation and regulates metabolic disorders of the ccRCC microenvironment. Additionally, elevated FASN mRNA expression is significantly correlated to the abdominal obesity distribution, especially VAT%, which is a significant predictor of a poor prognosis for ccRCC patients.
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Xiaoxin Hu
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Jun Wang
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in Southern China, Guangzhou, China
| | - Wangrui Liu
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Wenkai Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Chunguang Ma
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Fangning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
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24
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Song W, Shao Y, He X, Gong P, Yang Y, Huang S, Zeng Y, Wei L, Zhang J. IGFLR1 as a Novel Prognostic Biomarker in Clear Cell Renal Cell Cancer Correlating With Immune Infiltrates. Front Mol Biosci 2020; 7:565173. [PMID: 33324675 PMCID: PMC7726438 DOI: 10.3389/fmolb.2020.565173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
Objective Insulin Growth Factor-Like receptor 1 (IGFLR1) reflects progressive disease and confers a poor prognosis in clear cell renal cell cancer (ccRCC). However, extensive studies highlighting the mechanisms involved in how IGFLR1 triggers the progression of ccRCC remain lacking. Methods In the present study, the expression level of IGFLR1 mRNA and correlation between IGFLR1 expression and prognosis of ccRCC were analyzed based on The Cancer Genome Atlas (TCGA) ccRCC cohort. Further, we analyzed methylation and copy number variation to try to explain the difference in IGFLR1 expression. Subsequently, we investigated the correlation between IGFLR1 and tumor-infiltrating immune cells with the aid of TIMER (Tumor Immune Estimation Resource). The potential candidates' genes associated with IGFLR1 were screened by variation analysis, which were used for further enrichment analysis of signaling pathways and immune gene sets to infer the certain function and corresponding mechanisms in which IGFLR1 was involved in ccRCC. Finally, we establish prognostic risk models using multivariate Cox regression analysis and analyzed the possible involvement of IGFLR1 in chemotherapeutic drug resistance. Results The results showed that upregulated IGFLR1 was detected in ccRCC compared with para-cancer tissues and significantly affected the prognosis of ccRCC (overall survival: Logrank p < 0.0001; disease free survival: Logrank p = 0.022). Univariate and multivariate analyses indicated that IGFLR1 was an independent prognostic factor for ccRCC (HR = 2.064, p = 0.006) and the risk prognostic model based on age, M, level of platelet and calcium and IGFLR1 expression had satisfying predictive ability. The correlation analysis showed that the expression level of IGFLR1 was positively correlated with the abundance of myeloid derived suppressor cell and their marker genes in ccRCC significantly. IGFLR1 may be related to the regulatory activation, intercellular adhesion of lymphocytes and drug resistance in cancer. Conclusion These findings suggested that IGFLR1 was significantly associated with the prognosis in a variety of cancers, particularly ccRCC. IGFLR1 may play an important role in tumor related immune infiltration and showed potential diagnostic, therapeutic and prognostic value in ccRCC.
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Affiliation(s)
- Wenjing Song
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Youcheng Shao
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xin He
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Pengju Gong
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Yan Yang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Sirui Huang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Yifan Zeng
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Lei Wei
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jingwei Zhang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
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25
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Xu WH, Xu Y, Tian X, Anwaier A, Liu WR, Wang J, Zhu WK, Cao DL, Wang HK, Shi GH, Qu YY, Zhang HL, Ye DW. Large-scale transcriptome profiles reveal robust 20-signatures metabolic prediction models and novel role of G6PC in clear cell renal cell carcinoma. J Cell Mol Med 2020; 24:9012-9027. [PMID: 32567187 PMCID: PMC7417710 DOI: 10.1111/jcmm.15536] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/26/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common and highly malignant pathological type of kidney cancer. We sought to establish a metabolic signature to improve post‐operative risk stratification and identify novel targets in the prediction models for ccRCC patients. A total of 58 metabolic differential expressed genes (MDEGs) were identified with significant prognostic value. LASSO regression analysis constructed 20‐mRNA signatures models, metabolic prediction models (MPMs), in ccRCC patients from two cohorts. Risk score of MPMs significantly predicts prognosis for ccRCC patients in TCGA (P < 0.001, HR = 3.131, AUC = 0.768) and CPTAC cohorts (P = 0.046, HR = 2.893, AUC = 0.777). In addition, G6PC, a hub gene in PPI network of MPMs, shows significantly prognostic value in 718 ccRCC patients from multiply cohorts. Next, G6Pase was detected high expressed in normal kidney tissues than ccRCC tissues. It suggested that low G6Pase expression significantly correlated with poor prognosis (P < 0.0001, HR = 0.316) and aggressive progression (P < 0.0001, HR = 0.414) in 322 ccRCC patients from FUSCC cohort. Meanwhile, promoter methylation level of G6PC was significantly higher in ccRCC samples with aggressive progression status. G6PC significantly participates in abnormal immune infiltration of ccRCC microenvironment, showing significantly negative association with check‐point immune signatures, dendritic cells, Th1 cells, etc. In conclusion, this study first provided the opportunity to comprehensively elucidate the prognostic MDEGs landscape, established novel prognostic model MPMs using large‐scale ccRCC transcriptome data and identified G6PC as potential prognostic target in 1,040 ccRCC patients from multiply cohorts. These finding could assist in managing risk assessment and shed valuable insights into treatment strategies of ccRCC.
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Affiliation(s)
- Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Xu
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, China.,Medical College, Soochow University, Suzhou, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wang-Rui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical College for Nationalities, Guangxi, China
| | - Jun Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Kai Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hong-Kai Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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