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Hwang J, Bang S, Choi MH, Hong SH, Kim SW, Lee HE, Yang JH, Park US, Choi YJ. Discovery and Validation of Survival-Specific Genes in Papillary Renal Cell Carcinoma Using a Customized Next-Generation Sequencing Gene Panel. Cancers (Basel) 2024; 16:2006. [PMID: 38893126 PMCID: PMC11171119 DOI: 10.3390/cancers16112006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
PURPOSE Papillary renal cell carcinoma (PRCC), the second most common kidney cancer, is morphologically, genetically, and molecularly heterogeneous with diverse clinical manifestations. Genetic variations of PRCC and their association with survival are not yet well-understood. This study aimed to identify and validate survival-specific genes in PRCC and explore their clinical utility. MATERIALS AND METHODS Using machine learning, 293 patients from the Cancer Genome Atlas-Kidney Renal Papillary Cell Carcinoma (TCGA-KIRP) database were analyzed to derive genes associated with survival. To validate these genes, DNAs were extracted from the tissues of 60 Korean PRCC patients. Next generation sequencing was conducted using a customized PRCC gene panel of 202 genes, including 171 survival-specific genes. Kaplan-Meier and Log-rank tests were used for survival analysis. Fisher's exact test was performed to assess the clinical utility of variant genes. RESULTS A total of 40 survival-specific genes were identified in the TCGA-KIRP database through machine learning and statistical analysis. Of them, 10 (BAP1, BRAF, CFDP1, EGFR, ITM2B, JAK1, NODAL, PCSK2, SPATA13, and SYT5) were validated in the Korean-KIRP database. Among these survival gene signatures, three genes (BAP1, PCSK2, and SPATA13) showed survival specificity in both overall survival (OS) (p = 0.00004, p = 1.38 × 10-7, and p = 0.026, respectively) and disease-free survival (DFS) (p = 0.00002, p = 1.21 × 10-7, and p = 0.036, respectively). Notably, the PCSK2 mutation demonstrated survival specificity uniquely in both the TCGA-KIRP (OS: p = 0.010 and DFS: p = 0.301) and Korean-KIRP (OS: p = 1.38 × 10-7 and DFS: p = 1.21 × 10-7) databases. CONCLUSIONS We discovered and verified genes specific for the survival of PRCC patients in the TCGA-KIRP and Korean-KIRP databases. The survival gene signature, including PCSK2 commonly obtained from the 40 gene signature of TCGA and the 10 gene signature of the Korean database, is expected to provide insight into predicting the survival of PRCC patients and developing new treatment.
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Affiliation(s)
- Jia Hwang
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (J.H.); (H.E.L.)
| | - Seokhwan Bang
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.B.); (S.-H.H.); (S.W.K.)
| | - Moon Hyung Choi
- Department of Radiology, College of Medicine, Eunpyeong St. Mary’s Hospital, The Catholic University of Korea, Seoul 03312, Republic of Korea;
| | - Sung-Hoo Hong
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.B.); (S.-H.H.); (S.W.K.)
| | - Sae Woong Kim
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.B.); (S.-H.H.); (S.W.K.)
| | - Hye Eun Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (J.H.); (H.E.L.)
| | - Ji Hoon Yang
- Department of Computer Science and Engineering, Sogang University, Seoul 04107, Republic of Korea; (J.H.Y.); (U.S.P.)
| | - Un Sang Park
- Department of Computer Science and Engineering, Sogang University, Seoul 04107, Republic of Korea; (J.H.Y.); (U.S.P.)
| | - Yeong Jin Choi
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (J.H.); (H.E.L.)
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Bao-Caamano A, Costa-Fraga N, Cayrefourcq L, Rodriguez-Casanova A, Muinelo-Romay L, López-López R, Alix-Panabières C, Díaz-Lagares A. Epigenomic reprogramming of therapy-resistant circulating tumor cells in colon cancer. Front Cell Dev Biol 2023; 11:1291179. [PMID: 38188020 PMCID: PMC10771310 DOI: 10.3389/fcell.2023.1291179] [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: 09/08/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Therapy resistance is a major challenge in colorectal cancer management. Epigenetic changes, such as DNA methylation, in tumor cells are involved in the development of acquired resistance during treatment. Here, we characterized the DNA methylation landscape of colon circulating tumor cells (CTCs) during cancer progression and therapy resistance development. To this aim, we used nine permanent CTC lines that were derived from peripheral blood samples of a patient with metastatic colon cancer collected before treatment initiation (CTC-MCC-41) and during treatment and cancer progression (CTC-MCC-41.4 and CTC-MCC-41.5 [A-G]). We analyzed the DNA methylome of these nine CTC lines using EPIC arrays and also assessed the association between DNA methylation and gene expression profiles. We confirmed DNA methylation and gene expression results by pyrosequencing and RT-qPCR, respectively. The global DNA methylation profiles were different in the pre-treatment CTC line and in CTC lines derived during therapy resistance development. These resistant CTC lines were characterized by a more hypomethylated profile compared with the pre-treatment CTC line. Most of the observed DNA methylation differences were localized at CpG-poor regions and some in CpG islands, shore regions and promoters. We identified a distinctive DNA methylation signature that clearly differentiated the pre-treatment CTC line from the others. Of note, the genes involved in this signature were associated with cancer-relevant pathways, including PI3K/AKT, MAPK, Wnt signaling and metabolism. We identified several epigenetically deregulated genes associated with therapy resistance in CTCs, such as AP2M1. Our results bring new knowledge on the epigenomic landscape of therapy-resistant CTCs, providing novel mechanisms of resistance as well as potential biomarkers and therapeutic targets for advanced CRC management.
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Affiliation(s)
- Aida Bao-Caamano
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Nicolás Costa-Fraga
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Laure Cayrefourcq
- Laboratory of Rare Human Circulating Cells–The Liquid Biopsy Lab, University Medical Center of Montpellier, Montpellier, France
- Centre for Ecological and Evolutionary Cancer Research, Maladies infectieuses et vecteurs: génétique, èvolution et contrôle, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Aitor Rodriguez-Casanova
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Laura Muinelo-Romay
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, Madrid, Spain
| | - Rafael López-López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells–The Liquid Biopsy Lab, University Medical Center of Montpellier, Montpellier, France
- Centre for Ecological and Evolutionary Cancer Research, Maladies infectieuses et vecteurs: génétique, èvolution et contrôle, University of Montpellier, CNRS, IRD, Montpellier, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Angel Díaz-Lagares
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, Madrid, Spain
- Department of Clinical Analysis, University Hospital Complex of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
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Chen Y, Zhou X, Xie Y, Wu J, Li T, Yu T, Pang Y, Du W. Establishment of a Seven-Gene Signature Associated with CD8 + T Cells through the Utilization of Both Single-Cell and Bulk RNA-Sequencing Techniques in Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2023; 24:13729. [PMID: 37762031 PMCID: PMC10530336 DOI: 10.3390/ijms241813729] [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: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Tumor immune microenvironment constituents, such as CD8+ T cells, have emerged as crucial focal points for cancer immunotherapy. Given the absence of reliable biomarkers for clear cell renal cell carcinoma (ccRCC), we aimed to ascertain a molecular signature that could potentially be linked to CD8+ T cells. The differentially expressed genes (DEGs) linked to CD8+ T cells were identified through an analysis of single-cell RNA sequencing (scRNA-seq) data obtained from the Gene Expression Omnibus (GEO) database. Subsequently, immune-associated genes were obtained from the InnateDB and ImmPort datasets and were cross-referenced with CD8+ T-cell-associated DEGs to generate a series of DEGs linked to immune response and CD8+ T cells. Patients with ccRCC from the Cancer Genome Atlas (TCGA) were randomly allocated into testing and training groups. A gene signature was established by conducting LASSO-Cox analysis and subsequently confirmed using both the testing and complete groups. The efficacy of this signature in evaluating immunotherapy response was assessed on the IMvigor210 cohort. Finally, we employed various techniques, including CIBERSORT, ESTIMATE, ssGSEA, and qRT-PCR, to examine the immunological characteristics, drug responses, and expression of the signature genes in ccRCC. Our findings revealed 206 DEGs linked to immune response and CD8+ T cells, among which 65 genes were correlated with overall survival (OS) in ccRCC. A risk assessment was created utilizing a set of seven genes: RARRES2, SOCS3, TNFSF14, XCL1, GRN, CLDN4, and RBP7. The group with a lower risk showed increased expression of CD274 (PD-L1), suggesting a more favorable response to anti-PD-L1 treatment. The seven-gene signature demonstrated accurate prognostic prediction for ccRCC and holds potential as a clinical reference for treatment decisions.
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Affiliation(s)
- Yubin Chen
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China; (Y.C.); (X.Z.); (Y.X.); (J.W.); (T.L.); (T.Y.); (Y.P.)
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China
| | - Xinyu Zhou
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China; (Y.C.); (X.Z.); (Y.X.); (J.W.); (T.L.); (T.Y.); (Y.P.)
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China
| | - Yanwei Xie
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China; (Y.C.); (X.Z.); (Y.X.); (J.W.); (T.L.); (T.Y.); (Y.P.)
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China
| | - Jianan Wu
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China; (Y.C.); (X.Z.); (Y.X.); (J.W.); (T.L.); (T.Y.); (Y.P.)
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China
| | - Tingting Li
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China; (Y.C.); (X.Z.); (Y.X.); (J.W.); (T.L.); (T.Y.); (Y.P.)
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China
| | - Tian Yu
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China; (Y.C.); (X.Z.); (Y.X.); (J.W.); (T.L.); (T.Y.); (Y.P.)
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China
| | - Yipeng Pang
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China; (Y.C.); (X.Z.); (Y.X.); (J.W.); (T.L.); (T.Y.); (Y.P.)
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China
| | - Wenlong Du
- Department of Bioinformatics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China; (Y.C.); (X.Z.); (Y.X.); (J.W.); (T.L.); (T.Y.); (Y.P.)
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou 221004, China
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Zheng Z, Li H, Yang R, Guo H. Role of the membrane-spanning 4A gene family in lung adenocarcinoma. Front Genet 2023; 14:1162787. [PMID: 37533433 PMCID: PMC10390740 DOI: 10.3389/fgene.2023.1162787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023] Open
Abstract
Lung adenocarcinoma, which is the second most prevalent cancer in the world, has a poor prognosis and a low 5-year survival rate. The MS4A protein family is crucial to disease development and progression, particularly for cancers, allergies, metabolic disorders, autoimmune diseases, infections, and neurodegenerative disorders. However, its involvement in lung adenocarcinoma remains unclear. In this study, we found that 11 MS4A family genes were upregulated or downregulated in lung adenocarcinoma. Furthermore, we described the genetic variation landscape of the MS4A family in lung adenocarcinoma. Notably, through functional enrichment analysis, we discovered that the MS4A family is involved in the immune response regulatory signaling pathway and the immune response regulatory cell surface receptor signaling pathway. According to the Kaplan-Meier curve, patients with lung adenocarcinoma having poor expression of MS4A2, MS4A7, MS4A14, and MS4A15 had a low overall survival rate. These four prognostic genes are substantially associated with immune-infiltrating cells, and a prognosis model incorporating them may more accurately predict the overall survival rate of patients with lung adenocarcinoma than current models. The findings of this study may offer creative suggestions and recommendations for the identification and management of lung adenocarcinoma.
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Thokerunga E, Bongolo CC, Rugera SP, Akankwatsa G, Tu JC. FKBP11 upregulation promotes proliferation and migration in hepatocellular carcinoma. Cancer Biomark 2023:CBM220440. [PMID: 37248890 DOI: 10.3233/cbm-220440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the leading causes of cancer related deaths world over. Early diagnosis and effective treatment monitoring significantly improves patients' outcomes. FKBP11 gene is highly expressed in HCC and could play a role in its development, early diagnosis and treatment. OBJECTIVE This study aimed to evaluate the expression of FKBP11 in HCC, its correlation with patients' clinical characteristics and potential role in HCC development. METHODS Expression was determined by bioinformatics analysis, quantitative real-time PCR, western blot, and immunohistochemistry. CCK-8, Transwell and wound healing assays were used to investigate involvement in HCC development. RESULTS FKBP11 was significantly upregulated in HCC cells, tissues and blood (all p< 0.001). Its receiver operator characteristic (ROC) curve had an AUC of 0.864 (95% CI: 0.823-0.904), at a sensitivity of 0.86 and specificity of 0.78 indicating a good diagnostic potential in HCC. Its expression was markedly reduced after surgery (p< 0.0001), indicating a potential application in HCC treatment follow-up. Knockdown of FKBP11 in HCC cells attenuated proliferation and migration, suggesting a possible role in HCC pathogenesis. CONCLUSION This study thus found that FKBP11 is upregulated in HCC, and the upregulation promotes HCC development. FKBP11 levels are significantly reduced post-surgery and could be a potential diagnostic and prognostic marker for HCC.
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Affiliation(s)
- Erick Thokerunga
- Program and Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Christian Cedric Bongolo
- Program and Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Simon Peter Rugera
- Department of Medical Laboratory Science, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Gilbert Akankwatsa
- Department of Medical Laboratory Science, School of Allied Health Sciences, Kampala International University, Bushenyi, Uganda
| | - Jian-Cheng Tu
- Program and Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
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SLC9A1 Binding mTOR Signaling Pathway-Derived Risk Score Predicting Survival and Immune in Clear Cell Renal Cell Carcinoma. JOURNAL OF ONCOLOGY 2023. [DOI: 10.1155/2023/3937352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Objective. Clear cell renal cell carcinoma (ccRCC) is one of the common renal cell carcinomas (RCC) with a high risk of recurrence. Considering that SLC9A1 is involved in various cellular physiological processes and probably mediates the course of mTOR signaling in tumors, this study constructed a risk model for SLC9A1 combined with mTOR signaling in ccRCC, aiming at better predicting the prognosis of patients. Methods. ccRCC expression matrices were downloaded from TCGA and ICGC databases to compare the expression of SLC9A1 in TCGA, and qRT-PCR was adopted to validate the SLC9A1 expression in different RCC cells and normal kidney cells. The CIBERSORT and ESTIMATE algorithms were used to assess samples for immunity. mTOR signaling-associated genes were downloaded from the KEGG website, and then the genes were adopted to screen genes associated with SLC9A1 expression and mTOR signaling pathway colleagues, based on which univariate COX regression and lasso regression Cox analyses were conducted to construct a ccRCC prognostic risk model. ROC curves and nomograms were used to assess the validity of the models. Results. ccRCC tumor samples showed lower SLC9A1 expression than normal samples, as also evidenced by qRT-PCR. The SLC9A1 expression was highly correlated with tumor immunity. Totally, 564 key genes associated with both SLC9A1 expression and mTOR signaling were screened out, and the risk model consisting of 11 gene signatures was constructed in ccRCC based on the 564 genes. Since patients at a high risk had poorer survival outcomes, the high-risk group presented poorer immunotherapy outcomes. Moreover, a higher clinical grade of patients suggested a higher risk score. The risk score can serve as one independent prognostic factor for the prognosis prediction of ccRCC patients. Conclusion. An extremely promising prognostic indicator for ccRCC based on SLCA9A1 and mTOR signaling has been constructed to provide reference for clinical treatment.
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Zhang C, Li Y, Qian J, Zhu Z, Huang C, He Z, Zhou L, Gong Y. Identification of a claudin-low subtype in clear cell renal cell carcinoma with implications for the evaluation of clinical outcomes and treatment efficacy. Front Immunol 2022; 13:1020729. [PMID: 36479115 PMCID: PMC9719924 DOI: 10.3389/fimmu.2022.1020729] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/01/2022] [Indexed: 11/22/2022] Open
Abstract
Background In bladder and breast cancer, the claudin-low subtype is widely identified, revealing a distinct tumor microenvironment (TME) and immunological feature. Although we have previously identified individual claudin members as prognostic biomarkers in clear cell renal cell carcinoma (ccRCC), the existence of an intrinsic claudin-low subtype and its interplay with TME and clinical outcomes remains unclear. Methods Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA)- kidney clear cell carcinoma (KIRC) cohort and E-MTAB-1980 were derived as the training and validation cohorts, respectively. In addition, GSE40435, GSE53757, International Cancer Genome Consortium (ICGC) datasets, and RNA-sequencing data from local ccRCC patients were utilized as validation cohorts for claudin clustering based on silhouette scores. Using weighted correlation network analysis (WGCNA) and multiple machine learning algorithms, including least absolute shrinkage and selection operator (LASSO), CoxBoost, and random forest, we constructed a claudin-TME related (CTR) risk signature. Furthermore, the CTR associated genomic characteristics, immunity, and treatment sensitivity were evaluated. Results A claudin-low phenotype was identified and associated with an inferior survival and distinct TME and cancer immunity characteristics. Based on its interaction with TME, a risk signature was developed with robust prognostic prediction accuracy. Moreover, we found its association with a claudin-low, stem-like phenotype and advanced clinicopathological features. Intriguingly, it was also effective in kidney chromophobe and renal papillary cell carcinoma. The high CTR group exhibited genomic characteristics similar to those of claudin-low phenotype, including increased chromosomal instability (such as deletions at 9p) and risk genomic alterations (especially BAP1 and SETD2). In addition, a higher abundance of CD8 T cells and overexpression of immune checkpoints, such as LAG3, CTLA4 and PDCD1, were identified in the high CTR group. Notably, ccRCC patients with high CTR were potentially more sensitive to immune checkpoint inhibitors; their counterparts could have more clinical benefits when treated with antiangiogenic drugs, mTOR, or HIF inhibitors. Conclusion We comprehensively evaluated the expression features of claudin genes and identified a claudin-low phenotype in ccRCC. In addition, its related signature could robustly predict the prognosis and provide guide for personalizing management strategies.
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Affiliation(s)
- Cuijian Zhang
- Department of Urology, Peking University First Hospital, Beijing, China,Institute of Urology, Peking University, Beijing, China,National Urological Cancer Center, Peking University First Hospital, Beijing, China
| | - Yifan Li
- Department of Urology, Peking University First Hospital, Beijing, China,Institute of Urology, Peking University, Beijing, China,National Urological Cancer Center, Peking University First Hospital, Beijing, China
| | - Jinqin Qian
- Department of Urology, Peking University First Hospital, Beijing, China,Institute of Urology, Peking University, Beijing, China,National Urological Cancer Center, Peking University First Hospital, Beijing, China
| | - Zhenpeng Zhu
- Department of Urology, Peking University First Hospital, Beijing, China,Institute of Urology, Peking University, Beijing, China,National Urological Cancer Center, Peking University First Hospital, Beijing, China
| | - Cong Huang
- Department of Urology, Peking University First Hospital, Beijing, China,Institute of Urology, Peking University, Beijing, China,National Urological Cancer Center, Peking University First Hospital, Beijing, China
| | - Zhisong He
- Department of Urology, Peking University First Hospital, Beijing, China,Institute of Urology, Peking University, Beijing, China,National Urological Cancer Center, Peking University First Hospital, Beijing, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China,Institute of Urology, Peking University, Beijing, China,National Urological Cancer Center, Peking University First Hospital, Beijing, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, China,Institute of Urology, Peking University, Beijing, China,National Urological Cancer Center, Peking University First Hospital, Beijing, China,*Correspondence: Yanqing Gong,
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