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Buczyńska A, Kościuszko M, Sidorkiewicz I, Wiatr AA, Adamska A, Siewko K, Dzięcioł J, Szelachowska M, Krętowski AJ, Popławska-Kita A. Enhancing Angioinvasion Assessment in Papillary Thyroid Cancer Via a Biomarker Panel Involving TAC, 8-OHdG, and Sortilin. J Clin Endocrinol Metab 2024; 109:1866-1872. [PMID: 38181425 PMCID: PMC11180501 DOI: 10.1210/clinem/dgae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/06/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024]
Abstract
CONTEXT Papillary thyroid cancer (PTC) aggressiveness and metastatic potential are closely associated with angioinvasion. Identifying angioinvasion accurately is imperative for treatment planning and prognosis. OBJECTIVE This study explores serum biomarkers, including 8-hydroxydeoxyguanosine (8-OHdG) and oxidative status markers (total oxidative capacity, total antioxidant capacity [TAC], and sortilin), as potential indicators of angioinvasion in PTC. DESIGN A cross-sectional study involving 50 angioinvasive patients with PTC (study group) and 30 patients with PTC with low-risk features (reference group). Serum levels of biomarkers were analyzed to determine their association with angioinvasion. SETTING Patients were recruited from Department of Endocrinology, Diabetology, and Internal Diseases, Medical University of Bialystok, Poland, ensuring representation from a diverse clinical context. PATIENTS OR OTHER PARTICIPANTS Participants included patients with PTC, with 50 in the study group and 30 in the reference group. Selection criteria, matching characteristics, and participant completion rates were duly recorded. INTERVENTION(S) Serum biomarkers were measured to evaluate their association with PTC angioinvasion. MAIN OUTCOME MEASURE(S) Primary outcome measures included serum levels of 8-OHdG, total oxidative capacity, TAC, and sortilin. RESULTS Serum levels of 8-OHdG and sortilin were significantly elevated in angioinvasive PTC, whereas TAC showed a notable decrease (all P < .01). A regression panel combining TAC, 8-OHdG, and sortilin demonstrated a high area under the curve value (0.963) for angioinvasion discernment. CONCLUSION Measuring TAC, 8-OHdG, and sortilin levels may serve as potential biomarkers for identifying angioinvasion in PTC. The combined assessment of these biomarkers enhances angioinvasion discernment, aiding risk stratification and personalized treatment decisions. Further validation studies are required before integrating these biomarkers into routine clinical practice. The study adheres to the provided structure, providing concise and supported conclusions based on the results.
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Affiliation(s)
- Angelika Buczyńska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Maria Kościuszko
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Iwona Sidorkiewicz
- Clinical Research Support Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | | | - Agnieszka Adamska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Katarzyna Siewko
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Janusz Dzięcioł
- Department of Human Anatomy, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Małgorzata Szelachowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Adam Jacek Krętowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Anna Popławska-Kita
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
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Evergren E, Mills IG, Kennedy G. Adaptations of membrane trafficking in cancer and tumorigenesis. J Cell Sci 2024; 137:jcs260943. [PMID: 38770683 PMCID: PMC11166456 DOI: 10.1242/jcs.260943] [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] [Indexed: 05/22/2024] Open
Abstract
Membrane trafficking, a fundamental cellular process encompassing the transport of molecules to specific organelles, endocytosis at the plasma membrane and protein secretion, is crucial for cellular homeostasis and signalling. Cancer cells adapt membrane trafficking to enhance their survival and metabolism, and understanding these adaptations is vital for improving patient responses to therapy and identifying therapeutic targets. In this Review, we provide a concise overview of major membrane trafficking pathways and detail adaptations in these pathways, including COPII-dependent endoplasmic reticulum (ER)-to-Golgi vesicle trafficking, COPI-dependent retrograde Golgi-to-ER trafficking and endocytosis, that have been found in cancer. We explore how these adaptations confer growth advantages or resistance to cell death and conclude by discussing the potential for utilising this knowledge in developing new treatment strategies and overcoming drug resistance for cancer patients.
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Affiliation(s)
- Emma Evergren
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Ian G. Mills
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Grace Kennedy
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
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Chen J, Gao G, He Y, Zhang Y, Wu H, Dai P, Zheng Q, Huang H, Weng J, Zheng Y, Huang Y. Construction and validation of a novel lysosomal signature for hepatocellular carcinoma prognosis, diagnosis, and therapeutic decision-making. Sci Rep 2023; 13:22624. [PMID: 38114725 PMCID: PMC10730614 DOI: 10.1038/s41598-023-49985-3] [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: 09/11/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Lysosomes is a well-recognized oncogenic driver and chemoresistance across variable cancer types, and has been associated with tumor invasiveness, metastasis, and poor prognosis. However, the significance of lysosomes in hepatocellular carcinoma (HCC) is not well understood. Lysosomes-related genes (LRGs) were downloaded from Genome Enrichment Analysis (GSEA) databases. Lysosome-related risk score (LRRS), including eight LRGs, was constructed via expression difference analysis (DEGs), univariate and LASSO-penalized Cox regression algorithm based on the TCGA cohort, while the ICGC cohort was obtained for signature validation. Based on GSE149614 Single-cell RNA sequencing data, model gene expression and liver tumor niche were further analyzed. Moreover, the functional enrichments, tumor microenvironment (TME), and genomic variation landscape between LRRSlow/LRRShigh subgroup were systematically investigated. A total of 15 Lysosomes-related differentially expressed genes (DELRGs) in HCC were detected, and then 10 prognosis DELRGs were screened out. Finally, the 8 optimal DELRGs (CLN3, GBA, CTSA, BSG, APLN, SORT1, ANXA2, and LAPTM4B) were selected to construct the LRRS prognosis signature of HCC. LRRS was considered as an independent prognostic factor and was associated with advanced clinicopathological features. LRRS also proved to be a potential marker for HCC diagnosis, especially for early-stage HCC. Then, a nomogram integrating the LRRS and clinical parameters was set up displaying great prognostic predictive performance. Moreover, patients with high LRRS showed higher tumor stemness, higher heterogeneity, and higher genomic alteration status than those in the low LRRS group and enriched in metabolism-related pathways, suggesting its underlying role in the progression and development of liver cancer. Meanwhile, the LRRS can affect the proportion of immunosuppressive cell infiltration, making it a vital immunosuppressive factor in the tumor microenvironment. Additionally, HCC patients with low LRRS were more sensitive to immunotherapy, while patients in the high LRRS group responded better to chemotherapy. Upon single-cell RNA sequencing, CLN3, GBA, and LAPTM4B were found to be specially expressed in hepatocytes, where they promoted cell progression. Finally, RT-qPCR and external datasets confirmed the mRNA expression levels of model genes. This study provided a direct links between LRRS signature and clinical characteristics, tumor microenvironment, and clinical drug-response, highlighting the critical role of lysosome in the development and treatment resistance of liver cancer, providing valuable insights into the prognosis prediction and treatment response of HCC, thereby providing valuable insights into prognostic prediction, early diagnosis, and therapeutic response of HCC.
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Affiliation(s)
- Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
- Central Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Gan Gao
- Department of Clinical Laboratory, Liuzhou Hospital, Guangzhou Women and Children's Medical Center, Liuzhou, 545616, Guangxi, China
- Guangxi Clinical Research Center for Obstetrics and Gynecology, Liuzhou, 545616, Guangxi, China
| | - Yufang He
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
| | - Yi Zhang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Haixia Wu
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
| | - Peng Dai
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Qingzhu Zheng
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Hengbin Huang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Jiamiao Weng
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Yue Zheng
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Yi Huang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China.
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
- Central Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
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Chan KKS, Au KY, Suen LH, Leung B, Wong CY, Leow WQ, Lim TKH, Ng IOL, Chung CYS, Lo RCL. Sortilin-Driven Cancer Secretome Enhances Tumorigenic Properties of Hepatocellular Carcinoma via de Novo Lipogenesis. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:2156-2171. [PMID: 37673328 DOI: 10.1016/j.ajpath.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/18/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
A growing body of evidence suggests de novo lipogenesis as a key metabolic pathway adopted by cancers to fuel tumorigenic processes. While increased de novo lipogenesis has also been reported in hepatocellular carcinoma (HCC), understanding on molecular mechanisms driving de novo lipogenesis remains limited. In the present study, the functional role of sortilin, a member of the vacuolar protein sorting 10 protein receptor family, in HCC was investigated. Sortilin was overexpressed in HCC and was associated with poorer survival outcome. In functional studies, sortilin-overexpressing cells conferred tumorigenic phenotypes, namely, self-renewal and metastatic potential, of HCC cells via the cancer secretome. Proteomic profiling highlighted fatty acid metabolism as a potential molecular pathway associated with sortilin-driven cancer secretome. This finding was validated by the increased lipid content and expression of fatty acid synthase (FASN) in HCC cells treated with conditioned medium collected from sortilin-overexpressing cells. The enhanced tumorigenic properties endowed by sortilin-driven cancer secretome were partly abrogated by co-administration of FASN inhibitor C75. Further mechanistic dissection suggested protein stabilization by post-translational modification with O-GlcNAcylation as a major mechanism leading to augmented FASN expression. In conclusion, the present study uncovered the role of sortilin in hepatocarcinogenesis via modulation of the cancer secretome and deregulated lipid metabolism.
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Affiliation(s)
- Kristy Kwan-Shuen Chan
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwan-Yung Au
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Long-Hin Suen
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Bernice Leung
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Cheuk-Yan Wong
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wei-Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital & Duke-NUS Medical School, Singapore
| | - Tony Kiat-Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital & Duke-NUS Medical School, Singapore
| | - Irene Oi-Lin Ng
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, China
| | - Clive Yik-Sham Chung
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Regina Cheuk-Lam Lo
- Department of Pathology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, China.
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Sun Z, Chen X, Huang X, Wu Y, Shao L, Zhou S, Zheng Z, Lin Y, Chen S. Cuproptosis and Immune-Related Gene Signature Predicts Immunotherapy Response and Prognosis in Lung Adenocarcinoma. Life (Basel) 2023; 13:1583. [PMID: 37511958 PMCID: PMC10381686 DOI: 10.3390/life13071583] [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: 05/06/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Cuproptosis and associated immune-related genes (IRG) have been implicated in tumorigenesis and tumor progression. However, their effects on lung adenocarcinoma (LUAD) have not been elucidated. Therefore, we investigated the impact of cuproptosis-associated IRGs on the immunotherapy response and prognosis of LUAD using a bioinformatical approach and in vitro experiments analyzing clinical samples. Using the cuproptosis-associated IRG signature, we classified LUAD into two subtypes, cluster 1 and cluster 2, and identified three key cuproptosis-associated IRGs, NRAS, TRAV38-2DV8, and SORT1. These three genes were employed to establish a risk model and nomogram, and to classify the LUAD cohort into low- and high-risk subgroups. Biofunctional annotation revealed that cluster 2, remarkably downregulating epigenetic, stemness, and proliferation pathways activity, had a higher overall survival (OS) and immunoinfiltration abundance compared to cluster 1. Real-time quantitative PCR (RT-qPCR) validated the differential expression of these three genes in both subgroups. scRNA-seq demonstrated elevated expression of NRAS and SORT1 in macrophages. Immunity and oncogenic and stromal activation pathways were dramatically enriched in the low-risk subgroup, and patients in this subgroup responded better to immunotherapy. Our data suggest that the cuproptosis-associated IRG signature can be used to effectively predict the immunotherapy response and prognosis in LUAD. Our work provides enlightenment for immunotherapy response assessment, prognosis prediction, and the development of potential prognostic biomarkers for LUAD patients.
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Affiliation(s)
- Zihao Sun
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Xiujing Chen
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Xiaoning Huang
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Yanfen Wu
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Lijuan Shao
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
| | - Suna Zhou
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Zhu Zheng
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Yiguang Lin
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
- Research & Development Division, Guangzhou Anjie Biomedical Technology Co., Ltd., Guangzhou 510535, China
| | - Size Chen
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
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Marsland M, Dowdell A, Faulkner S, Gedye C, Lynam J, Griffin CP, Marsland J, Jiang CC, Hondermarck H. The Membrane Protein Sortilin Is a Potential Biomarker and Target for Glioblastoma. Cancers (Basel) 2023; 15:cancers15092514. [PMID: 37173980 PMCID: PMC10177035 DOI: 10.3390/cancers15092514] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Glioblastoma (GBM) is a devastating brain cancer with no effective treatment, and there is an urgent need for developing innovative biomarkers as well as therapeutic targets for better management of the disease. The membrane protein sortilin has recently been shown to participate in tumor cell invasiveness in several cancers, but its involvement and clinical relevance in GBM is unclear. In the present study, we explored the expression of sortilin and its potential as a clinical biomarker and therapeutic target for GBM. Sortilin expression was investigated by immunohistochemistry and digital quantification in a series of 71 clinical cases of invasive GBM vs. 20 non-invasive gliomas. Sortilin was overexpressed in GBM and, importantly, higher expression levels were associated with worse patient survival, pointing to sortilin tissue expression as a potential prognostic biomarker for GBM. Sortilin was also detectable in the plasma of GBM patients by enzyme-linked immunosorbent assay (ELISA), but no differences were observed between sortilin levels in the blood of GBM vs. glioma patients. In vitro, sortilin was detected in 11 brain-cancer-patient-derived cell lines at the anticipated molecular weight of 100 kDa. Interestingly, targeting sortilin with the orally bioavailable small molecule inhibitor AF38469 resulted in decreased GBM invasiveness, but cancer cell proliferation was not affected, showing that sortilin is targetable in GBM. Together, these data suggest the clinical relevance for sortilin in GBM and support further investigation of GBM as a clinical biomarker and therapeutic target.
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Affiliation(s)
- Mark Marsland
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
| | - Amiee Dowdell
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
| | - Sam Faulkner
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
| | - Craig Gedye
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Department of Medical Oncology, Calvary Mater, Newcastle, NSW 2298, Australia
| | - James Lynam
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Department of Medical Oncology, Calvary Mater, Newcastle, NSW 2298, Australia
| | - Cassandra P Griffin
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
- Hunter Cancer Biobank, NSW Regional Biospecimen and Research Services, University of Newcastle, Callaghan, NSW 2305, Australia
| | - Joanne Marsland
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
| | - Chen Chen Jiang
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW 2305, Australia
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Lin XH, Li DP, Liu ZY, Zhang S, Tang WQ, Chen RX, Weng SQ, Tseng YJ, Xue RY, Dong L. Six immune-related promising biomarkers may promote hepatocellular carcinoma prognosis: a bioinformatics analysis and experimental validation. Cancer Cell Int 2023; 23:52. [PMID: 36959615 PMCID: PMC10035283 DOI: 10.1186/s12935-023-02888-9] [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: 12/07/2021] [Accepted: 02/23/2023] [Indexed: 03/25/2023] Open
Abstract
Background Abnormal miRNA and mRNA expression and dysregulated immune microenvironment have been found to frequently induce the progression of hepatocellular carcinoma (HCC) in recent reports. In particular, the immune-related competing endogenous RNAs (ceRNA) mechanism plays a crucial role in HCC progression. However, the underlying mechanisms remain unclear. Methods Differentially expressed immune-related genes were obtained from the Immport, GEO, and TCGA databases. The mRNA and protein expression levels in HCC tissues and adjacent normal tissues were confirmed, and we further investigated the methylation levels of these biomarkers to explore their function. Then, the TIMER and TISCH databases were used to assess the relationship between immune infiltration and hub genes. Survival analysis and univariate and multivariate Cox models were used to evaluate the association between hub genes and HCC diagnosis. Hub gene expression was experimentally validated in six HCC cell lines and 15 HCC samples using qRT-PCR and immunohistochemistry. The hub genes were uploaded to DSigDB for drug prediction enrichment analysis. Results We identified that patients with abnormal miRNAs (hsa-miR-125b-5p and hsa-miR-21-5p) and their targeted genes (NTF3, PSMD14, CD320, and SORT1) had a worse prognosis. Methylation analysis of miRNA-targeted genes suggested that alteration of methylation levels is also a factor in the induction of tumorigenesis. We also found that the development of HCC progression caused by miRNA-mRNA interactions may be closely correlated with the infiltration of immunocytes. Moreover, the GSEA, GO, and KEGG analysis suggested that several common immune-related biological processes and pathways were related to miRNA-targeted genes. The results of qRT-PCR, immunohistochemistry, and western blotting were consistent with our bioinformatics results, suggesting that abnormal miRNAs and their targeted genes may affect HCC progression. Conclusions Briefly, our study systematically describes the mechanisms of miRNA-mRNA interactions in HCC and predicts promising biomarkers that are associated with immune filtration for HCC progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-023-02888-9.
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Affiliation(s)
- Xia-Hui Lin
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Dong-ping Li
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Zhi-Yong Liu
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Si Zhang
- grid.8547.e0000 0001 0125 2443Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Wen-qing Tang
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Rong-xin Chen
- grid.8547.e0000 0001 0125 2443Key Laboratory of Carcinogenesis and Cancer Invasion, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
| | - Shu-qiang Weng
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Yu-jen Tseng
- grid.8547.e0000 0001 0125 2443Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040 China
| | - Ru-yi Xue
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Ling Dong
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
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8
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Chi H, Zhao S, Yang J, Gao X, Peng G, Zhang J, Xie X, Song G, Xu K, Xia Z, Chen S, Zhao J. T-cell exhaustion signatures characterize the immune landscape and predict HCC prognosis via integrating single-cell RNA-seq and bulk RNA-sequencing. Front Immunol 2023; 14:1137025. [PMID: 37006257 PMCID: PMC10050519 DOI: 10.3389/fimmu.2023.1137025] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/22/2023] [Indexed: 03/17/2023] Open
Abstract
BackgroundHepatocellular carcinoma (HCC), the third most prevalent cause of cancer-related death, is a frequent primary liver cancer with a high rate of morbidity and mortality. T-cell depletion (TEX) is a progressive decline in T-cell function due to continuous stimulation of the TCR in the presence of sustained antigen exposure. Numerous studies have shown that TEX plays an essential role in the antitumor immune process and is significantly associated with patient prognosis. Hence, it is important to gain insight into the potential role of T cell depletion in the tumor microenvironment. The purpose of this study was to develop a trustworthy TEX-based signature using single-cell RNA-seq (scRNA-seq) and high-throughput RNA sequencing, opening up new avenues for evaluating the prognosis and immunotherapeutic response of HCC patients.MethodsThe International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) databases were used to download RNA-seq information for HCC patients. The 10x scRNA-seq. data of HCC were downloaded from GSE166635, and UMAP was used for clustering descending, and subgroup identification. TEX-related genes were identified by gene set variance analysis (GSVA) and weighted gene correlation network analysis (WGCNA). Afterward, we established a prognostic TEX signature using LASSO-Cox analysis. External validation was performed in the ICGC cohort. Immunotherapy response was assessed by the IMvigor210, GSE78220, GSE79671, and GSE91061cohorts. In addition, differences in mutational landscape and chemotherapy sensitivity between different risk groups were investigated. Finally, the differential expression of TEX genes was verified by qRT-PCR.Result11 TEX genes were thought to be highly predictive of the prognosis of HCC and substantially related to HCC prognosis. Patients in the low-risk group had a greater overall survival rate than those in the high-risk group, according to multivariate analysis, which also revealed that the model was an independent predictor of HCC. The predictive efficacy of columnar maps created from clinical features and risk scores was strong.ConclusionTEX signature and column line plots showed good predictive performance, providing a new perspective for assessing pre-immune efficacy, which will be useful for future precision immuno-oncology studies.
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Affiliation(s)
- Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Songyun Zhao
- Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Jinyan Yang
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xinrui Gao
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Gaoge Peng
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Jinhao Zhang
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xixi Xie
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Guobin Song
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Ke Xu
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
- *Correspondence: Shi Chen, ; Jinqiu Zhao, ; Zhijia Xia,
| | - Shi Chen
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Shi Chen, ; Jinqiu Zhao, ; Zhijia Xia,
| | - Jinqiu Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Shi Chen, ; Jinqiu Zhao, ; Zhijia Xia,
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9
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Zhong G, Lin Y, Huang Z. Identification of a novel circRNA-miRNA-mRNA regulatory axis in hepatocellular carcinoma based on bioinformatics analysis. Sci Rep 2023; 13:3728. [PMID: 36878930 PMCID: PMC9988886 DOI: 10.1038/s41598-023-30567-2] [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: 10/22/2022] [Accepted: 02/25/2023] [Indexed: 03/08/2023] Open
Abstract
In recent years, circular RNAs (circRNAs) have been found to play an essential regulatory role in hepatocellular carcinoma (HCC) through various mechanisms, particularly the endogenous competitive RNA (ceRNA) mechanism. Therefore, it is significant to explore the circRNAs in hepatoma. In this study, we constructed the ceRNA and survival network using Cytoscape. We also used R, Perl software, and multiple online databases and platforms, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), to perform overall survival, immune cell infiltration, immune checkpoints, pathway activity, and anticancer drug sensitivity analysis of the genes. Finally, the receiver operator characteristic curve (ROC) analysis was performed to identify the diagnosis value of the genes. KEGG analysis revealed the T cell receptor signaling pathway as the main enrichment pathway. A total of 29 genes related to survival and prognosis were screened out. The findings suggest that ZNF544, WDR76, ACTG1, RASSF3, E2F3, ASRGL1, and POGK are associated with multilevel immune cell infiltration. Additionally, immune checkpoint analysis screened out the ACTG1, E2F3, RASSF3, and WDR76. It was also revealed that the WDR76, E2F3, ASRGL1, and POGK mainly activated the cell cycle and DNA damage response (DDR) pathway. The results suggest that the sensitivity toward trametinib, refametinib (RDEA119), and selumetinib correlates to the expression of WDR76. ROC analysis showed that the area under the curve (AUC) of all genes in the regulatory axis was greater than 0.7. The identified hsa_circ_0000417/hsa_circ_0002688/hsa_circ_0001387--hsa-miR-199a-5p--WDR76 regulatory axis may provide new insights into the progression, clinical diagnosis, and treatment of HCC.
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Affiliation(s)
- Guoqiang Zhong
- Department of Gastroenterology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.,The Graduate School, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Yan Lin
- Department of Gastroenterology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.,The Graduate School, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Zansong Huang
- Department of Gastroenterology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China. .,The Graduate School, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China.
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10
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Feng S, Yang C, Wang J, Fan X, Ying X. Aggrephagy-related LncRNAs index: A predictor for HCC prognosis, immunotherapy efficacy, and chemosensitivity. Technol Health Care 2023:THC220738. [PMID: 36872811 DOI: 10.3233/thc-220738] [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: 03/06/2023]
Abstract
BACKGROUND Due to the complexity and heterogeneity of hepatocellular carcinoma, the existing clinical staging criterias are insufficient to accurately reflect the tumor microenvironment and predict the prognosis of HCC patients. Aggrephagy, as a type of selective autophagy, is associated with various phenotypes of malignant tumors. OBJECTIVE This study aimed to identify and validate a prognostic model based on aggrephagy-related LncRNAs to assess the prognosis and immunotherapeutic response of HCC patients. METHODS Based on the TCGA-LIHC cohort, aggrephagy-related LncRNAs were identified. Univariate Cox regression analysis and lasso and multivariate Cox regression were used to construct a risk-scoring system based on eight ARLs. CIBERSORT, ssGSEA, and other algorithms were used to evaluate and present the immune landscape of tumor microenvironment. RESULTS The high-risk group had a worse overall survival (OS) than the low-risk group. Patients in the high-risk group are more likely to benefit from immunotherapy because of their high infiltration level and high immune checkpoint expression. CONCLUSION The ARLs signature is a powerful predictor of prognosis for HCC patients, and the nomogram based on this model can help clinicians accurately determine the prognosis of HCC patients and screen for specific subgroups of patients who are more sensitive to immunotherapy and chemotherapy.
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Affiliation(s)
- Shengchun Feng
- Department of Clinical Laboratory, Jinhua Municipal Central Hospital, Jinhua, Zhejiang, China.,Department of Clinical Laboratory, Jinhua Municipal Central Hospital, Jinhua, Zhejiang, China
| | - Chunyan Yang
- Department of Ultrasound Medicine, Chongqing University Cancer Hospital, Chongqing, China.,Department of Clinical Laboratory, Jinhua Municipal Central Hospital, Jinhua, Zhejiang, China
| | - Jun Wang
- Department of Hepatopancreatobiliary Surgery, The People's Hospital of Lishui, Lishui, Zhejiang, China
| | - Xiaopeng Fan
- Department of Hepatopancreatobiliary Surgery, The People's Hospital of Lishui, Lishui, Zhejiang, China
| | - Xiaowei Ying
- Department of Hepatopancreatobiliary Surgery, The People's Hospital of Lishui, Lishui, Zhejiang, China
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11
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Shen J, Zhao C, Zhang H, Zhou P, Li Z. Classification of tuberculosis-related programmed cell death-related patient subgroups and associated immune cell profiling. Front Immunol 2023; 14:1159713. [PMID: 37205113 PMCID: PMC10185908 DOI: 10.3389/fimmu.2023.1159713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Background Tuberculosis (TB) is the deadliest communicable disease in the world with the exception of the ongoing COVID-19 pandemic. Programmed cell death (PCD) patterns play key roles in the development and progression of many disease states such that they may offer value as effective biomarkers or therapeutic targets that can aid in identifying and treating TB patients. Materials and methods The Gene Expression Omnibus (GEO) was used to gather TB-related datasets after which immune cell profiles in these data were analyzed to examine the potential TB-related loss of immune homeostasis. Profiling of differentially expressed PCD-related genes was performed, after which candidate hub PCD-associated genes were selected via a machine learning approach. TB patients were then stratified into two subsets based on the expression of PCD-related genes via consensus clustering. The potential roles of these PCD-associated genes in other TB-related diseases were further examined. Results In total, 14 PCD-related differentially expressed genes (DEGs) were identified and highly expressed in TB patient samples and significantly correlated with the abundance of many immune cell types. Machine learning algorithms enabled the selection of seven hub PCD-related genes that were used to establish PCD-associated patient subgroups, followed by the validation of these subgroups in independent datasets. These findings, together with GSVA results, indicated that immune-related pathways were significantly enriched in TB patients exhibiting high levels of PCD-related gene expression, whereas metabolic pathways were significantly enriched in the other patient group. Single cell RNA-seq (scRNA-seq) further highlighted significant differences in the immune status of these different TB patient samples. Furthermore, we used CMap to predict five potential drugs for TB-related diseases. Conclusion These results highlight clear enrichment of PCD-related gene expression in TB patients and suggest that this PCD activity is closely associated with immune cell abundance. This thus indicates that PCD may play a role in TB progression through the induction or dysregulation of an immune response. These findings provide a foundation for further research aimed at clarifying the molecular drivers of TB, the selection of appropriate diagnostic biomarkers, and the design of novel therapeutic interventions aimed at treating this deadly infectious disease.
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Affiliation(s)
- Jie Shen
- School of Medical Laboratory, Weifang Medical University, Weifang, China
| | - Chao Zhao
- Office of Academic Affairs, Weifang Medical University, Weifang, China
| | - Hong Zhang
- School of Public Health, Weifang Medical University, Weifang, China
| | - Peipei Zhou
- School of Medical Laboratory, Weifang Medical University, Weifang, China
| | - Zhenpeng Li
- School of Medical Laboratory, Weifang Medical University, Weifang, China
- *Correspondence: Zhenpeng Li,
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Hypoxia-Inducible Factor-2-Altered Urothelial Carcinoma: Clinical and Genomic Features. Curr Oncol 2022; 29:8638-8649. [PMID: 36421334 PMCID: PMC9689673 DOI: 10.3390/curroncol29110681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Hypoxia is recognized as a key feature of cancer growth and is involved in various cellular processes, including proliferation, angiogenesis, and immune surveillance. Besides hypoxia-inducible factor 1-alpha (HIF-1α), which is the main mediator of hypoxia effects and can also be activated under normoxic conditions, little is known about its counterpart, HIF-2. This study focused on investigating the clinical and molecular landscape of HIF-2-altered urothelial carcinoma (UC). Methods: Publicly available next-generation sequencing (NGS) data from muscle-invasive UC cell lines and patient tumor samples from the MSK/TCGA 2020 cohort (n = 476) were interrogated for the level of expression (mRNA, protein) and presence of mutations, copy number variations, structural variants in the EPAS1 gene encoding HIF-2, and findings among various clinical (stage, grade, progression-free and overall survival) and molecular (tumor mutational burden, enriched gene expression) parameters were compared between altered and unaltered tumors. Results: 19% (7/37) of UC cell lines and 7% (27/380) of patients with muscle-invasive UC display high EPAS1 mRNA and protein expression or/and EPAS1 alterations. EPAS1-altered tumors are associated with higher stage, grade, and lymph node metastasis as well as with shorter PFS (14 vs. 51 months, q = 0.01) and OS (15 vs. 55 months, q = 0.01). EPAS1 mRNA expression is directly correlated with that of its target-genes, including VEGF, FLT1, KDR, DLL4, CDH5, ANGPT1 (q < 0.001). While there is a slightly higher tumor mutational burden in EPAS1-altered tumors (9.9 vs. 4.9 mut/Mb), they are enriched in and associated with genes promoting immune evasion, including ARID5B, SPINT1, AAK1, CLIC3, SORT1, SASH1, and FGFR3, respectively (q < 0.001). Conclusions: HIF-2-altered UC has an aggressive clinical and a distinct genomic and immunogenomic profile enriched in angiogenesis- and immune evasion-promoting genes.
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