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Liu Y, Qi L, Ye B, Wang A, Lu J, Qu L, Luo P, Wang L, Jiang A. MOICS, a novel classier deciphering immune heterogeneity and aid precise management of clear cell renal cell carcinoma at multiomics level. Cancer Biol Ther 2024; 25:2345977. [PMID: 38659199 PMCID: PMC11057626 DOI: 10.1080/15384047.2024.2345977] [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: 02/19/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
Recent studies have indicated that the tumor immune microenvironment plays a pivotal role in the initiation and progression of clear cell renal cell carcinoma (ccRCC). However, the characteristics and heterogeneity of tumor immunity in ccRCC, particularly at the multiomics level, remain poorly understood. We analyzed immune multiomics datasets to perform a consensus cluster analysis and validate the clustering results across multiple internal and external ccRCC datasets; and identified two distinctive immune phenotypes of ccRCC, which we named multiomics immune-based cancer subtype 1 (MOICS1) and subtype 2 (MOICS2). The former, MOICS1, is characterized by an immune-hot phenotype with poor clinical outcomes, marked by significant proliferation of CD4+ and CD8+ T cells, fibroblasts, and high levels of immune inhibitory signatures; the latter, MOICS2, exhibits an immune-cold phenotype with favorable clinical characteristics, characterized by robust immune activity and high infiltration of endothelial cells and immune stimulatory signatures. Besides, a significant negative correlation between immune infiltration and angiogenesis were identified. We further explored the mechanisms underlying these differences, revealing that negatively regulated endopeptidase activity, activated cornification, and neutrophil degranulation may promote an immune-deficient phenotype, whereas enhanced monocyte recruitment could ameliorate this deficiency. Additionally, significant differences were observed in the genomic landscapes between the subtypes: MOICS1 exhibited mutations in TTN, BAP1, SETD2, MTOR, MUC16, CSMD3, and AKAP9, while MOICS2 was characterized by notable alterations in the TGF-β pathway. Overall, our work demonstrates that multi-immune omics remodeling analysis enhances the understanding of the immune heterogeneity in ccRCC and supports precise patient management.
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Affiliation(s)
- Ying Liu
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, Hunan, China
| | - Bicheng Ye
- School of Clinical Medicine, Medical College of Yangzhou Polytechnic College, Yangzhou, China
| | - Anbang Wang
- Department of Urology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Juan Lu
- Vocational Education Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
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2
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Li GX, Chen L, Hsiao Y, Mannan R, Zhang Y, Luo J, Petralia F, Cho H, Hosseini N, Leprevost FDV, Calinawan A, Li Y, Anand S, Dagar A, Geffen Y, Kumar-Sinha C, Chugh S, Le A, Ponce S, Guo S, Zhang C, Schnaubelt M, Al Deen NN, Chen F, Caravan W, Houston A, Hopkins A, Newton CJ, Wang X, Polasky DA, Haynes S, Yu F, Jing X, Chen S, Robles AI, Mesri M, Thiagarajan M, An E, Getz GA, Linehan WM, Hostetter G, Jewell SD, Chan DW, Wang P, Omenn GS, Mehra R, Ricketts CJ, Ding L, Chinnaiyan AM, Cieslik MP, Dhanasekaran SM, Zhang H, Nesvizhskii AI. Comprehensive proteogenomic characterization of rare kidney tumors. Cell Rep Med 2024; 5:101547. [PMID: 38703764 PMCID: PMC11148773 DOI: 10.1016/j.xcrm.2024.101547] [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: 03/20/2023] [Revised: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.
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Affiliation(s)
- Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanbyul Cho
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Aniket Dagar
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seema Chugh
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Shenghao Guo
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Alex Hopkins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Xiaoming Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaojun Jing
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Gad A Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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3
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Sindhu KK, Dovey Z, Thompson M, Nehlsen AD, Skalina KA, Malachowska B, Hasan S, Guha C, Tang J, Salgado LR. The potential role of precision medicine to alleviate racial disparities in prostate, bladder and renal urological cancer care. BJUI COMPASS 2024; 5:405-425. [PMID: 38633827 PMCID: PMC11019243 DOI: 10.1002/bco2.323] [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: 09/24/2023] [Revised: 12/11/2023] [Accepted: 12/23/2023] [Indexed: 04/19/2024] Open
Abstract
Background Racial disparities in oncological outcomes resulting from differences in social determinants of health (SDOH) and tumour biology are well described in prostate cancer (PCa) but similar inequities exist in bladder (BCa) and renal cancers (RCCs). Precision medicine (PM) aims to provide personalized treatment based on individual patient characteristics and has the potential to reduce these inequities in GU cancers. Objective This article aims to review the current evidence outlining racial disparities in GU cancers and explore studies demonstrating improved oncological outcomes when PM is applied to racially diverse patient populations. Evidence acquisition Evidence was obtained from Pubmed and Web of Science using keywords prostate, bladder and renal cancer, racial disparity and precision medicine. Because limited studies were found, preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were not applied but rather related articles were studied to explore existing debates, identify the current status and speculate on future applications. Results Evidence suggests addressing SDOH for PCa can reverse racial inequities in oncological outcomes but differences in incidence remain. Similar disparities in BCa and RCC are seen, and it would be reasonable to suggest achieving parity in SDOH for all races would do the same. Research applying a PM approach to different ethnicities is lacking although in African Americans (AAs) with metastatic castrate-resistant prostate cancer (mCRPCa) better outcomes have been shown with androgen receptor inhibitors, radium-223 and sipuleucel. Exploiting the abscopal effect with targeted radiation therapy (RT) and immunotherapy has promise but requires further study, as does defining actionable mutations in specific patient groups to tailor treatments as appropriate. Conclusion For all GU cancers, the historical underrepresentation of ethnic minorities in clinical trials still exists and there is an urgent need for recruitment strategies to address this. PM is a promising development with the potential to reduce inequities in GU cancers, however, both improved understanding of race-specific tumour biology, and enhanced recruitment of minority populations into clinical trials are required. Without this, the benefits of PM will be limited.
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Affiliation(s)
- Kunal K. Sindhu
- Department of Radiation OncologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Zachary Dovey
- Department of UrologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Marcher Thompson
- Department of Radiation OncologyAIS Cancer Center/Adventist HealthBakersfieldCAUSA
| | - Anthony D. Nehlsen
- Department of Radiation OncologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Karin A. Skalina
- Department of Radiation OncologyMontefiore Medical Center/Albert Einstein College of MedicineBronxNYUSA
| | - Beata Malachowska
- Department of Radiation OncologyMontefiore Medical Center/Albert Einstein College of MedicineBronxNYUSA
| | - Shaakir Hasan
- Department of Radiation OncologyMontefiore Medical Center/Albert Einstein College of MedicineBronxNYUSA
| | - Chandan Guha
- Department of Radiation OncologyMontefiore Medical Center/Albert Einstein College of MedicineBronxNYUSA
| | - Justin Tang
- Department of Radiation OncologyMontefiore Medical Center/Albert Einstein College of MedicineBronxNYUSA
| | - Lucas Resende Salgado
- Department of Radiation OncologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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4
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Jani Y, Jansen CS, Gerke MB, Bilen MA. Established and emerging biomarkers of immunotherapy in renal cell carcinoma. Immunotherapy 2024; 16:405-426. [PMID: 38264827 DOI: 10.2217/imt-2023-0267] [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] [Indexed: 01/25/2024] Open
Abstract
Immunotherapies, such as immune checkpoint inhibitors, have heralded impressive progress for patient care in renal cell carcinoma (RCC). Despite this success, some patients' disease fails to respond, and other patients experience significant side effects. Thus, development of biomarkers is needed to ensure that patients can be selected to maximize benefit from immunotherapies. Improving clinicians' ability to predict which patients will respond to immunotherapy and which are most at risk of adverse events - namely through clinical biomarkers - is indispensable for patient safety and therapeutic efficacy. Accordingly, an evolving suite of therapeutic biomarkers continues to be investigated. This review discusses biomarkers for immunotherapy in RCC, highlighting current practices and emerging innovations, aiming to contribute to improved outcomes for patients with RCC.
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Affiliation(s)
- Yash Jani
- Mercer University, Macon, GA 31207, USA
| | - Caroline S Jansen
- Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Margo B Gerke
- Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mehmet Asim Bilen
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
- Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
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5
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Wang XM, Mannan R, Zhang Y, Chinnaiyan A, Rangaswamy R, Chugh S, Su F, Cao X, Wang R, Skala SL, Hafez KS, Vaishampayan U, Mckenney J, Picken MM, Gupta S, Alaghehbandan R, Tretiakova M, Argani P, Chinnaiyan AM, Dhanasekaran SM, Mehra R. Hybrid Oncocytic Tumors (HOTs) in Birt-Hogg-Dubé Syndrome Patients-A Tale of Two Cities: Sequencing Analysis Reveals Dual Lineage Markers Capturing the 2 Cellular Populations of HOT. Am J Surg Pathol 2024; 48:163-173. [PMID: 37994665 PMCID: PMC10871670 DOI: 10.1097/pas.0000000000002152] [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: 11/24/2023]
Abstract
Birt-Hogg-Dubé (BHD) syndrome is associated with an increased risk of multifocal renal tumors, including hybrid oncocytic tumor (HOT) and chromophobe renal cell carcinoma (chRCC). HOT exhibits heterogenous histologic features overlapping with chRCC and benign renal oncocytoma, posing challenges in diagnosis of HOT and renal tumor entities resembling HOT. In this study, we performed integrative analysis of bulk and single-cell RNA sequencing data from renal tumors and normal kidney tissues, and nominated candidate biomarkers of HOT, L1CAM, and LINC01187 , which are also lineage-specific markers labeling the principal cell and intercalated cell lineages of the distal nephron, respectively. Our findings indicate the principal cell lineage marker L1CAM and intercalated cell lineage marker LINC01187 to be expressed mutually exclusively in a unique checkered pattern in BHD-associated HOTs, and these 2 lineage markers collectively capture the 2 distinct tumor epithelial populations seen to co-exist morphologically in HOTs. We further confirmed that the unique checkered expression pattern of L1CAM and LINC01187 distinguished HOT from chRCC, renal oncocytoma, and other major and rare renal cell carcinoma subtypes. We also characterized the histopathologic features and immunophenotypic features of oncocytosis in the background kidney of patients with BHD, as well as the intertumor and intratumor heterogeneity seen within HOT. We suggest that L1CAM and LINC01187 can serve as stand-alone diagnostic markers or as a panel for the diagnosis of HOT. These lineage markers will inform future studies on the evolution and interaction between the 2 transcriptionally distinct tumor epithelial populations in such tumors.
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Affiliation(s)
- Xiao-Ming Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
- Michigan Center for Translational Pathology, Ann Arbor, MI
| | - Rahul Mannan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
- Michigan Center for Translational Pathology, Ann Arbor, MI
| | - Yuping Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
- Michigan Center for Translational Pathology, Ann Arbor, MI
| | | | | | - Seema Chugh
- Michigan Center for Translational Pathology, Ann Arbor, MI
| | - Fengyun Su
- Michigan Center for Translational Pathology, Ann Arbor, MI
| | - Xuhong Cao
- Michigan Center for Translational Pathology, Ann Arbor, MI
| | - Rui Wang
- Michigan Center for Translational Pathology, Ann Arbor, MI
| | - Stephanie L Skala
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Khaled S Hafez
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI
| | | | | | | | | | | | - Maria Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Pedram Argani
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
- Michigan Center for Translational Pathology, Ann Arbor, MI
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI
- Howard Hughes Medical Institute, Ann Arbor, MI
| | - Saravana M. Dhanasekaran
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
- Michigan Center for Translational Pathology, Ann Arbor, MI
| | - Rohit Mehra
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
- Michigan Center for Translational Pathology, Ann Arbor, MI
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI
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6
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Wei S, Krause HB, Geynisman DM, Elliott A, Kutikov A, Uzzo RG, Pei J, Barata P, Carneiro B, Heath E, Ryan C, Farrell A, Nabhan C, Ali-Fehmi R, Naqash AR, Argani P, McKay RR. Molecular Characterization of TFE3-Rearranged Renal Cell Carcinoma: A Comparative Study With Papillary and Clear Cell Renal Cell Carcinomas. Mod Pathol 2024; 37:100404. [PMID: 38104891 DOI: 10.1016/j.modpat.2023.100404] [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: 06/04/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
TFE3-rearranged renal cell carcinoma (rRCC) is a rare subtype of renal cell carcinomas belonging to the MiT family translocation RCC. To further elucidate the co-alterations that occur along with TFE3 fusions in rRCC, we characterized the genomic, transcriptional, and immune landscapes in comparison to clear cell (ccRCC) and papillary renal cell carcinoma (pRCC). Next-generation sequencing of RNA (whole transcriptome) and DNA (592-gene panel or whole exome) for rRCC (N = 20), pRCC (N = 20), and ccRCC samples (N = 392) was performed. Patients with rRCC were significantly younger and more frequently female (median 44.5 years, 75.0% female) as compared with patients with pRCC (68.5 years, 25.0% female; P < .05) and ccRCC (62.0 years, 27.8% female; P < .05). A total of 8 unique fusion partners were observed, including a novel fusion with SRRM2::TFE3 in 2 patients. ccRCC exhibited significantly higher mutation rates of VHL (0% rRCC, 0% pRCC, 78.7% ccRCC; P < .05) and PBMR1 (0% rRCC, 5.0% pRCC, 49.4% ccRCC; P < .05). The genomic landscapes of rRCC were sparse with no mutations occurring with a prevalence higher than 10% other than pTERT (18.2% rRCC, 0% pRCC, 9.2% ccRCC). rRCC were associated with significantly less M1 macrophages (0.8%) as compared with pRCC (1.4%) and ccRCC (2.7%) (P < .05), suggesting a cold tumor-immune microenvironment. However, rRCC were more commonly PD-L1+ (rRCC 50%, pRCC 19.0%, ccRCC 12.2%; P < .05). Gene set enrichment analysis showed that rRCC are enriched in genes related to oxidative phosphorylation when compared with both ccRCC and pRCC. Despite having a colder tumor-immune microenvironment than pRCC and ccRCC, increased PDL1+ rates in rRCC suggest a potential benefit from immune checkpoint inhibitor therapy.
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Affiliation(s)
- Shuanzeng Wei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
| | | | - Daniel M Geynisman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Alexander Kutikov
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Robert G Uzzo
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jianming Pei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pedro Barata
- Division of Solid Tumor Oncology, Department of Medicine, University Hospitals Seidman Cancer Center, Cleveland, Ohio
| | - Benedito Carneiro
- Division of Hematology/Oncology, Department of Medicine, Lifespan Health System, Brown University, Providence, Rhode Islands
| | - Elisabeth Heath
- Department of Oncology, Karmanos Cancer Institute, Detroit, Michigan
| | - Charles Ryan
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | | | | | - Rouba Ali-Fehmi
- Department of Pathology, Karmanos Cancer Institute, Detroit, Michigan
| | - Abdul Rafeh Naqash
- Medical Oncology, Stephenson Cancer Center, The University of Oklahoma Health Sciences, Oklahoma City, Oklahoma
| | - Pedram Argani
- Department of Pathology, The Johns Hopkins University School of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland
| | - Rana R McKay
- Department of Medicine, University of California San Diego, San Diego, California
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7
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Fukagawa A, Hama N, Totoki Y, Nakamura H, Arai Y, Saito-Adachi M, Maeshima A, Matsui Y, Yachida S, Ushiku T, Shibata T. Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort. Nat Commun 2023; 14:8383. [PMID: 38104198 PMCID: PMC10725467 DOI: 10.1038/s41467-023-44159-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
Renal cell carcinoma (RCC) comprises several histological types characterised by different genomic and epigenomic aberrations; however, the molecular pathogenesis of each type still requires further exploration. We perform whole-genome sequencing of 128 Japanese RCC cases of different histology to elucidate the significant somatic alterations and mutagenesis processes. We also perform transcriptomic and epigenomic sequencing to identify distinguishing features, including assay for transposase-accessible chromatin sequencing (ATAC-seq) and methyl sequencing. Genomic analysis reveals that the mutational signature differs among the histological types, suggesting that different carcinogenic factors drive each histology. From the ATAC-seq results, master transcription factors are identified for each histology. Furthermore, clear cell RCC is classified into three epi-subtypes, one of which expresses highly immune checkpoint molecules with frequent loss of chromosome 14q. These genomic and epigenomic features may lead to the development of effective therapeutic strategies for RCC.
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Affiliation(s)
- Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akiko Maeshima
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshiyuki Matsui
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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8
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Murali R, Gopalakrishnan AV. Molecular insight into renal cancer and latest therapeutic approaches to tackle it: an updated review. Med Oncol 2023; 40:355. [PMID: 37955787 DOI: 10.1007/s12032-023-02225-0] [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: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023]
Abstract
Renal cell carcinoma (RCC) is one of the most lethal genitourinary cancers, with the highest mortality rate, and may remain undetected throughout its development. RCC can be sporadic or hereditary. Exploring the underlying genetic abnormalities in RCC will have important implications for understanding the origins of nonhereditary renal cancers. The treatment of RCC has evolved over centuries from the era of cytokines to targeted therapy to immunotherapy. A surgical cure is the primary treatment modality, especially for organ-confined diseases. Furthermore, the urologic oncology community focuses on nephron-sparing surgical approaches and ablative procedures when small renal masses are detected incidentally in conjunction with interventional radiologists. In addition to new combination therapies approved for RCC treatment, several trials have been conducted to investigate the potential benefits of certain drugs. This may lead to durable responses and more extended survival benefits for patients with metastatic RCC (mRCC). Several approved drugs have reduced the mortality rate of patients with RCC by targeting VEGF signaling and mTOR. This review better explains the signaling pathways involved in the RCC progression, oncometabolites, and essential biomarkers in RCC that can be used for its diagnosis. Further, it provides an overview of the characteristics of RCC carcinogenesis to assist in combating treatment resistance, as well as details about the current management and future therapeutic options. In the future, multimodal and integrated care will be available, with new treatment options emerging as we learn more about the disease.
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Affiliation(s)
- Reshma Murali
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology VIT, Vellore, Tamil Nadu, 632014, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology VIT, Vellore, Tamil Nadu, 632014, India.
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9
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van der Wijngaart H, Beekhof R, Knol JC, Henneman AA, de Goeij-de Haas R, Piersma SR, Pham TV, Jimenez CR, Verheul HMW, Labots M. Candidate biomarkers for treatment benefit from sunitinib in patients with advanced renal cell carcinoma using mass spectrometry-based (phospho)proteomics. Clin Proteomics 2023; 20:49. [PMID: 37940875 PMCID: PMC10631096 DOI: 10.1186/s12014-023-09437-6] [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: 04/10/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
The tyrosine kinase inhibitor sunitinib is an effective first-line treatment for patients with advanced renal cell carcinoma (RCC). Hypothesizing that a functional read-out by mass spectrometry-based (phospho, p-)proteomics will identify predictive biomarkers for treatment outcome of sunitinib, tumor tissues of 26 RCC patients were analyzed. Eight patients had primary resistant (RES) and 18 sensitive (SENS) RCC. A 78 phosphosite signature (p < 0.05, fold-change > 2) was identified; 22 p-sites were upregulated in RES (unique in RES: BCAR3, NOP58, EIF4A2, GDI1) and 56 in SENS (35 unique). EIF4A1/EIF4A2 were differentially expressed in RES at the (p-)proteome and, in an independent cohort, transcriptome level. Inferred kinase activity of MAPK3 (p = 0.026) and EGFR (p = 0.045) as determined by INKA was higher in SENS. Posttranslational modifications signature enrichment analysis showed that different p-site-centric signatures were enriched (p < 0.05), of which FGF1 and prolactin pathways in RES and, in SENS, vanadate and thrombin treatment pathways, were most significant. In conclusion, the RCC (phospho)proteome revealed differential p-sites and kinase activities associated with sunitinib resistance and sensitivity. Independent validation is warranted to develop an assay for upfront identification of patients who are intrinsically resistant to sunitinib.
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Affiliation(s)
- Hanneke van der Wijngaart
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Robin Beekhof
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Alex A Henneman
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Richard de Goeij-de Haas
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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10
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de Vries-Brilland M, Rioux-Leclercq N, Meylan M, Dauvé J, Passot C, Spirina-Menand E, Flippot R, Fromont G, Gravis G, Geoffrois L, Chevreau C, Rolland F, Blanc E, Lefort F, Ravaud A, Gross-Goupil M, Escudier B, Negrier S, Albiges L. Comprehensive analyses of immune tumor microenvironment in papillary renal cell carcinoma. J Immunother Cancer 2023; 11:e006885. [PMID: 37935564 PMCID: PMC10649801 DOI: 10.1136/jitc-2023-006885] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Papillary renal cell carcinoma (pRCC) is the most common non-clear cell RCC, and associated with poor outcomes in the metastatic setting. In this study, we aimed to comprehensively evaluate the immune tumor microenvironment (TME), largely unknown, of patients with metastatic pRCC and identify potential therapeutic targets. METHODS We performed quantitative gene expression analysis of TME using Microenvironment Cell Populations-counter (MCP-counter) methodology, on two independent cohorts of localized pRCC (n=271 and n=98). We then characterized the TME, using immunohistochemistry (n=38) and RNA-sequencing (RNA-seq) (n=30) on metastatic pRCC from the prospective AXIPAP trial cohort. RESULTS Unsupervised clustering identified two "TME subtypes", in each of the cohorts: the "immune-enriched" and the "immune-low". Within AXIPAP trial cohort, the "immune-enriched" cluster was significantly associated with a worse prognosis according to the median overall survival to 8 months (95% CI, 6 to 29) versus 37 months (95% CI, 20 to NA, p=0.001). The two immune signatures, Teff and JAVELIN Renal 101 Immuno signature, predictive of response to immune checkpoint inhibitors (CPI) in clear cell RCC, were significantly higher in the "immune-enriched" group (adjusted p<0.05). Finally, five differentially overexpressed genes were identified, corresponding mainly to B lymphocyte populations. CONCLUSION For the first time, using RNA-seq and immunohistochemistry, we have highlighted a specific immune TME subtype of metastatic pRCC, significantly more infiltrated with T and B immune population. This "immune-enriched" group appears to have a worse prognosis and could have a potential predictive value for response to immunotherapy, justifying the confirmation of these results in a cohort of metastatic pRCC treated with CPI and in combination with targeted therapies. TRIAL REGISTRATION NUMBER NCT02489695.
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Affiliation(s)
- Manon de Vries-Brilland
- Department of Medical Oncology, Integrated Centers of Oncology (ICO) Paul Papin, Angers, France
| | | | - Maxime Meylan
- Equipe inflammation, complément et cancer, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, Paris, France
| | - Jonathan Dauvé
- Department of Clinical Biology, Integrated Centers of Oncology (ICO) Paul Papin, Angers, France
| | - Christophe Passot
- Department of Clinical Biology, Integrated Centers of Oncology (ICO) Paul Papin, Angers, France
| | - Elena Spirina-Menand
- Department of Clinical Biology, Integrated Centers of Oncology (ICO) Paul Papin, Angers, France
| | - Ronan Flippot
- Medical Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | | | - Lionnel Geoffrois
- Department of Medical Oncology, Institut de Cancérologie de Lorraine, Vandoeuvre-les-Nancy, France
| | - Christine Chevreau
- Department of Medical Oncology, IUCT-Oncopôle Institut Claudius Regaud, Toulouse, France
| | - Fréderic Rolland
- Department of Medical Oncology, Integrated Centers of Oncology (ICO) René Gauducheau, Nantes, France
| | - Ellen Blanc
- Department of Clinical Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Félix Lefort
- Department of Medical Oncology, University Hospital of Bordeaux, Bordeaux, France
| | - Alain Ravaud
- Department of Medical Oncology, University Hospital of Bordeaux, Bordeaux, France
| | - Marine Gross-Goupil
- Department of Medical Oncology, University Hospital of Bordeaux, Bordeaux, France
| | - Bernard Escudier
- Medical Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- U1015 INSERM, Gustave Roussy Cancer Campus, Paris-Saclay University, Villejuif, France
| | - Sylvie Negrier
- Department of Medical Oncology, Lyon I University, Lyon, France
| | - Laurence Albiges
- Medical Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
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11
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Tang J, Yao F, Yao Z, Xing XL. Characterization of tumor microenvironment and sensitive chemotherapy drugs based on cuproptosis-related signatures in renal cell carcinoma. Aging (Albany NY) 2023; 15:9695-9717. [PMID: 37728407 PMCID: PMC10564438 DOI: 10.18632/aging.205043] [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: 05/01/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023]
Abstract
Cuproptosis is a novel type of copper-induced cell death and is considered as a new therapeutic target for many cancers. Distant metastases occur in about 40% of patients with advanced renal cell carcinoma (RCC), with a poor 5-year prognosis of about 10%. Through a series of comprehensive analyses, four differentially expressed cuproptosis-related lncRNAs (DECRLs) were identified as candidate biomarkers for RCC. The risk model constructed by using these four DECRLs can better predict the prognosis of patients with RCC, which is determined by the receiver operating characteristic (Time dependent area under curve value at 1-year, 3-year, 5-year, and 10-year were 0.82, 0.80, 0.76, and 0.73 respectively). There were significant differences in immune status between high-risk and low-risk RCC patients. The differentially expressed gene enrichment terms between high- and low-risk patients was also dominated by immune-related terms. The risk score was also correlated with immunotherapy as measured by the tumor immune dysfunction and exclusion (TIDE) score. In addition, we also found that the sensitivity of many chemotherapy drugs varies widely between high- and low-risk patients. The sensitivity of the three chemotherapy drugs (AZD4547, Vincristine, and WEHI-539) varied among high- and low-risk patients, and was significantly negatively correlated with risk values, suggesting that they could be used as clinical treatment drugs for RCC. Our study not only obtained four potential biomarkers, but also provided guidance for immunotherapy and chemotherapy treatment of RCC, as well as new research strategies for the screening of other cancer biomarkers and sensitive drugs.
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Affiliation(s)
- Jiefu Tang
- The First Affiliated Hospital of Hunan University of Medicine, School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, Hunan, P.R. China
| | - Fan Yao
- The First Affiliated Hospital of Hunan University of Medicine, School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, Hunan, P.R. China
| | - Zhiyong Yao
- The First Affiliated Hospital of Hunan University of Medicine, School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, Hunan, P.R. China
| | - Xiao-Liang Xing
- The First Affiliated Hospital of Hunan University of Medicine, School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, Hunan, P.R. China
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12
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Mannan R, Wang X, Bawa PS, Zhang Y, Skala SL, Chinnaiyan AK, Dagar A, Wang L, Zelenka-Wang SB, McMurry LM, Daniel N, Cao X, Sangoi AR, Gupta S, Vaishampayan UN, Hafez KS, Morgan TM, Spratt DE, Tretiakova MS, Argani P, Chinnaiyan AM, Dhanasekaran SM, Mehra R. Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms. Int J Surg Pathol 2023; 31:1027-1040. [PMID: 36250542 DOI: 10.1177/10668969221125793] [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] [Indexed: 09/09/2023]
Abstract
Introduction. Chromophobe renal cell carcinoma (chromophobe RCC) is the third major subcategory of renal tumors after clear cell RCC and papillary RCC, accounting for approximately 5% of all RCC subtypes. Other oncocytic neoplasms seen commonly in surgical pathology practice include the eosinophilic variant of chromophobe RCC, renal oncocytoma, and low-grade oncocytic unclassified RCC. Methods. In our recent next-generation sequencing based study, we nominated a lineage-specific novel biomarker LINC01187 (long intergenic non-protein coding RNA 1187) which was found to be enriched in chromophobe RCC. Like KIT (cluster of differentiation 117; CD117), a clinically utilized chromophobe RCC related biomarker, LINC01187 is expressed in intercalated cells of the nephron. In this follow-up study, we performed KIT immunohistochemistry and LINC01187 RNA in situ hybridization (RNA-ISH) on a cohort of chromophobe RCC and other renal neoplasms, characterized the expression patterns, and quantified the expression signals of the two biomarkers in both primary and metastatic settings. Results. LINC01187, in comparison to KIT, exhibits stronger and more uniform expression within tumors while maintaining temporal and spatial consistency. LINC01187 also is devoid of intra-tumoral heterogeneous expression pattern, a phenomenon commonly noted with KIT. Conclusions. LINC01187 expression can augment the currently utilized KIT assay and help facilitate easy microscopic analyses in routine surgical pathology practice.
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Affiliation(s)
- Rahul Mannan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Xiaoming Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Pushpinder S Bawa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Stephanie L Skala
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Aniket Dagar
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Sylvia B Zelenka-Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Lisa M McMurry
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Nikita Daniel
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Ann Arbor, MI, USA
| | - Ankur R Sangoi
- Department of Pathology, El Camino Hospital, Mountain View, CA, USA
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ulka N Vaishampayan
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Khaled S Hafez
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Maria S Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pedram Argani
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
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13
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Perelli L, Carbone F, Zhang L, Huang JK, Le C, Khan H, Citron F, Del Poggetto E, Gutschner T, Tomihara H, Soeung M, Minelli R, Srinivasan S, Peoples M, Lam TNA, Lundgren S, Xia R, Zhu C, Mohamed AMT, Zhang J, Sircar K, Sgambato A, Gao J, Jonasch E, Draetta GF, Futreal A, Bakouny Z, Van Allen EM, Choueiri T, Signoretti S, Msaouel P, Litchfield K, Turajlic S, Wang L, Chen YB, Di Natale RG, Hakimi AA, Giuliani V, Heffernan TP, Viale A, Bristow CA, Tannir NM, Carugo A, Genovese G. Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer. NATURE CANCER 2023; 4:984-1000. [PMID: 37365326 PMCID: PMC10368532 DOI: 10.1038/s43018-023-00584-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/18/2023] [Indexed: 06/28/2023]
Abstract
Molecular routes to metastatic dissemination are critical determinants of aggressive cancers. Through in vivo CRISPR-Cas9 genome editing, we generated somatic mosaic genetically engineered models that faithfully recapitulate metastatic renal tumors. Disruption of 9p21 locus is an evolutionary driver to systemic disease through the rapid acquisition of complex karyotypes in cancer cells. Cross-species analysis revealed that recurrent patterns of copy number variations, including 21q loss and dysregulation of the interferon pathway, are major drivers of metastatic potential. In vitro and in vivo genomic engineering, leveraging loss-of-function studies, along with a model of partial trisomy of chromosome 21q, demonstrated a dosage-dependent effect of the interferon receptor genes cluster as an adaptive mechanism to deleterious chromosomal instability in metastatic progression. This work provides critical knowledge on drivers of renal cell carcinoma progression and defines the primary role of interferon signaling in constraining the propagation of aneuploid clones in cancer evolution.
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Affiliation(s)
- Luigi Perelli
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Federica Carbone
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Nerviano Medical Sciences, NMS Group Spa, Milan, Italy
| | - Li Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin K Huang
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Courtney Le
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hania Khan
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francesca Citron
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edoardo Del Poggetto
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tony Gutschner
- Junior Research Group 'RNA Biology and Pathogenesis', Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Hideo Tomihara
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melinda Soeung
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosalba Minelli
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanjana Srinivasan
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Peoples
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Truong Nguyen Anh Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sebastian Lundgren
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruohan Xia
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cihui Zhu
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alaa M T Mohamed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanishka Sircar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessandro Sgambato
- Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - JianJun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Toni Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sabina Signoretti
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ying Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Renzo G Di Natale
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Ari Hakimi
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Virginia Giuliani
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy P Heffernan
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher A Bristow
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessandro Carugo
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Biology, IRBM S.p.A., Rome, Italy.
| | - Giannicola Genovese
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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14
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Shankar V, Vijayalakshmi K, Nolley R, Sonn GA, Kao CS, Zhao H, Wen R, Eberlin LS, Tibshirani R, Zare RN, Brooks JD. Distinguishing Renal Cell Carcinoma From Normal Kidney Tissue Using Mass Spectrometry Imaging Combined With Machine Learning. JCO Precis Oncol 2023; 7:e2200668. [PMID: 37285559 PMCID: PMC10309512 DOI: 10.1200/po.22.00668] [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] [Received: 12/03/2022] [Revised: 02/26/2023] [Accepted: 04/10/2023] [Indexed: 06/09/2023] Open
Abstract
PURPOSE Accurately distinguishing renal cell carcinoma (RCC) from normal kidney tissue is critical for identifying positive surgical margins (PSMs) during partial and radical nephrectomy, which remains the primary intervention for localized RCC. Techniques that detect PSM with higher accuracy and faster turnaround time than intraoperative frozen section (IFS) analysis can help decrease reoperation rates, relieve patient anxiety and costs, and potentially improve patient outcomes. MATERIALS AND METHODS Here, we extended our combined desorption electrospray ionization mass spectrometry imaging (DESI-MSI) and machine learning methodology to identify metabolite and lipid species from tissue surfaces that can distinguish normal tissues from clear cell RCC (ccRCC), papillary RCC (pRCC), and chromophobe RCC (chRCC) tissues. RESULTS From 24 normal and 40 renal cancer (23 ccRCC, 13 pRCC, and 4 chRCC) tissues, we developed a multinomial lasso classifier that selects 281 total analytes from over 27,000 detected molecular species that distinguishes all histological subtypes of RCC from normal kidney tissues with 84.5% accuracy. On the basis of independent test data reflecting distinct patient populations, the classifier achieves 85.4% and 91.2% accuracy on a Stanford test set (20 normal and 28 RCC) and a Baylor-UT Austin test set (16 normal and 41 RCC), respectively. The majority of the model's selected features show consistent trends across data sets affirming its stable performance, where the suppression of arachidonic acid metabolism is identified as a shared molecular feature of ccRCC and pRCC. CONCLUSION Together, these results indicate that signatures derived from DESI-MSI combined with machine learning may be used to rapidly determine surgical margin status with accuracies that meet or exceed those reported for IFS.
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Affiliation(s)
- Vishnu Shankar
- Program in Immunology, Stanford University School of Medicine, Stanford, CA
| | | | - Rosalie Nolley
- Department of Urology, Stanford University School of Medicine, Stanford, CA
| | - Geoffrey A. Sonn
- Department of Urology, Stanford University School of Medicine, Stanford, CA
| | - Chia-Sui Kao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Hongjuan Zhao
- Department of Urology, Stanford University School of Medicine, Stanford, CA
| | - Ru Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA
| | | | - Robert Tibshirani
- Department of Biomedical Data Science, and Statistics, Stanford University, Stanford, CA
| | | | - James D. Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA
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15
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Gupta A, Patil A, Patel D, Singh AG, Ganpule AP, Sabnis RB, Desai MR. Stage Migration in Renal Malignancies in COVID Era: A Single-Center Analysis. Indian J Surg Oncol 2023:1-6. [PMID: 37363712 PMCID: PMC10187501 DOI: 10.1007/s13193-023-01771-3] [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: 08/29/2022] [Accepted: 05/10/2023] [Indexed: 06/28/2023] Open
Abstract
The COVID-19 disease, caused by SARS-CoV-2 virus, attained the status of a pandemic by March 2020. There was apprehension among patients suffering from renal malignancies about balancing cancer treatment and preventing COVID-19 infection transmission. We analyzed 184 patients with renal malignancies retrospectively, who presented to our institute over 2 years: 91 patients of renal malignancies in pre-COVID era (March 2019-Feb 2020) and 93 patients in COVID era (March 2020-Feb 2021). The parameters analyzed were age, tumor size, clinical presentation, clinical stage, pathological stage, nuclear grade, and presence of metastasis. Level of significance was kept at 95%, and p value <0.05 was considered significant. The age of patients was comparable in both groups (p: 0.381). Clinical presentation was also similar in both groups whereas there were more cases diagnosed during routine evaluation in pre-COVID era (p: 0.022). Tumor size was 5.84 ± 3.03cm vs. 7.10±3.83cm (p: 0.017) in pre-COVID vs. COVID era, respectively. Patients in COVID era had significantly higher clinical stage (p = 0.041), pathological stage (p =0.027), nuclear grade (p = 0.007), and presence of metastasis (p = 0.005) as compared to pre-COVID era. Patients, who underwent Nephron-sparing surgery, also had higher pathological stage in COVID era. COVID overshadowed the management of renal malignancies. There was a clear shift and stage migration in patients of renal malignancies in COVID era as compared to pre-COVID era, probably because of less routine health check-ups and patients deferring hospital visits due to fear of contracting COVID infection.
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16
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Badoiu SC, Greabu M, Miricescu D, Stanescu-Spinu II, Ilinca R, Balan DG, Balcangiu-Stroescu AE, Mihai DA, Vacaroiu IA, Stefani C, Jinga V. PI3K/AKT/mTOR Dysregulation and Reprogramming Metabolic Pathways in Renal Cancer: Crosstalk with the VHL/HIF Axis. Int J Mol Sci 2023; 24:8391. [PMID: 37176098 PMCID: PMC10179314 DOI: 10.3390/ijms24098391] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Renal cell carcinoma (RCC) represents 85-95% of kidney cancers and is the most frequent type of renal cancer in adult patients. It accounts for 3% of all cancer cases and is in 7th place among the most frequent histological types of cancer. Clear cell renal cell carcinoma (ccRCC), accounts for 75% of RCCs and has the most kidney cancer-related deaths. One-third of the patients with ccRCC develop metastases. Renal cancer presents cellular alterations in sugars, lipids, amino acids, and nucleic acid metabolism. RCC is characterized by several metabolic dysregulations including oxygen sensing (VHL/HIF pathway), glucose transporters (GLUT 1 and GLUT 4) energy sensing, and energy nutrient sensing cascade. Metabolic reprogramming represents an important characteristic of the cancer cells to survive in nutrient and oxygen-deprived environments, to proliferate and metastasize in different body sites. The phosphoinositide 3-kinase-AKT-mammalian target of the rapamycin (PI3K/AKT/mTOR) signaling pathway is usually dysregulated in various cancer types including renal cancer. This molecular pathway is frequently correlated with tumor growth and survival. The main aim of this review is to present renal cancer types, dysregulation of PI3K/AKT/mTOR signaling pathway members, crosstalk with VHL/HIF axis, and carbohydrates, lipids, and amino acid alterations.
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Affiliation(s)
- Silviu Constantin Badoiu
- Department of Anatomy and Embryology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Maria Greabu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Daniela Miricescu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Iulia-Ioana Stanescu-Spinu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Radu Ilinca
- Department of Medical Informatics and Biostatistics, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Daniela Gabriela Balan
- Department of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania; (D.G.B.); (A.-E.B.-S.)
| | - Andra-Elena Balcangiu-Stroescu
- Department of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania; (D.G.B.); (A.-E.B.-S.)
| | - Doina-Andrada Mihai
- Department of Diabetes, Nutrition and Metabolic Diseases, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Ileana Adela Vacaroiu
- Department of Nephrology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Constantin Stefani
- Department of Family Medicine and Clinical Base, Dr. Carol Davila Central Military Emergency University Hospital, 134 Calea Plevnei, 010825 Bucharest, Romania;
| | - Viorel Jinga
- Department of Urology, “Prof. Dr. Theodor Burghele” Hospital, 050653 Bucharest, Romania
- “Prof. Dr. Theodor Burghele” Clinical Hospital, University of Medicine and Pharmacy Carol Davila, 050474 Bucharest, Romania
- Medical Sciences Section, Academy of Romanian Scientists, 050085 Bucharest, Romania
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17
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Cheng J, Yan J, Liu Y, Shi J, Wang H, Zhou H, Zhou Y, Zhang T, Zhao L, Meng X, Gong H, Zhang X, Zhu H, Jiang P. Cancer-cell-derived fumarate suppresses the anti-tumor capacity of CD8 + T cells in the tumor microenvironment. Cell Metab 2023:S1550-4131(23)00171-7. [PMID: 37178684 DOI: 10.1016/j.cmet.2023.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/06/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Metabolic alterations in the microenvironment significantly modulate tumor immunosensitivity, but the underlying mechanisms remain obscure. Here, we report that tumors depleted of fumarate hydratase (FH) exhibit inhibition of functional CD8+ T cell activation, expansion, and efficacy, with enhanced malignant proliferative capacity. Mechanistically, FH depletion in tumor cells accumulates fumarate in the tumor interstitial fluid, and increased fumarate can directly succinate ZAP70 at C96 and C102 and abrogate its activity in infiltrating CD8+ T cells, resulting in suppressed CD8+ T cell activation and anti-tumor immune responses in vitro and in vivo. Additionally, fumarate depletion by increasing FH expression strongly enhances the anti-tumor efficacy of anti-CD19 CAR T cells. Thus, these findings demonstrate a role for fumarate in controlling TCR signaling and suggest that fumarate accumulation in the tumor microenvironment (TME) is a metabolic barrier to CD8+ T cell anti-tumor function. And potentially, fumarate depletion could be an important strategy for tumor immunotherapy.
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Affiliation(s)
- Jie Cheng
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jinxin Yan
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiangzhou Shi
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Hubei 430081, China
| | - Haoyu Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hanyang Zhou
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinglin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tongcun Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Hubei 430081, China
| | - Lina Zhao
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xianbin Meng
- National Center for Protein Science, Tsinghua University, Beijing 100084, China
| | - Haipeng Gong
- School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xinxiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Haichuan Zhu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Hubei 430081, China.
| | - Peng Jiang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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18
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Saout JR, Lecuyer G, Léonard S, Evrard B, Kammerer-Jacquet SF, Noël L, Khene ZE, Mathieu R, Brunot A, Rolland AD, Bensalah K, Rioux-Leclercq N, Lardenois A, Chalmel F. Single-cell Deconvolution of a Specific Malignant Cell Population as a Poor Prognostic Biomarker in Low-risk Clear Cell Renal Cell Carcinoma Patients. Eur Urol 2023; 83:441-451. [PMID: 36801089 DOI: 10.1016/j.eururo.2023.02.008] [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: 09/12/2022] [Revised: 12/10/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Intratumor heterogeneity (ITH) is a key feature in clear cell renal cell carcinomas (ccRCCs) that impacts outcomes such as aggressiveness, response to treatments, or recurrence. In particular, it may explain tumor relapse after surgery in clinically low-risk patients who did not benefit from adjuvant therapy. Recently, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool to unravel expression ITH (eITH) and might enable better assessment of clinical outcomes in ccRCC. OBJECTIVE To explore eITH in ccRCC with a focus on malignant cells (MCs) and assess its relevance to improve prognosis for low-risk patients. DESIGN, SETTING, AND PARTICIPANTS We performed scRNA-seq on tumor samples from five untreated ccRCC patients ranging from pT1a to pT3b. Data were complemented with a published dataset composed of pairs of matched normal and ccRCC samples. INTERVENTION Radical or partial nephrectomy on untreated ccRCC patients. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Viability and cell type proportions were determined by flow cytometry. Following scRNA-seq, a functional analysis was performed and tumor progression trajectories were inferred. A deconvolution approach was applied on an external cohort, and Kaplan-Meier survival curves were estimated with respect to the prevalence of malignant clusters. RESULTS AND LIMITATIONS We analyzed 54 812 cells and identified 35 cell subpopulations. The eITH analysis revealed that each tumor contained various degrees of clonal diversity. The transcriptomic signatures of MCs in one particularly heterogeneous sample were used to design a deconvolution-based strategy that allowed the risk stratification of 310 low-risk ccRCC patients. CONCLUSIONS We described eITH in ccRCCs, and used this information to establish significant cell population-based prognostic signatures and better discriminate ccRCC patients. This approach has the potential to improve the stratification of clinically low-risk patients and their therapeutic management. PATIENT SUMMARY We sequenced the RNA content of individual cell subpopulations composed of clear cell renal cell carcinomas and identified specific malignant cells the genetic information of which can be used to predict tumor progression.
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Affiliation(s)
- Judikael R Saout
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Gwendoline Lecuyer
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Simon Léonard
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France; INSERM, EFS, UMR S1236, Univ Rennes, Rennes, France
| | - Bertrand Evrard
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Solène-Florence Kammerer-Jacquet
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Pathology Department, University Hospital of Rennes, Rennes, France
| | - Laurence Noël
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | | | - Romain Mathieu
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Urology Department, University Hospital of Rennes, Rennes, France
| | - Angélique Brunot
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Antoine D Rolland
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Karim Bensalah
- Urology Department, University Hospital of Rennes, Rennes, France
| | - Nathalie Rioux-Leclercq
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Pathology Department, University Hospital of Rennes, Rennes, France
| | - Aurélie Lardenois
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Frédéric Chalmel
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
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19
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Choi JM, Park C, Chae H. meth-SemiCancer: a cancer subtype classification framework via semi-supervised learning utilizing DNA methylation profiles. BMC Bioinformatics 2023; 24:168. [PMID: 37101254 PMCID: PMC10131478 DOI: 10.1186/s12859-023-05272-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/05/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Identification of the cancer subtype plays a crucial role to provide an accurate diagnosis and proper treatment to improve the clinical outcomes of patients. Recent studies have shown that DNA methylation is one of the key factors for tumorigenesis and tumor growth, where the DNA methylation signatures have the potential to be utilized as cancer subtype-specific markers. However, due to the high dimensionality and the low number of DNA methylome cancer samples with the subtype information, still, to date, a cancer subtype classification method utilizing DNA methylome datasets has not been proposed. RESULTS In this paper, we present meth-SemiCancer, a semi-supervised cancer subtype classification framework based on DNA methylation profiles. The proposed model was first pre-trained based on the methylation datasets with the cancer subtype labels. After that, meth-SemiCancer generated the pseudo-subtypes for the cancer datasets without subtype information based on the model's prediction. Finally, fine-tuning was performed utilizing both the labeled and unlabeled datasets. CONCLUSIONS From the performance comparison with the standard machine learning-based classifiers, meth-SemiCancer achieved the highest average F1-score and Matthews correlation coefficient, outperforming other methods. Fine-tuning the model with the unlabeled patient samples by providing the proper pseudo-subtypes, encouraged meth-SemiCancer to generalize better than the supervised neural network-based subtype classification method. meth-SemiCancer is publicly available at https://github.com/cbi-bioinfo/meth-SemiCancer .
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Affiliation(s)
- Joung Min Choi
- Department of Computer Science, Virginia Tech, Blacksburg, USA
| | - Chaelin Park
- Division of Computer Science, Sookmyung Women's University, Seoul, Republic of Korea
| | - Heejoon Chae
- Division of Computer Science, Sookmyung Women's University, Seoul, Republic of Korea.
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20
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Lang M, Schmidt LS, Wilson KM, Ricketts CJ, Sourbier C, Vocke CD, Wei D, Crooks DR, Yang Y, Gibbs BK, Zhang X, Klumpp-Thomas C, Chen L, Guha R, Ferrer M, McKnight C, Itkin Z, Wangsa D, Wangsa D, James A, Difilippantonio S, Karim B, Morís F, Ried T, Merino MJ, Srinivasan R, Thomas CJ, Linehan WM. High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma. J Exp Clin Cancer Res 2023; 42:99. [PMID: 37095531 PMCID: PMC10127337 DOI: 10.1186/s13046-023-02667-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND MiT-Renal Cell Carcinoma (RCC) is characterized by genomic translocations involving microphthalmia-associated transcription factor (MiT) family members TFE3, TFEB, or MITF. MiT-RCC represents a specific subtype of sporadic RCC that is predominantly seen in young patients and can present with heterogeneous histological features making diagnosis challenging. Moreover, the disease biology of this aggressive cancer is poorly understood and there is no accepted standard of care therapy for patients with advanced disease. Tumor-derived cell lines have been established from human TFE3-RCC providing useful models for preclinical studies. METHODS TFE3-RCC tumor derived cell lines and their tissues of origin were characterized by IHC and gene expression analyses. An unbiased high-throughput drug screen was performed to identify novel therapeutic agents for treatment of MiT-RCC. Potential therapeutic candidates were validated in in vitro and in vivo preclinical studies. Mechanistic assays were conducted to confirm the on-target effects of drugs. RESULTS The results of a high-throughput small molecule drug screen utilizing three TFE3-RCC tumor-derived cell lines identified five classes of agents with potential pharmacological efficacy, including inhibitors of phosphoinositide-3-kinase (PI3K) and mechanistic target of rapamycin (mTOR), and several additional agents, including the transcription inhibitor Mithramycin A. Upregulation of the cell surface marker GPNMB, a specific MiT transcriptional target, was confirmed in TFE3-RCC and evaluated as a therapeutic target using the GPNMB-targeted antibody-drug conjugate CDX-011. In vitro and in vivo preclinical studies demonstrated efficacy of the PI3K/mTOR inhibitor NVP-BGT226, Mithramycin A, and CDX-011 as potential therapeutic options for treating advanced MiT-RCC as single agents or in combination. CONCLUSIONS The results of the high-throughput drug screen and validation studies in TFE3-RCC tumor-derived cell lines have provided in vitro and in vivo preclinical data supporting the efficacy of the PI3K/mTOR inhibitor NVP-BGT226, the transcription inhibitor Mithramycin A, and GPNMB-targeted antibody-drug conjugate CDX-011 as potential therapeutic options for treating advanced MiT-RCC. The findings presented here should provide the basis for designing future clinical trials for patients with MiT-driven RCC.
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Affiliation(s)
- Martin Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, 39100, Italy
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carole Sourbier
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Darmood Wei
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Youfeng Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin K Gibbs
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Carleen Klumpp-Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Crystal McKnight
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Zina Itkin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Darawalee Wangsa
- Genetics Branch, Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danny Wangsa
- Genetics Branch, Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy James
- Laboratory of Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simone Difilippantonio
- Laboratory of Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Baktir Karim
- Laboratory of Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Francisco Morís
- EntreChem SL, Vivero Ciencias de la Salud, Calle Colegio Santo Domingo Guzmán, Oviedo, AS, 33011, Spain
| | - Thomas Ried
- Genetics Branch, Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria J Merino
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ramaprasad Srinivasan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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21
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Xi Y, Song L, Wang S, Zhou H, Ren J, Zhang R, Fu F, Yang Q, Duan G, Wang J. Identification of basement membrane-related prognostic signature for predicting prognosis, immune response and potential drug prediction in papillary renal cell carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:10694-10724. [PMID: 37322956 DOI: 10.3934/mbe.2023474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Papillary renal cell carcinoma (PRCC) is a malignant neoplasm of the kidney and is highly interesting due to its increasing incidence. Many studies have shown that the basement membrane (BM) plays an important role in the development of cancer, and structural and functional changes in the BM can be observed in most renal lesions. However, the role of BM in the malignant progression of PRCC and its impact on prognosis has not been fully studied. Therefore, this study aimed to explore the functional and prognostic value of basement membrane-associated genes (BMs) in PRCC patients. We identified differentially expressed BMs between PRCC tumor samples and normal tissue and systematically explored the relevance of BMs to immune infiltration. Moreover, we constructed a risk signature based on these differentially expressed genes (DEGs) using Lasso regression analysis and demonstrated their independence using Cox regression analysis. Finally, we predicted 9 small molecule drugs with the potential to treat PRCC and compared the differences in sensitivity to commonly used chemotherapeutic agents between high and low-risk groups to better target patients for more precise treatment planning. Taken together, our study suggested that BMs might play a crucial role in the development of PRCC, and these results might provide new insights into the treatment of PRCC.
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Affiliation(s)
- Yujia Xi
- Department of Urology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Liying Song
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Shuang Wang
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Haonan Zhou
- First School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Jieying Ren
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Ran Zhang
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Feifan Fu
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Qian Yang
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Guosheng Duan
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Jingqi Wang
- Department of Urology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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22
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de Alwis R, Schoch S, Islam M, Möller C, Ljungberg B, Axelson H. Identification and validation of NFIA as a novel prognostic marker in renal cell carcinoma. J Pathol Clin Res 2023. [PMID: 36947439 DOI: 10.1002/cjp2.316] [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: 10/03/2022] [Revised: 01/10/2023] [Accepted: 02/24/2023] [Indexed: 03/23/2023]
Abstract
Prognostic tools are an essential component of the clinical management of patients with renal cell carcinoma (RCC). Although tumour stage and grade can provide important information, they fail to consider patient- and tumour-specific biology. In this study, we set out to find a novel molecular marker of RCC by using hepatocyte nuclear factor 4A (HNF4A), a transcription factor implicated in RCC progression and malignancy, as a blueprint. Through transcriptomic analyses, we show that the nuclear factor I A (NFIA)-driven transcription network is active in primary RCC and that higher levels of NFIA confer a survival benefit. We validate our findings using immunohistochemical staining and analysis of a 363-patient tissue microarray (TMA), showing for the first time that NFIA can independently predict poor cancer-specific survival in clear cell RCC (ccRCC) patients (hazard ratio = 0.46, 95% CI = 0.24-0.85, p value = 0.014). Furthermore, we confirm the association of HNF4A with higher grades and stages in ccRCC in our TMA cohort. We present novel data that show HNF4A protein expression does not confer favourable prognosis in papillary RCC, confirming our survival analysis with publicly available HNF4A RNA expression data. Further work is required to elucidate the functional role of NFIA in RCC as well as the testing of these markers on patient material from diverse multi-centre cohorts, to establish their value for the prognostication of RCC.
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Affiliation(s)
- Roger de Alwis
- Division of Translational Cancer Research, Department of Laboratory Medicine Lund University, Lund, Sweden
| | - Sarah Schoch
- Division of Translational Cancer Research, Department of Laboratory Medicine Lund University, Lund, Sweden
| | - Mazharul Islam
- Division of Translational Cancer Research, Department of Laboratory Medicine Lund University, Lund, Sweden
| | - Christina Möller
- Division of Translational Cancer Research, Department of Laboratory Medicine Lund University, Lund, Sweden
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine Lund University, Lund, Sweden
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23
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Jin J, Xie Y, Zhang JS, Wang JQ, Dai SJ, He WF, Li SY, Ashby CR, Chen ZS, He Q. Sunitinib resistance in renal cell carcinoma: From molecular mechanisms to predictive biomarkers. Drug Resist Updat 2023; 67:100929. [PMID: 36739809 DOI: 10.1016/j.drup.2023.100929] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
Currently, renal cell carcinoma (RCC) is the most prevalent type of kidney cancer. Targeted therapy has replaced radiation therapy and chemotherapy as the main treatment option for RCC due to the lack of significant efficacy with these conventional therapeutic regimens. Sunitinib, a drug used to treat gastrointestinal tumors and renal cell carcinoma, inhibits the tyrosine kinase activity of a number of receptor tyrosine kinases, including vascular endothelial growth factor receptor (VEGFR), platelet-derived growth factor receptor (PDGFR), c-Kit, rearranged during transfection (RET) and fms-related receptor tyrosine kinase 3 (Flt3). Although sunitinib has been shown to be efficacious in the treatment of patients with advanced RCC, a significant number of patients have primary resistance to sunitinib or acquired drug resistance within the 6-15 months of therapy. Thus, in order to develop more efficacious and long-lasting treatment strategies for patients with advanced RCC, it will be crucial to ascertain how to overcome sunitinib resistance that is produced by various drug resistance mechanisms. In this review, we discuss: 1) molecular mechanisms of sunitinib resistance; 2) strategies to overcome sunitinib resistance and 3) potential predictive biomarkers of sunitinib resistance.
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Affiliation(s)
- Juan Jin
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310003, China
| | - Yuhao Xie
- Institute for Biotechnology, St. John's University, Queens, NY 11439, USA; Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Jin-Shi Zhang
- Urology & Nephrology Center, Department of Nephrology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Shi-Jie Dai
- Zhejiang Eyoung Pharmaceutical Research and Development Center, Hangzhou, Zhejiang 311258, China
| | - Wen-Fang He
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310003, China
| | - Shou-Ye Li
- Zhejiang Eyoung Pharmaceutical Research and Development Center, Hangzhou, Zhejiang 311258, China
| | - Charles R Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Zhe-Sheng Chen
- Institute for Biotechnology, St. John's University, Queens, NY 11439, USA; Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA.
| | - Qiang He
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310003, China.
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24
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Zhang Y, Chen F, Creighton CJ. Pan-cancer molecular subtypes of metastasis reveal distinct and evolving transcriptional programs. Cell Rep Med 2023; 4:100932. [PMID: 36731467 PMCID: PMC9975284 DOI: 10.1016/j.xcrm.2023.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/22/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023]
Abstract
Molecular mechanisms underlying cancer metastasis span diverse tissues of origin. Here, we synthesize and collate the transcriptomes of patient-derived xenografts and patient tumor metastases, and these data collectively represent 38 studies and over 3,000 patients and 4,000 tumors. We identify four expression-based subtypes of metastasis transcending tumor lineage. The first subtype has extensive copy alterations, higher expression of MYC transcriptional targets and DNA repair genes, and bromodomain inhibitor response association. The second subtype has higher expression of genes involving metabolism and prostaglandin synthesis and regulation. The third subtype has evidence of neuronal differentiation, higher expression of DNA and histone methylation genes and EZH2 transcriptional targets, and BCL2 inhibitor response association. The fourth subtype has higher expression of immune checkpoint and Notch pathway genes. The metastasis subtypes reflect expression differences from paired primaries, with subtype switching being common. These subtypes facilitate understanding of the molecular underpinnings of metastases beyond tissue-oriented domains, with therapeutic implications.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS305, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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25
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Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun 2023; 14:346. [PMID: 36681680 PMCID: PMC9867739 DOI: 10.1038/s41467-023-35833-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
While the mutational and transcriptional landscapes of renal cell carcinoma (RCC) are well-known, the epigenome is poorly understood. We characterize the epigenome of clear cell (ccRCC), papillary (pRCC), and chromophobe RCC (chRCC) by using ChIP-seq, ATAC-Seq, RNA-seq, and SNP arrays. We integrate 153 individual data sets from 42 patients and nominate 50 histology-specific master transcription factors (MTF) to define RCC histologic subtypes, including EPAS1 and ETS-1 in ccRCC, HNF1B in pRCC, and FOXI1 in chRCC. We confirm histology-specific MTFs via immunohistochemistry including a ccRCC-specific TF, BHLHE41. FOXI1 overexpression with knock-down of EPAS1 in the 786-O ccRCC cell line induces transcriptional upregulation of chRCC-specific genes, TFCP2L1, ATP6V0D2, KIT, and INSRR, implicating FOXI1 as a MTF for chRCC. Integrating RCC GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data reveals that risk-variants are significantly enriched in allelically-imbalanced peaks. This epigenomic atlas in primary human samples provides a resource for future investigation.
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Affiliation(s)
- Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan C Baca
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elio Adib
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Talal El Zarif
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - David A Braun
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Heng Du
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Abdallah Flaifel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michel Alchoueiry
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sayed G Matar
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Andres Acosta
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yue Hou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jacob E Berchuck
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elizabeth Henske
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Toni K Choueiri
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
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26
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Copper Death Inducer, FDX1, as a Prognostic Biomarker Reshaping Tumor Immunity in Clear Cell Renal Cell Carcinoma. Cells 2023; 12:cells12030349. [PMID: 36766692 PMCID: PMC9913648 DOI: 10.3390/cells12030349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Progress in the diagnosis and treatment of clear cell renal cell carcinoma (ccRCC) has significantly prolonged patient survival. However, ccRCC displays an extreme heterogenous characteristic and metastatic tendency, which limit the benefit of targeted or immune therapy. Thus, identifying novel biomarkers and therapeutic targets for ccRCC is of great importance. METHOD Pan cancer datasets, including the expression profile, DNA methylation, copy number variation, and single nucleic variation, were introduced to decode the aberrance of copper death regulators (CDRs). Then, FDX1 was systematically analyzed in ccRCC to evaluate its impact on clinical characteristics, prognosis, biological function, immune infiltration, and therapy response. Finally, in vivo experiments were utilized to decipher FDX1 in ccRCC malignancy and its role in tumor immunity. RESULT Copper death regulators were identified at the pancancer level, especially in ccRCC. FDX1 played a protective role in ccRCC, and its expression level was significantly decreased in tumor tissues, which might be regulated via CNV events. At the molecular mechanism level, FDX1 positively regulated fatty acid metabolism and oxidative phosphorylation. In addition, FDX1 overexpression restrained ccRCC cell line malignancy and enhanced tumor immunity by increasing the secretion levels of IL2 and TNFγ. CONCLUSIONS Our research illustrated the role of FDX1 in ccRCC patients' clinical outcomes and its impact on tumor immunity, which could be treated as a promising target for ccRCC patients.
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27
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Renal Carcinoma and Angiogenesis: Therapeutic Target and Biomarkers of Response in Current Therapies. Cancers (Basel) 2022; 14:cancers14246167. [PMID: 36551652 PMCID: PMC9776425 DOI: 10.3390/cancers14246167] [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: 10/27/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Due to the aberrant hypervascularization and the high immune infiltration of renal tumours, current therapeutic regimens of renal cell carcinoma (RCC) target angiogenic or immunosuppressive pathways or both. Tumour angiogenesis plays an essential role in tumour growth and immunosuppression. Indeed, the aberrant vasculature promotes hypoxia and can also exert immunosuppressive functions. In addition, pro-angiogenic factors, including VEGF-A, have an immunosuppressive action on immune cells. Despite the progress of treatments in RCC, there are still non responders or acquired resistance. Currently, no biomarkers are used in clinical practice to guide the choice between the different available treatments. Considering the role of angiogenesis in RCC, angiogenesis-related markers are interesting candidates. They have been studied in the response to antiangiogenic drugs (AA) and show interest in predicting the response. They have been less studied in immunotherapy alone or combined with AA. In this review, we will discuss the role of angiogenesis in tumour growth and immune escape and the place of angiogenesis-targeted biomarkers to predict response to current therapies in RCC.
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28
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Creighton CJ. Clinical proteomics towards multiomics in cancer. MASS SPECTROMETRY REVIEWS 2022:e21827. [PMID: 36495097 DOI: 10.1002/mas.21827] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent technological advancements in mass spectrometry (MS)-based proteomics technologies have accelerated its application to study greater and greater numbers of human tumor specimens. Over the last several years, the Clinical Proteomic Tumor Analysis Consortium, the International Cancer Proteogenome Consortium, and others have generated MS-based proteomic profiling data combined with corresponding multiomics data on thousands of human tumors to date. Proteomic data sets in the public domain can be re-examined by other researchers with different questions in mind from what the original studies explored. In this review, we examine the increasing role of proteomics in studying cancer, along with the potential for previous studies and their associated data sets to contribute to improving the diagnosis and treatment of cancer in the clinical setting. We also explore publicly available proteomics and multi-omics data from cancer cell line models to show how such data may aid in identifying therapeutic strategies for cancer subsets.
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Affiliation(s)
- Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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29
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Taylor AS, Skala SL. Tumors masquerading as type 2 papillary renal cell carcinoma: pathologists' ever-expanding differential diagnosis for a heterogeneous group of entities. Urol Oncol 2022; 40:499-511. [PMID: 34116938 DOI: 10.1016/j.urolonc.2021.04.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/22/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
Although papillary renal cell carcinoma has historically been classified as either type 1 or type 2, data from The Cancer Genome Atlas (TCGA) has demonstrated significant genomic heterogeneity in tumors classified as "type 2 papillary renal cell carcinoma" (T2PRCC). Papillary renal cell carcinoma is expected to have a favorable clinical course compared to clear cell renal cell carcinoma (CCRCC). However, tumors with poor outcome more similar to CCRCC were included in the T2PRCC cohort studied by the TCGA. The differential diagnosis for T2PRCC includes a variety of other renal tumors, including aggressive entities such as TFE3 translocation-associated renal cell carcinoma, TFEB-amplified renal cell carcinoma, fumarate hydratase-deficient renal cell carcinoma, high-grade CCRCC, and collecting duct carcinoma. Accurate classification of these tumors is important for prognostication and selection of therapy.
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Affiliation(s)
- Alexander S Taylor
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Stephanie L Skala
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI.
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30
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Valcarcel-Jimenez L, Rogerson C, Yong C, Schmidt C, Yang M, Cremades-Rodelgo M, Harle V, Offord V, Wong K, Mora A, Speed A, Caraffini V, Tran MGB, Maher ER, Stewart GD, Vanharanta S, Adams DJ, Frezza C. HIRA loss transforms FH-deficient cells. SCIENCE ADVANCES 2022; 8:eabq8297. [PMID: 36269833 PMCID: PMC9586478 DOI: 10.1126/sciadv.abq8297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/31/2022] [Indexed: 05/03/2023]
Abstract
Fumarate hydratase (FH) is a mitochondrial enzyme that catalyzes the reversible hydration of fumarate to malate in the tricarboxylic acid (TCA) cycle. Germline mutations of FH lead to hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a cancer syndrome characterized by a highly aggressive form of renal cancer. Although HLRCC tumors metastasize rapidly, FH-deficient mice develop premalignant cysts in the kidneys, rather than carcinomas. How Fh1-deficient cells overcome these tumor-suppressive events during transformation is unknown. Here, we perform a genome-wide CRISPR-Cas9 screen to identify genes that, when ablated, enhance the proliferation of Fh1-deficient cells. We found that the depletion of the histone cell cycle regulator (HIRA) enhances proliferation and invasion of Fh1-deficient cells in vitro and in vivo. Mechanistically, Hira loss activates MYC and its target genes, increasing nucleotide metabolism specifically in Fh1-deficient cells, independent of its histone chaperone activity. These results are instrumental for understanding mechanisms of tumorigenesis in HLRCC and the development of targeted treatments for patients.
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Affiliation(s)
- Lorea Valcarcel-Jimenez
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Connor Rogerson
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Cissy Yong
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christina Schmidt
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Ming Yang
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Monica Cremades-Rodelgo
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Victoria Harle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kim Wong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ariane Mora
- School of Chemistry and Molecular Biosciences, University of Queensland, Molecular Biosciences Building 76, St. Lucia, QLD 4072, Australia
| | - Alyson Speed
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Veronica Caraffini
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Maxine Gia Binh Tran
- UCL Division of Surgery and Interventional Science, Specialist Centre for Kidney Cancer, Royal Free Hospital, Pond Street, London NW3 2QG, UK
| | - Eamonn R. Maher
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sakari Vanharanta
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- Translational Cancer Medicine Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - David J. Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Christian Frezza
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
- CECAD Research Centre, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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Brech D, Herbstritt AS, Diederich S, Straub T, Kokolakis E, Irmler M, Beckers J, Büttner FA, Schaeffeler E, Winter S, Schwab M, Nelson PJ, Noessner E. Dendritic Cells or Macrophages? The Microenvironment of Human Clear Cell Renal Cell Carcinoma Imprints a Mosaic Myeloid Subtype Associated with Patient Survival. Cells 2022; 11:3289. [PMID: 36291154 PMCID: PMC9600747 DOI: 10.3390/cells11203289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 09/29/2023] Open
Abstract
Since their initial description by Elie Metchnikoff, phagocytes have sparked interest in a variety of biologic disciplines. These important cells perform central functions in tissue repair and immune activation as well as tolerance. Myeloid cells can be immunoinhibitory, particularly in the tumor microenvironment, where their presence is generally associated with poor patient prognosis. These cells are highly adaptable and plastic, and can be modulated to perform desired functions such as antitumor activity, if key programming molecules can be identified. Human clear cell renal cell carcinoma (ccRCC) is considered immunogenic; yet checkpoint blockades that target T cell dysfunction have shown limited clinical efficacy, suggesting additional layers of immunoinhibition. We previously described "enriched-in-renal cell carcinoma" (erc) DCs that were often found in tight contact with dysfunctional T cells. Using transcriptional profiling and flow cytometry, we describe here that ercDCs represent a mosaic cell type within the macrophage continuum co-expressing M1 and M2 markers. The polarization state reflects tissue-specific signals that are characteristic of RCC and renal tissue homeostasis. ErcDCs are tissue-resident with increasing prevalence related to tumor grade. Accordingly, a high ercDC score predicted poor patient survival. Within the profile, therapeutic targets (VSIG4, NRP1, GPNMB) were identified with promise to improve immunotherapy.
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Affiliation(s)
- Dorothee Brech
- Immunoanalytics/Tissue Control of Immunocytes, Helmholtz Zentrum München, 81377 Munich, Germany
| | - Anna S. Herbstritt
- Immunoanalytics/Tissue Control of Immunocytes, Helmholtz Zentrum München, 81377 Munich, Germany
| | - Sarah Diederich
- Immunoanalytics/Tissue Control of Immunocytes, Helmholtz Zentrum München, 81377 Munich, Germany
| | - Tobias Straub
- Bioinformatics Core Unit, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg, Germany
| | - Evangelos Kokolakis
- Immunoanalytics/Tissue Control of Immunocytes, Helmholtz Zentrum München, 81377 Munich, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Chair of Experimental Genetics, Technical University of Munich, 85354 Freising, Germany
| | - Florian A. Büttner
- Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tuebingen, 72074 Tuebingen, Germany
| | - Elke Schaeffeler
- Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tuebingen, 72074 Tuebingen, Germany
| | - Stefan Winter
- Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tuebingen, 72074 Tuebingen, Germany
| | - Matthias Schwab
- Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tuebingen, 72074 Tuebingen, Germany
- Department of Clinical Pharmacology, University of Tuebingen, 72074 Tuebingen, Germany
- Department of Pharmacy and Biochemistry, University of Tuebingen, 72074 Tuebingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tuebingen, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Peter J. Nelson
- Medizinische Klinik und Poliklinik IV, University of Munich, 80336 Munich, Germany
| | - Elfriede Noessner
- Immunoanalytics/Tissue Control of Immunocytes, Helmholtz Zentrum München, 81377 Munich, Germany
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Raghubar AM, Roberts MJ, Wood S, Healy HG, Kassianos AJ, Mallett AJ. Cellular milieu in clear cell renal cell carcinoma. Front Oncol 2022; 12:943583. [PMID: 36313721 PMCID: PMC9614096 DOI: 10.3389/fonc.2022.943583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is globally the most prevalent renal cancer. The cells of origin in ccRCC have been identified as proximal tubular epithelial cells (PTEC); however, the transcriptomic pathways resulting in the transition from normal to malignant PTEC state have remained unclear. Immunotherapy targeting checkpoints have revolutionized the management of ccRCC, but a sustained clinical response is achieved in only a minority of ccRCC patients. This indicates that our understanding of the mechanisms involved in the malignant transition and resistance to immune checkpoint therapy in ccRCC is unclear. This review examines recent single-cell transcriptomics studies of ccRCC to clarify the transition of PTEC in ccRCC development, and the immune cell types, states, and interactions that may limit the response to targeted immune therapy, and finally suggests stromal cells as key drivers in recurrent and locally invasive ccRCC. These and future single-cell transcriptomics studies will continue to clarify the cellular milieu in the ccRCC microenvironment, thus defining actional clinical, therapeutic, and prognostic characteristics of ccRCC.
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Affiliation(s)
- Arti M. Raghubar
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Matthew J. Roberts
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Department of Urology, Royal Brisbane and Women’s Hospital, Brisbane, QLD, Australia
- Department of Urology, Redcliffe Hospital, Redcliffe, QLD, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Simon Wood
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Department of Urology, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Helen G. Healy
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Andrew J. Kassianos
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Andrew J. Mallett
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- College of Medicine & Dentistry, James Cook University, Townsville, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- *Correspondence: Andrew J. Mallett,
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Chang A, Chakiryan NH, Du D, Stewart PA, Zhang Y, Tian Y, Soupir AC, Bowers K, Fang B, Morganti A, Teer JK, Kim Y, Spiess PE, Chahoud J, Noble JD, Putney RM, Berglund AE, Robinson TJ, Koomen JM, Wang L, Manley BJ. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. Eur Urol 2022; 82:354-362. [PMID: 35718636 PMCID: PMC11075093 DOI: 10.1016/j.eururo.2022.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/24/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Alternative mRNA splicing can be dysregulated in cancer, resulting in the generation of aberrant splice variants (SVs). Given the paucity of actionable genomic mutations in clear cell renal cell carcinoma (ccRCC), aberrant SVs may be an avenue to novel mechanisms of pathogenesis. OBJECTIVE To identify and characterize aberrant SVs enriched in ccRCC. DESIGN, SETTING, AND PARTICIPANTS Using RNA-seq data from the Cancer Cell Line Encyclopedia, we identified neojunctions uniquely expressed in ccRCC. Candidate SVs were then checked for expression across normal tissue in the Genotype-Tissue Expression Project and primary tumor tissue from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and our institutional Total Cancer Care database. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Clinicopathologic, genomic, and survival data were available for all cohorts. Epigenetic data were available for the TCGA and CPTAC cohorts. Proteomic data were available for the CPTAC cohort. The association of aberrant SV expression with these variables was examined using the Kruskal-Wallis test, pairwise t test, Spearman correlation test, and Cox regression analysis. RESULTS AND LIMITATIONS Our pipeline identified 16 ccRCC-enriched SVs. EGFR, HPCAL1-SV and RNASET2-SV expression was negatively correlated with gene-specific CpG methylation. We derived a survival risk score based primarily on the expression of five SVs (RNASET2, FGD1, PDZD2, COBLL1, and PTPN14), which was consistent and applicable across multiple cohorts on multivariate analysis. The splicing factor RBM4, which modulates splicing of HIF-1α, exhibited significantly lower expression at the protein level in the high-risk group, as defined by our SV-based score. CONCLUSIONS We describe 16 aberrant SVs enriched in ccRCC, many of which are associated with disease biology and/or clinical outcomes. This study provides a novel strategy for identifying and characterizing disease-specific aberrant SVs. PATIENT SUMMARY We describe a method to identify disease targets and biomarkers using transcriptomic analysis beyond somatic mutations or gene expression. Kidney tumors express unique splice variants that may provide additional prognostic information following surgery.
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Affiliation(s)
- Andrew Chang
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
| | - Nicholas H Chakiryan
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Dongliang Du
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Yonghong Zhang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Yijun Tian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alex C Soupir
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kiah Bowers
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Bin Fang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ashley Morganti
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Philippe E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jad Chahoud
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jerald D Noble
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Radiation Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ryan M Putney
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Timothy J Robinson
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Brandon J Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
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Rossi SH, Newsham I, Pita S, Brennan K, Park G, Smith CG, Lach RP, Mitchell T, Huang J, Babbage A, Warren AY, Leppert JT, Stewart GD, Gevaert O, Massie CE, Samarajiwa SA. Accurate detection of benign and malignant renal tumor subtypes with MethylBoostER: An epigenetic marker-driven learning framework. SCIENCE ADVANCES 2022; 8:eabn9828. [PMID: 36170366 PMCID: PMC9519038 DOI: 10.1126/sciadv.abn9828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Current gold standard diagnostic strategies are unable to accurately differentiate malignant from benign small renal masses preoperatively; consequently, 20% of patients undergo unnecessary surgery. Devising a more confident presurgical diagnosis is key to improving treatment decision-making. We therefore developed MethylBoostER, a machine learning model leveraging DNA methylation data from 1228 tissue samples, to classify pathological subtypes of renal tumors (benign oncocytoma, clear cell, papillary, and chromophobe RCC) and normal kidney. The prediction accuracy in the testing set was 0.960, with class-wise ROC AUCs >0.988 for all classes. External validation was performed on >500 samples from four independent datasets, achieving AUCs >0.89 for all classes and average accuracies of 0.824, 0.703, 0.875, and 0.894 for the four datasets. Furthermore, consistent classification of multiregion samples (N = 185) from the same patient demonstrates that methylation heterogeneity does not limit model applicability. Following further clinical studies, MethylBoostER could facilitate a more confident presurgical diagnosis to guide treatment decision-making in the future.
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Affiliation(s)
- Sabrina H. Rossi
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Izzy Newsham
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Sara Pita
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Kevin Brennan
- Stanford Centre for Biomedical Informatics Research, Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Gahee Park
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Christopher G. Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Centre, Cambridge, UK
| | - Radoslaw P. Lach
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas Mitchell
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Junfan Huang
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Babbage
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Y. Warren
- Department of Histopathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - John T. Leppert
- Department of Urology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Urology Surgical Service, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - Olivier Gevaert
- Stanford Centre for Biomedical Informatics Research, Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Charles E. Massie
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Shamith A. Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
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Büttner FA, Winter S, Stühler V, Rausch S, Hennenlotter J, Füssel S, Zastrow S, Meinhardt M, Toma M, Jerónimo C, Henrique R, Miranda-Gonçalves V, Kröger N, Ribback S, Hartmann A, Agaimy A, Stöhr C, Polifka I, Fend F, Scharpf M, Comperat E, Wasinger G, Moch H, Stenzl A, Gerlinger M, Bedke J, Schwab M, Schaeffeler E. A novel molecular signature identifies mixed subtypes in renal cell carcinoma with poor prognosis and independent response to immunotherapy. Genome Med 2022; 14:105. [PMID: 36109798 PMCID: PMC9476269 DOI: 10.1186/s13073-022-01105-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/10/2022] [Indexed: 12/30/2022] Open
Abstract
Background Renal cell carcinoma (RCC) is a heterogeneous disease comprising histologically defined subtypes. For therapy selection, precise subtype identification and individualized prognosis are mandatory, but currently limited. Our aim was to refine subtyping and outcome prediction across main subtypes, assuming that a tumor is composed of molecular features present in distinct pathological subtypes. Methods Individual RCC samples were modeled as linear combination of the main subtypes (clear cell (ccRCC), papillary (pRCC), chromophobe (chRCC)) using computational gene expression deconvolution. The new molecular subtyping was compared with histological classification of RCC using the Cancer Genome Atlas (TCGA) cohort (n = 864; ccRCC: 512; pRCC: 287; chRCC: 65) as well as 92 independent histopathologically well-characterized RCC. Predicted continuous subtypes were correlated to cancer-specific survival (CSS) in the TCGA cohort and validated in 242 independent RCC. Association with treatment-related progression-free survival (PFS) was studied in the JAVELIN Renal 101 (n = 726) and IMmotion151 trials (n = 823). CSS and PFS were analyzed using the Kaplan–Meier and Cox regression analysis. Results One hundred seventy-four signature genes enabled reference-free molecular classification of individual RCC. We unambiguously assign tumors to either ccRCC, pRCC, or chRCC and uncover molecularly heterogeneous tumors (e.g., with ccRCC and pRCC features), which are at risk of worse outcome. Assigned proportions of molecular subtype-features significantly correlated with CSS (ccRCC (P = 4.1E − 10), pRCC (P = 6.5E − 10), chRCC (P = 8.6E − 06)) in TCGA. Translation into a numerical RCC-R(isk) score enabled prognosis in TCGA (P = 9.5E − 11). Survival modeling based on the RCC-R score compared to pathological categories was significantly improved (P = 3.6E − 11). The RCC-R score was validated in univariate (P = 3.2E − 05; HR = 3.02, 95% CI: 1.8–5.08) and multivariate analyses including clinicopathological factors (P = 0.018; HR = 2.14, 95% CI: 1.14–4.04). Heterogeneous PD-L1-positive RCC determined by molecular subtyping showed increased PFS with checkpoint inhibition versus sunitinib in the JAVELIN Renal 101 (P = 3.3E − 04; HR = 0.52, 95% CI: 0.36 − 0.75) and IMmotion151 trials (P = 0.047; HR = 0.69, 95% CI: 0.48 − 1). The prediction of PFS significantly benefits from classification into heterogeneous and unambiguous subtypes in both cohorts (P = 0.013 and P = 0.032). Conclusion Switching from categorical to continuous subtype classification across most frequent RCC subtypes enables outcome prediction and fosters personalized treatment strategies.
Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01105-y.
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36
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Xu Y, Morales AJ, Towlerton AMH, Akilesh S, Miller CP, Tykodi SS, Warren EH. Integrated TCR repertoire analysis and single-cell transcriptomic profiling of tumor-infiltrating T cells in renal cell carcinoma identifies shared and tumor-restricted expanded clones with unique phenotypes. Front Oncol 2022; 12:952252. [PMID: 36185254 PMCID: PMC9515957 DOI: 10.3389/fonc.2022.952252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Objective responses of metastatic renal cell carcinoma (RCC) associated with systemic immunotherapies suggest the potential for T-cell-mediated tumor clearance. Recent analyses associate clonally expanded T cells present in the tumor at diagnosis with responses to immune checkpoint inhibitors (ICIs). To identify and further characterize tumor-associated, clonally expanded T cells, we characterized the density, spatial distribution, T-cell receptor (TCR) repertoire, and transcriptome of tumor-infiltrating T cells from 14 renal tumors at the time of resection and compared them with T cells in peripheral blood and normal adjacent kidney. Multiplex immunohistochemistry revealed that T-cell density was higher in clear cell RCC (ccRCC) than in other renal tumor histologies with spatially nonuniform T-cell hotspots and exclusion zones. TCR repertoire analysis also revealed increased clonal expansion in ccRCC tumors compared with non-clear cell histologies or normal tissues. Expanded T-cell clones were most frequently CD8+ with some detectable in peripheral blood or normal kidney and others found exclusively within the tumor. Divergent expression profiles for chemokine receptors and ligands and the Ki67 proliferation marker distinguished tumor-restricted T-cell clones from those also present in blood suggesting a distinct phenotype for subsets of clonally expanded T cells that also differed for upregulated markers of T-cell activation and exhaustion. Thus, our single-cell level stratification of clonally expanded tumor infiltrating T-cell subpopulations provides a framework for further analysis. Future studies will address the spatial orientation of these clonal subsets within tumors and their association with treatment outcomes for ICIs or other therapeutic modalities.
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Affiliation(s)
- Yuexin Xu
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- *Correspondence: Yuexin Xu,
| | - Alicia J. Morales
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | | | - Shreeram Akilesh
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Chris P. Miller
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Scott S. Tykodi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Medicine, Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, United States
| | - Edus H. Warren
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Department of Medicine, Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, United States
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37
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Dong Y, Song N, Wang J, Shi L, Zhang Z, Du J. Driver Gene Alterations in Malignant Progression of Gastric Cancer. Front Oncol 2022; 12:920207. [PMID: 35903675 PMCID: PMC9315095 DOI: 10.3389/fonc.2022.920207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
The identification of driver genes is of great importance in modern medical research. It is also an essential factor in the development of individualization and has a positive effect on understanding the causes of cancer. Gene mutations are the primary cause of the outcomes of the process of tumorigenesis. Driver genes can be used as therapeutic targets for tumor-specific mutation-dependent overexpression. This study sought to identify mutation-based driver genes in gastric cancer (GC) by applying comprehensive gene expression and copy number analysis. Multiplatform analysis was used to identify four major genomic subtypes of GC. The most prominent cancer-related variations observed in this cohort were TTN mutations (found in 56% of tumors), followed by TP53 (51%), MUC16 (7%), and LRP1B (6%) mutations. In our analysis, mutation characteristics were mainly related to the DNA mismatch repair system. In addition, 34 candidate driver oncogenes were identified in GC. Further research identified six GC-related driver genes associated with the levels of immune infiltration of different immune cells and the majority of immune markers. Our mutation-based study of driver oncogenes identified potential drug targets in GC.
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Affiliation(s)
| | | | | | | | | | - Jianjun Du
- *Correspondence: Ziqiang Zhang, ; Jianjun Du,
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38
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Jamadar A, Dwivedi N, Mathew S, Calvet JP, Thomas SM, Rao R. Vasopressin Receptor Type-2 Mediated Signaling in Renal Cell Carcinoma Stimulates Stromal Fibroblast Activation. Int J Mol Sci 2022; 23:7601. [PMID: 35886951 PMCID: PMC9325308 DOI: 10.3390/ijms23147601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023] Open
Abstract
Vasopressin type-2 receptor (V2R) is ectopically expressed and plays a pathogenic role in clear cell renal cell carcinoma (ccRCC) tumor cells. Here we examined how V2R signaling within human ccRCC tumor cells (Caki1 cells) stimulates stromal cancer-associated fibroblasts (CAFs). We found that cell culture conditioned media from Caki1 cells increased activation, migration, and proliferation of fibroblasts in vitro, which was inhibited by V2R gene silencing in Caki1 cells. Analysis of the conditioned media and mRNA of the V2R gene silenced and control Caki1 cells showed that V2R regulates the production of CAF-activating factors. Some of these factors were also found to be regulated by YAP in these Caki1 cells. YAP expression colocalized and correlated with V2R expression in ccRCC tumor tissue. V2R gene silencing or V2R antagonist significantly reduced YAP in Caki1 cells. Moreover, the V2R antagonist reduced YAP expression and myofibroblasts in mouse xenograft tumors. These results suggest that V2R plays an important role in secreting pro-fibrotic factors that stimulate fibroblast activation by a YAP-dependent mechanism in ccRCC tumors. Our results demonstrate a novel role for the V2R-YAP axis in the regulation of myofibroblasts in ccRCC and a potential therapeutic target.
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Affiliation(s)
- Abeda Jamadar
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA; (A.J.); (N.D.); (J.P.C.)
| | - Nidhi Dwivedi
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA; (A.J.); (N.D.); (J.P.C.)
| | - Sijo Mathew
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, Fargo, ND 58105, USA;
| | - James P. Calvet
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA; (A.J.); (N.D.); (J.P.C.)
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sufi M. Thomas
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Reena Rao
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA; (A.J.); (N.D.); (J.P.C.)
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Medicine, 5040 WHE, The Jared Grantham Kidney Institute, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
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39
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Dwyer DB, Buciuman MO, Ruef A, Kambeitz J, Sen Dong M, Stinson C, Kambeitz-Ilankovic L, Degenhardt F, Sanfelici R, Antonucci LA, Lalousis PA, Wenzel J, Urquijo-Castro MF, Popovic D, Oeztuerk OF, Haas SS, Weiske J, Hauke D, Neufang S, Schmidt-Kraepelin C, Ruhrmann S, Penzel N, Lichtenstein T, Rosen M, Chisholm K, Riecher-Rössler A, Egloff L, Schmidt A, Andreou C, Hietala J, Schirmer T, Romer G, Michel C, Rössler W, Maj C, Borisov O, Krawitz PM, Falkai P, Pantelis C, Lencer R, Bertolino A, Borgwardt S, Noethen M, Brambilla P, Schultze-Lutter F, Meisenzahl E, Wood SJ, Davatzikos C, Upthegrove R, Salokangas RKR, Koutsouleris N. Clinical, Brain, and Multilevel Clustering in Early Psychosis and Affective Stages. JAMA Psychiatry 2022; 79:677-689. [PMID: 35583903 PMCID: PMC9118078 DOI: 10.1001/jamapsychiatry.2022.1163] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Importance Approaches are needed to stratify individuals in early psychosis stages beyond positive symptom severity to investigate specificity related to affective and normative variation and to validate solutions with premorbid, longitudinal, and genetic risk measures. Objective To use machine learning techniques to cluster, compare, and combine subgroup solutions using clinical and brain structural imaging data from early psychosis and depression stages. Design, Setting, and Participants A multisite, naturalistic, longitudinal cohort study (10 sites in 5 European countries; including major follow-up intervals at 9 and 18 months) with a referred patient sample of those with clinical high risk for psychosis (CHR-P), recent-onset psychosis (ROP), recent-onset depression (ROD), and healthy controls were recruited between February 1, 2014, to July 1, 2019. Data were analyzed between January 2020 and January 2022. Main Outcomes and Measures A nonnegative matrix factorization technique separately decomposed clinical (287 variables) and parcellated brain structural volume (204 gray, white, and cerebrospinal fluid regions) data across CHR-P, ROP, ROD, and healthy controls study groups. Stability criteria determined cluster number using nested cross-validation. Validation targets were compared across subgroup solutions (premorbid, longitudinal, and schizophrenia polygenic risk scores). Multiclass supervised machine learning produced a transferable solution to the validation sample. Results There were a total of 749 individuals in the discovery group and 610 individuals in the validation group. Individuals included those with CHR-P (n = 287), ROP (n = 323), ROD (n = 285), and healthy controls (n = 464), The mean (SD) age was 25.1 (5.9) years, and 702 (51.7%) were female. A clinical 4-dimensional solution separated individuals based on positive symptoms, negative symptoms, depression, and functioning, demonstrating associations with all validation targets. Brain clustering revealed a subgroup with distributed brain volume reductions associated with negative symptoms, reduced performance IQ, and increased schizophrenia polygenic risk scores. Multilevel results distinguished between normative and illness-related brain differences. Subgroup results were largely validated in the external sample. Conclusions and Relevance The results of this longitudinal cohort study provide stratifications beyond the expression of positive symptoms that cut across illness stages and diagnoses. Clinical results suggest the importance of negative symptoms, depression, and functioning. Brain results suggest substantial overlap across illness stages and normative variation, which may highlight a vulnerability signature independent from specific presentations. Premorbid, longitudinal, and genetic risk validation suggested clinical importance of the subgroups to preventive treatments.
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Affiliation(s)
- Dominic B Dwyer
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Centre for Youth Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Madalina-Octavia Buciuman
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,International Max-Planck Research School for Translational Psychiatry, Munich, Germany
| | - Anne Ruef
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Joseph Kambeitz
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Mark Sen Dong
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Caedyn Stinson
- Max-Planck School of Cognition, Leipzig, Germany.,Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Lana Kambeitz-Ilankovic
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.,Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Rachele Sanfelici
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Max-Planck Institute of Psychiatry, Munich, Germany
| | - Linda A Antonucci
- Department of Education, Psychology, Communication, University of Bari Aldo Moro, Bari, Italy
| | - Paris Alexandros Lalousis
- Institute for Mental Health and Centre for Brain Health, University of Birmingham, Birmingham, United Kingdom
| | - Julian Wenzel
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | | | - David Popovic
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,International Max-Planck Research School for Translational Psychiatry, Munich, Germany
| | - Oemer Faruk Oeztuerk
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,International Max-Planck Research School for Translational Psychiatry, Munich, Germany
| | - Shalaila S Haas
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Johanna Weiske
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany
| | - Daniel Hauke
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland.,Early Intervention Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom.,Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Susanne Neufang
- Department of Psychiatry and Psychotherapy, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Stephan Ruhrmann
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Nora Penzel
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Theresa Lichtenstein
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Marlene Rosen
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Katharine Chisholm
- Institute for Mental Health and Centre for Brain Health, University of Birmingham, Birmingham, United Kingdom.,Department of Psychology, Aston University, Birmingham, United Kingdom
| | | | - Laura Egloff
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland
| | - André Schmidt
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland
| | - Christina Andreou
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland
| | - Jarmo Hietala
- Department of Psychiatry, University of Turku, Turku, Finland
| | - Timo Schirmer
- GE Healthcare GmbH (previously GE Global Research GmbH), Munich, Germany
| | - Georg Romer
- Department of Child and Adolescent Psychiatry, University of Münster, Münster, Germany
| | - Chantal Michel
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland
| | - Wulf Rössler
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry Zurich, Zurich, Switzerland
| | - Carlo Maj
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Max-Planck Institute of Psychiatry, Munich, Germany
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, University of Melbourne & Melbourne Health, Melbourne, Victoria, Australia
| | - Rebekka Lencer
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany.,Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Alessandro Bertolino
- Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Stefan Borgwardt
- Department of Psychiatry (Psychiatric University Hospital, UPK), University of Basel, Basel, Switzerland.,Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Markus Noethen
- Institute of Human Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Paolo Brambilla
- Department of Neurosciences and Mental Health, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Frauke Schultze-Lutter
- Department of Psychiatry and Psychotherapy, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany.,University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland.,Department of Psychology, Faculty of Psychology, Airlangga University, Surabaya, Indonesia
| | | | - Stephen J Wood
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Victoria, Australia.,Orygen, the National Centre of Excellence for Youth Mental Health, Melbourne, Victoria, Australia
| | - Christos Davatzikos
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Rachel Upthegrove
- Institute for Mental Health and Centre for Brain Health, University of Birmingham, Birmingham, United Kingdom.,Early Intervention Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | | | - Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University, Munich, Germany.,Max-Planck Institute of Psychiatry, Munich, Germany.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
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40
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Jikuya R, Murakami K, Nishiyama A, Kato I, Furuya M, Nakabayashi J, Ramilowski JA, Hamanoue H, Maejima K, Fujita M, Mitome T, Ohtake S, Noguchi G, Kawaura S, Odaka H, Kawahara T, Komeya M, Shinoki R, Ueno D, Ito H, Ito Y, Muraoka K, Hayashi N, Kondo K, Nakaigawa N, Hatano K, Baba M, Suda T, Kodama T, Fujii S, Makiyama K, Yao M, Shuch BM, Schmidt LS, Linehan WM, Nakagawa H, Tamura T, Hasumi H. Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers. iScience 2022; 25:104463. [PMID: 35874919 PMCID: PMC9301876 DOI: 10.1016/j.isci.2022.104463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/05/2022] [Accepted: 05/17/2022] [Indexed: 11/26/2022] Open
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41
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Wang H, Wang X, Xu L, Zhang J. PBX1, EMCN and ERG are associated with the sub-clusters and the prognosis of VHL mutant clear cell renal cell carcinoma. Sci Rep 2022; 12:8955. [PMID: 35624190 PMCID: PMC9142578 DOI: 10.1038/s41598-022-13148-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 05/20/2022] [Indexed: 12/30/2022] Open
Abstract
The molecular heterogeneity of primary clear cell renal cell carcinoma (ccRCC) has been reported. However, the classifications of Von Hippel-Lindau (VHL) mutant ccRCC are unclear. Here, VHL mutant ccRCC from The Cancer Genome Atlas and E-MTAB-1980 datasets were divided into two sub-clusters through non-negative matrix factorization algorithm. Most VHL mutant ccRCC patients in sub-cluster2 were with pathological T1 stage and VHL mutant ccRCC patients in sub-cluster1 were with decreased overall survival. DNA replication and homologous recombination scores were higher, while, WNT signaling pathway and regulation of autophagy scores were lower in sub-cluster1 VHL mutant ccRCC. Moreover, PBX1 transcriptional scores and mRNA expressions were lower in sub-cluster1 VHL mutant ccRCC patients and were associated with the overall survival of VHL mutant ccRCC. Furthermore, PBX1 associated genes EMCN and ERG were down-regulated in sub-cluster1 VHL mutant ccRCC and overall survival was decreased in EMCN or ERG lowly expressed VHL mutant ccRCC patients. Also, PBX1 and EMCN were down-regulated in ccRCC tissues, compared with normal kidney tissues. At last, we constructed risk models based on PBX1, EMCN and EGR expression features. With the increase of the risk score, the number of death of VHL mutant ccRCC patients was increased.
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Affiliation(s)
- Haiwei Wang
- Fujian Maternity and Child Health Hospital, Fujian Medical University, Fuzhou, Fujian, China.
| | - Xinrui Wang
- Fujian Maternity and Child Health Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Ji Zhang
- Shanghai Institute of Hematology, Rui-Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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42
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Zhang Y, Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. Nat Commun 2022; 13:2669. [PMID: 35562349 PMCID: PMC9106650 DOI: 10.1038/s41467-022-30342-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Mass-spectrometry-based proteomic data on human tumors—combined with corresponding multi-omics data—present opportunities for systematic and pan-cancer proteogenomic analyses. Here, we assemble a compendium dataset of proteomics data of 2002 primary tumors from 14 cancer types and 17 studies. Protein expression of genes broadly correlates with corresponding mRNA levels or copy number alterations (CNAs) across tumors, but with notable exceptions. Based on unsupervised clustering, tumors separate into 11 distinct proteome-based subtypes spanning multiple tissue-based cancer types. Two subtypes are enriched for brain tumors, one subtype associating with MYC, Wnt, and Hippo pathways and high CNA burden, and another subtype associating with metabolic pathways and low CNA burden. Somatic alteration of genes in a pathway associates with higher pathway activity as inferred by proteome or transcriptome data. A substantial fraction of cancers shows high MYC pathway activity without MYC copy gain but with mutations in genes with noncanonical roles in MYC. Our proteogenomics survey reveals the interplay between genome and proteome across tumor lineages. Pan-cancer proteomics analysis enables the analysis of protein expression across multiple cancer types. Here, the authors compare proteomics from 14 cancer types and show 11 distinct subtypes across multiple cancer types. Proteome data could link higher pathway activity levels with somatic alteration of specific genes in the pathway.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Darshan S Chandrashekar
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.,Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Sooryanarayana Varambally
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.,Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.,The Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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43
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Beck P, Selle B, Madenach L, Jones DTW, Vokuhl C, Gopisetty A, Nabbi A, Brecht IB, Ebinger M, Wegert J, Graf N, Gessler M, Pfister SM, Jäger N. The genomic landscape of pediatric renal cell carcinomas. iScience 2022; 25:104167. [PMID: 35445187 PMCID: PMC9014386 DOI: 10.1016/j.isci.2022.104167] [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: 11/16/2021] [Revised: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 12/08/2022] Open
Abstract
Pediatric renal cell carcinomas (RCC) differ from their adult counterparts not only in histologic subtypes but also in clinical characteristics and outcome. However, the underlying biology is still largely unclear. For this reason, we performed whole-exome and transcriptome sequencing analyses on a cohort of 25 pediatric RCC patients with various histologic subtypes, including 10 MiT family translocation (MiT) and 10 papillary RCCs. In this cohort of pediatric RCC, we find only limited genomic overlap with adult RCC, even within the same histologic subtype. Recurrent somatic mutations in genes not previously reported in RCC were detected, such as in CCDC168, PLEKHA1, VWF, and MAP3K9. Our papillary pediatric RCCs, which represent the largest cohort to date with comprehensive molecular profiling in this age group, appeared as a distinct genomic subtype differing in terms of gene mutations and gene expression patterns not only from MiT-RCC but also from their adult counterparts. WES and RNA-seq of 25 pediatric RCCs with various histologic subtypes Detected only limited genomic overlap with adult RCC Revealed recurrent somatic mutations in genes not previously reported in RCC Discovery of a CRK-PITPNA fusion gene in a pediatric papillary RCC
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Affiliation(s)
- Pengbo Beck
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Barbara Selle
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lukas Madenach
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Vokuhl
- Section of Pediatric Pathology, Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - Apurva Gopisetty
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Arash Nabbi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ines B Brecht
- Department of Pediatric Oncology and Hematology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Martin Ebinger
- Department of Pediatric Oncology and Hematology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Würzburg University & Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Saarland University, Homburg, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Würzburg University & Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
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44
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De Alwis R, Hansson J, Lindgren D, Schoch S, Tejera A, Scholtz B, Elfving P, Möller C, Nilsson H, Johansson M, Axelson H. Size‑based isolation and detection of renal carcinoma cells from whole blood. Mol Clin Oncol 2022; 16:101. [PMID: 35463211 PMCID: PMC9022084 DOI: 10.3892/mco.2022.2534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Abstract
Renal cell carcinoma (RCC) is a tumour type with an indolent growth pattern and rather vague symptoms. The present study developed a platform for liquid biopsy of RCC based upon the isolation of circulating tumour cells (CTCs). Founded on the observation that RCC tumour cells are considerably larger than leucocytes, the present study employed a microfluidics-based system for isolation of RCC CTCs from whole blood. Using this system, it was revealed that 66% of spiked-in RCC tumour cells could be retrieved using this approach. Furthermore, it was demonstrated that these cells could be molecularly detected with digital PCR using RCC-specific genes down to one tumour cell, whilst avoiding detection in samples lacking tumour cells. Finally, subtype specific transcripts were identified to distinguish the different subtypes of RCC, which were then validated in patient tumours. The present study established a novel workflow for the isolation of RCC CTCs from whole blood, with the potential to detect these cells irrespective of subtype.
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Affiliation(s)
- Roger De Alwis
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Jennifer Hansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - David Lindgren
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Sarah Schoch
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Alexander Tejera
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Bianca Scholtz
- Department of Urology, Skåne University Hospital, 214 28 Malmö, Sweden
| | - Peter Elfving
- Department of Urology, Skåne University Hospital, 214 28 Malmö, Sweden
| | - Christina Möller
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Helén Nilsson
- Center for Molecular Pathology, Department of Translational Medicine, Skåne University Hospital, 214 28 Malmö, Sweden
| | - Martin Johansson
- Center for Molecular Pathology, Department of Translational Medicine, Skåne University Hospital, 214 28 Malmö, Sweden
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
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45
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Wang PY, Yang S, Bao YJ. An Integrative Analysis Framework for Identifying the Prognostic Markers from Multidimensional RNA Data of Clear Cell Renal Cell Carcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:671-686. [PMID: 35063405 DOI: 10.1016/j.ajpath.2021.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/13/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
The altered regulatory status of long noncoding RNA (lncRNA), miRNA, and mRNA and their interactions play critical roles in tumor proliferation, metastasis, and progression, which ultimately influence cancer prognosis. However, there are limited studies of comprehensive identification of prognostic biomarkers from combined data sets of the three RNA types in the highly metastatic clear cell renal cell carcinoma (ccRCC). The current study employed an integrative analysis framework of functional genomics approaches and machine learning methods to the lncRNA, miRNA, and mRNA data and identified 16 RNAs (3 lncRNAs, 6 miRNAs, and 7 mRNAs) of prognostic value, with 9 of them novel. A 16 RNA-based score was established for prognosis prediction of ccRCC with significance (P < 0.0001). The area under the curve for the score model was 0.868 to 0.870 in the training cohort and 0.714 to 0.778 in the validation cohort. Construction of the lncRNA-miRNA-mRNA interaction network showed that the downstream mRNAs and upstream lncRNAs in the network initiated from the miRNA or lncRNA markers exhibit significant enrichment in functional classifications associated with cancer metastasis, proliferation, progression, or prognosis. The functional analysis provided clear support for the role of the RNA biomarkers in predicting cancer prognosis. This study provides promising biomarkers for predicting prognosis of ccRCC using multidimensional RNA data, and these findings are expected to facilitate potential clinical applications of the biomarkers.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Kaplan-Meier Estimate
- Male
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Prognosis
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Peng-Ying Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Yun-Juan Bao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China.
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Fumarate inhibits PTEN to promote tumorigenesis and therapeutic resistance of type2 papillary renal cell carcinoma. Mol Cell 2022; 82:1249-1260.e7. [PMID: 35216667 DOI: 10.1016/j.molcel.2022.01.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/10/2021] [Accepted: 01/28/2022] [Indexed: 12/22/2022]
Abstract
Fumarate is an oncometabolite. However, the mechanism underlying fumarate-exerted tumorigenesis remains unclear. Here, utilizing human type2 papillary renal cell carcinoma (PRCC2) as a model, we show that fumarate accumulates in cells deficient in fumarate hydratase (FH) and inhibits PTEN to activate PI3K/AKT signaling. Mechanistically, fumarate directly reacts with PTEN at cysteine 211 (C211) to form S-(2-succino)-cysteine. Succinated C211 occludes tethering of PTEN with the cellular membrane, thereby diminishing its inhibitory effect on the PI3K/AKT pathway. Functionally, re-expressing wild-type FH or PTEN C211S phenocopies an AKT inhibitor in suppressing tumor growth and sensitizing PRCC2 to sunitinib. Analysis of clinical specimens indicates that PTEN C211 succination levels are positively correlated with AKT activation in PRCC2. Collectively, these findings elucidate a non-metabolic, oncogenic role of fumarate in PRCC2 via direct post-translational modification of PTEN and further reveal potential stratification strategies for patients with FH loss by combinatorial AKTi and sunitinib therapy.
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Farhadi A, Namdari S, Chong PP, Geramizadeh B, Behzad-Behbahani A, Sekawi Z, Sharifzadeh S. Epstein-Barr virus infection is associated with the nuclear factor-kappa B p65 signaling pathway in renal cell carcinoma. BMC Urol 2022; 22:17. [PMID: 35130882 PMCID: PMC8822771 DOI: 10.1186/s12894-022-00964-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There have been few studies regarding viral involvement in the pathogenesis of renal cell carcinoma (RCC). The aim of this study was to examine the possible association of Epstein-Barr virus (EBV) infection with clinicopathological features and cellular biomarkers including p53, p16INK4a, Ki-67 and nuclear factor-kappa B (NF-κB) in RCC tumors. METHODS In this prospective study, 122 histologically confirmed Formalin-fixed Paraffin-embedded RCC tissue specimens along with 96 specimens of their corresponding peritumoral tissues and 23 samples of blunt renal injuries were subjected to nested polymerase chain reaction (nPCR) in order to amplify EBV DNA sequences. The expression of p53, p16INK4a, Ki-67 and NF-κB was investigated by immunohistochemistry (IHC) assay. Statistical analysis was employed to demonstrate the possible associations. RESULTS Infection with EBV was found to be significantly associated with RCC. Our results indicate that p65 NF-κB signaling pathway is probably involved in EBV-mediated RCC pathogenesis. Moreover, we found p53, Ki-67 and cytoplasmic NF-κB expression to be associated with tumor nuclear grade in RCC patients. The expression of p53 and Ki-67 was associated with primary tumor category as well. In addition, p53 overexpression was significantly more frequent among nonconventional RCC tumors than the conventional histologic type. CONCLUSIONS Infection with EBV is likely to play an important role in the development of RCC through the constitutive and permanent activation of NF-κB p65 signaling pathway. However, more experiments and supporting data are required to reach a decisive conclusion.
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Affiliation(s)
- Ali Farhadi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Sepide Namdari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pei Pei Chong
- School of Biosciences, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia
| | - Bita Geramizadeh
- Department of Pathology, Medical School of Shiraz University, Shiraz University of Medical Sciences, Shiraz, Iran.,Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zamberi Sekawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Sedigheh Sharifzadeh
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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Xiang X, Guo Y, Chen Z, Mo Z. Molecular Characterization of m6A Modifications in Non-Clear Cell Renal Cell Carcinoma and Potential Relationship with Pathological Types. Int J Gen Med 2022; 15:1595-1608. [PMID: 35210831 PMCID: PMC8858024 DOI: 10.2147/ijgm.s348343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/27/2022] [Indexed: 12/24/2022] Open
Abstract
Background N6-Methyladenosine (m6A) modification is a eukaryotic mRNA modification that modulates the fate of modified RNA and, therefore, the expression of proteins. m6A modifications are associated with important roles in several cancers. Most studies related to m6A modification are based on clear cell renal cell carcinoma (ccRCC) and little is known about its role in non-ccRCC. Methods We summarized the molecular features of different m6A modification patterns in non-ccRCC based on The Cancer Genome Atlas database and correlated them with phenotypes such as immune patterns and prognosis. We also computed the m6Ascore and assessed its prognostic value using multivariate Cox regression analysis. Results We found the immune-excluded phenotype to be predominant in non-ccRCC patients. We also found that in non-clear cell carcinoma, different m6A modification profiles determine different immune patterns and are associated with different prognosis. m6AgeneCluser typing strongly associated with pathological status. Based on our findings, we suggest that the m6Ascore can be used as an independent prognostic value for prognostic assessment in non-ccRCC. Conclusion This study confirms the important role of m6A modifications in non-ccRCC, reveals the heterogeneity of tumor immunity, and highlights the promise of non-ccRCC therapy.
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Affiliation(s)
- Xuebao Xiang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Yi Guo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Zhongyuan Chen
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
- Correspondence: Zengnan Mo, Email
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49
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Identification of Molecular Subtypes in Head and Neck Squamous Cell Carcinoma Based on Dysregulated Immune LncRNAs. JOURNAL OF ONCOLOGY 2022; 2022:9702789. [PMID: 35126519 PMCID: PMC8808126 DOI: 10.1155/2022/9702789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs (lncRNAs) perform indispensable functions in cancer pathologies and are involved in the onset and progression of multiple cancers. Multiple platforms were performed to comprehensively analyze the head and neck squamous cell carcinoma (HNSCC) for determining molecular subtypes. Molecular subtypes were clustered and analyzed by the “ConsensusClusterPlus” R package. The Limma software was utilized to screen for differentially expressed genes (DEGs). Functional enrichment analyses, including Gene Set Enrichment Analysis (GSEA), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO), were performed on the three database resources. Seventeen lncRNAs were determined as HNSCC-specific immune lncRNAs that were dysregulated. Our research identified and redefined two distinct molecular subtypes, C1 (230 samples) and C2 (269 samples). Moreover, the C1 subtype had a higher survival rate than the C2 subtype in HNSCC samples, as well as a prolonged median survival duration with activated immune response. 1531 DEGs, including 529 upmodulated genes and 1002 downmodulated genes, were identified in the above two subtypes. Functional enrichment analysis revealed that upmodulated genes in C2 were associated with tumorigenesis and development, while downregulated genes in C2 were associated with immune response. By comparing with the existing immunophenotyping group, it found that C1 had more overlaps with the existing Atypical and Basal, and C2 and Classical and Mesenchymal had a high degree of coincidence. On the basis of lncRNA, there were significant differences in the aspect of prognostic and immunological characteristics in the two identified molecular subtypes of HNSCC.
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50
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Wang Q, Zhang Y, Zhang B, Fu Y, Zhao X, Zhang J, Zuo K, Xing Y, Jiang S, Qin Z, Li E, Guo H, Liu Z, Yang J. Single-cell chromatin accessibility landscape in kidney identifies additional cell-of-origin in heterogenous papillary renal cell carcinoma. Nat Commun 2022; 13:31. [PMID: 35013217 PMCID: PMC8748507 DOI: 10.1038/s41467-021-27660-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/02/2021] [Indexed: 01/14/2023] Open
Abstract
Papillary renal cell carcinoma (pRCC) is the most heterogenous renal cell carcinoma. Patient survival varies and no effective therapies for advanced pRCC exist. Histological and molecular characterization studies have highlighted the heterogeneity of pRCC tumours. Recent studies identified the proximal tubule (PT) cell as a cell-of-origin for pRCC. However, it remains elusive whether other pRCC subtypes have different cell-of-origin. Here, by obtaining genome-wide chromatin accessibility profiles of normal human kidney cells using single-cell transposase-accessible chromatin-sequencing and comparing the profiles with pRCC samples, we discover that besides PT cells, pRCC can also originate from kidney collecting duct principal cells. We show pRCCs with different cell-of-origin exhibit different molecular characteristics and clinical behaviors. Further, metabolic reprogramming appears to mediate the progression of pRCC to the advanced state. Here, our results suggest that determining cell-of-origin and monitoring origin-dependent metabolism could potentially be useful for early diagnosis and treatment of pRCC.
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Affiliation(s)
- Qi Wang
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Yang Zhang
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Bolei Zhang
- School of Computer Science, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu, 210023, China
| | - Yao Fu
- Department of Pathology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Xiaozhi Zhao
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Jing Zhang
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Ke Zuo
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Yuexian Xing
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Song Jiang
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Erguang Li
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Hongqian Guo
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210008, China.
| | - Zhihong Liu
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China.
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China.
| | - Jingping Yang
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China.
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China.
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, 210093, China.
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