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Sensitivity of VHL mutant kidney cancers to HIF2 inhibitors does not require an intact p53 pathway. Proc Natl Acad Sci U S A 2022; 119:e2120403119. [PMID: 35357972 PMCID: PMC9168943 DOI: 10.1073/pnas.2120403119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
VHL tumor suppressor gene inactivation is a hallmark of clear cell renal cell carcinoma (ccRCC), the most common form of kidney cancer, and promotes tumor growth by stabilizing the hypoxia-inducible factor 2 (HIF2) transcription factor. HIF2 inhibitors appear to be helpful for some, but not all, ccRCC patients in clinical trials. Previous preclinical and clinical data suggested that only ccRCCs that can activate the p53 tumor suppressor in response to DNA damage would respond to HIF2 inhibitors. Here, we show that an intact p53 pathway is neither necessary nor sufficient for the sensitivity of ccRCCs to HIF2 inhibitors, suggesting that it would be premature to use p53 status to determine which ccRCC patients should be treated with a HIF2 inhibitor. Inactivation of the VHL tumor suppressor gene is the signature initiating event in clear cell renal cell carcinoma (ccRCC), which is the most common form of kidney cancer. The VHL tumor suppressor protein marks hypoxia-inducible factor 1 (HIF1) and HIF2 for proteasomal degradation when oxygen is present. The inappropriate accumulation of HIF2 drives tumor formation by VHL tumor suppressor protein (pVHL)–defective ccRCC. Belzutifan, a first-in-class allosteric HIF2 inhibitor, has advanced to phase 3 testing for advanced ccRCC and is approved for ccRCCs arising in patients with VHL disease, which is caused by germline VHL mutations. HIF2 can suppress p53 function in some settings and preliminary data suggested that an intact p53 pathway, as measured by activation in response to DNA damage, was necessary for HIF2 dependence. Here, we correlated HIF2 dependence and p53 status across a broader collection of ccRCC cell lines. We also genetically manipulated p53 function in ccRCC lines that were or were not previously HIF2-dependent and then assessed their subsequent sensitivity to HIF2 ablation using CRISPR-Cas9 or the HIF2 inhibitor PT2399, which is closely related to belzutifan. From these studies, we conclude that p53 status does not dictate HIF2 dependence, at least in preclinical models, and thus is unlikely to be a useful biomarker for predicting which ccRCC patients will respond to HIF2 inhibitors.
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202
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Andreou A, Yngvadottir B, Bassaganyas L, Clark G, Martin E, Whitworth J, Cornish AJ, Houlston RS, Rich P, Egan C, Hodgson SV, Warren AY, Snape K, Maher ER. Elongin C (ELOC/TCEB1)-associated von Hippel-Lindau disease. Hum Mol Genet 2022; 31:2728-2737. [PMID: 35323939 PMCID: PMC9402235 DOI: 10.1093/hmg/ddac066] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/02/2022] Open
Abstract
Around 95% of patients with clinical features that meet the diagnostic criteria for von Hippel-Lindau disease (VHL) have a detectable inactivating germline variant in VHL. The VHL protein (pVHL) functions as part of the E3 ubiquitin ligase complex comprising pVHL, elongin C, elongin B, cullin 2 and ring box 1 (VCB-CR complex), which plays a key role in oxygen sensing and degradation of hypoxia-inducible factors. To date, only variants in VHL have been shown to cause VHL disease. We undertook trio analysis by whole-exome sequencing in a proband with VHL disease but without a detectable VHL mutation. Molecular studies were also performed on paired DNA extracted from the proband's kidney tumour and blood and bioinformatics analysis of sporadic renal cell carcinoma (RCC) dataset was undertaken. A de novo pathogenic variant in ELOC NM_005648.4(ELOC):c.236A>G (p.Tyr79Cys) gene was identified in the proband. ELOC encodes elongin C, a key component [C] of the VCB-CR complex. The p.Tyr79Cys substitution is a mutational hotspot in sporadic VHL-competent RCC and has previously been shown to mimic the effects of pVHL deficiency on hypoxic signalling. Analysis of an RCC from the proband showed similar findings to that in somatically ELOC-mutated RCC (expression of hypoxia-responsive proteins, no somatic VHL variants and chromosome 8 loss). These findings are consistent with pathogenic ELOC variants being a novel cause for VHL disease and suggest that genetic testing for ELOC variants should be performed in individuals with suspected VHL disease with no detectable VHL variant.
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Affiliation(s)
- Avgi Andreou
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Bryndis Yngvadottir
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Laia Bassaganyas
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Graeme Clark
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Ezequiel Martin
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - James Whitworth
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | | | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Philip Rich
- Department of Neuroradiology, St. George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Catherine Egan
- NIHR Biomedical Research Center at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Shirley V Hodgson
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University NHS Foundation Trust, Cambridge CB2 OQQ, UK
| | - Katie Snape
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK,St George's University of London, UK
| | - Eamonn R Maher
- To whom correspondence should be addressed at: Department of Medical Genetics, University of Cambridge, Box 238, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK. Tel: +44 01223746715; Fax: +44 01223746777;
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203
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Lee CH, Voss MH, Carlo MI, Chen YB, Zucker M, Knezevic A, Lefkowitz RA, Shapnik N, Dadoun C, Reznik E, Shah NJ, Owens CN, McHugh DJ, Aggen DH, Laccetti AL, Kotecha R, Feldman DR, Motzer RJ. Phase II Trial of Cabozantinib Plus Nivolumab in Patients With Non-Clear-Cell Renal Cell Carcinoma and Genomic Correlates. J Clin Oncol 2022; 40:2333-2341. [PMID: 35298296 DOI: 10.1200/jco.21.01944] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE To assess the efficacy and safety of cabozantinib plus nivolumab in a phase II trial in patients with non-clear-cell renal cell carcinoma (RCC). PATIENTS AND METHODS Patients had advanced non-clear-cell renal carcinoma who underwent 0-1 prior systemic therapies excluding prior immune checkpoint inhibitors. Patients received cabozantinib 40 mg once daily plus nivolumab 240 mg once every 2 weeks or 480 mg once every 4 weeks. Cohort 1 enrolled patients with papillary, unclassified, or translocation-associated RCC; cohort 2 enrolled patients with chromophobe RCC. The primary end point was objective response rate (ORR) by RECIST 1.1; secondary end points included progression-free survival, overall survival, and safety. Next-generation sequencing results were correlated with response. RESULTS A total of 47 patients were treated with a median follow-up of 13.1 months. Objective response rate for cohort 1 (n = 40) was 47.5% (95% CI, 31.5 to 63.9), with median progression-free survival of 12.5 months (95% CI, 6.3 to 16.4) and median overall survival of 28 months (95% CI, 16.3 to not evaluable). In cohort 2 (n = 7), no responses were observed; one patient had stable disease > 1 year. Grade 3/4 treatment-related adverse events were observed in 32% treated patients. Cabozantinib and nivolumab were discontinued because of toxicity in 13% and 17% of patients, respectively. Common mutations included NF2 and FH in cohort 1 and TP53 and PTEN in cohort 2. Objective responses were seen in 10/12 patients with either NF2 or FH mutations. CONCLUSION Cabozantinib plus nivolumab showed promising efficacy in most non-clear-cell RCC variants tested in this trial, particularly those with prominent papillary features, whereas treatment effects were limited in chromophobe RCC. Genomic findings in non-clear-cell RCC variants warrant further study as predictors of response.
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Affiliation(s)
- Chung-Han Lee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Martin H Voss
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Maria Isabel Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Ying-Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Zucker
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrea Knezevic
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert A Lefkowitz
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Natalie Shapnik
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chloe Dadoun
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neil J Shah
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Colette Ngozi Owens
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Deaglan Joseph McHugh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - David Henry Aggen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Andrew Leonard Laccetti
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Ritesh Kotecha
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Robert J Motzer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
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204
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Therapeutic potential of CDK4/6 inhibitors in renal cell carcinoma. Nat Rev Urol 2022; 19:305-320. [PMID: 35264774 DOI: 10.1038/s41585-022-00571-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 12/12/2022]
Abstract
The treatment of advanced and metastatic kidney cancer has entered a golden era with the addition of more therapeutic options, improved survival and new targeted therapies. Tyrosine kinase inhibitors, mammalian target of rapamycin (mTOR) inhibitors and immune checkpoint blockade have all been shown to be promising strategies in the treatment of renal cell carcinoma (RCC). However, little is known about the best therapeutic approach for individual patients with RCC and how to combat therapeutic resistance. Cancers, including RCC, rely on sustained replicative potential. The cyclin-dependent kinases CDK4 and CDK6 are involved in cell-cycle regulation with additional roles in metabolism, immunogenicity and antitumour immune response. Inhibitors of CDK4 and CDK6 are now commonly used as approved and investigative treatments in breast cancer, as well as several other tumours. Furthermore, CDK4/6 inhibitors have been shown to work synergistically with other kinase inhibitors, including mTOR inhibitors, as well as with immune checkpoint inhibitors in preclinical cancer models. The effect of CDK4/6 inhibitors in kidney cancer is relatively understudied compared with other cancers, but the preclinical studies available are promising. Collectively, growing evidence suggests that targeting CDK4 and CDK6 in kidney cancer, alone and in combination with current therapeutics including mTOR and immune checkpoint inhibitors, might have therapeutic benefit and should be further explored.
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205
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Sun W, Wu W, Wang Q, Yao Q, Feng Q, Wang Y, Sun Y, Liu Y, Lai Q, Zhang G, Qi P, Sun Y, Qian C, Ren W, Luo Z, Chen J, Wang H, Xu Q, Zhou X, Sun W, Lin D. Clinical validation of a 90-gene expression test for tumor tissue of origin diagnosis: a large-scale multicenter study of 1417 patients. J Transl Med 2022; 20:114. [PMID: 35255924 PMCID: PMC8900384 DOI: 10.1186/s12967-022-03318-6] [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: 01/21/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022] Open
Abstract
Background Once malignancy tumors were diagnosed, the determination of tissue origin and tumor type is critical for clinical management. Although the significant advance in imaging techniques and histopathological approaches, the diagnosis remains challenging in patients with metastatic and poorly differentiated or undifferentiated tumors. Gene expression profiling has been demonstrated the ability to classify multiple tumor types. The present study aims to assess the performance of a 90-gene expression test for tumor classification (i.e. the determination of tumor tissue of origin) in real clinical settings. Methods Formalin-fixed paraffin-embedded samples and associated clinicopathologic information were collected from three cancer centers between January 2016 and January 2021. A total of 1417 specimens that met quality control criteria (RNA quality, tumor cell content ≥ 60% and so on) were analyzed by the 90-gene expression test to identify the tumor tissue of origin. The performance was evaluated by comparing the test results with histopathological diagnosis. Results The 1417 samples represent 21 main tumor types classified by common tissue origins and anatomic sites. Overall, the 90-gene expression test reached an accuracy of 94.4% (1338/1417, 95% CI: 0.93 to 0.96). Among different tumor types, sensitivities were ranged from 74.2% (head&neck tumor) to 100% (adrenal carcinoma, mesothelioma, and prostate cancer). Sensitivities for the most prevalent cancers of lung, breast, colorectum, and gastroesophagus are 95.0%, 98.4%, 93.9%, and 90.6%, respectively. Moreover, specificities for all 21 tumor types are greater than 99%. Conclusions These findings showed robust performance of the 90-gene expression test for identifying the tumor tissue of origin and support the use of molecular testing as an adjunct to tumor classification, especially to those poorly differentiated or undifferentiated tumors in clinical practice. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03318-6.
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206
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RNA-binding protein MEX3A controls G1/S transition via regulating the RB/E2F pathway in clear cell renal cell carcinoma. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:241-255. [PMID: 34976441 PMCID: PMC8703191 DOI: 10.1016/j.omtn.2021.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022]
Abstract
MEX3A is an RNA-binding protein that mediates mRNA decay through binding to 3′ untranslated regions. However, its role and mechanism in clear cell renal cell carcinoma remain unknown. In this study, we found that MEX3A expression was transcriptionally activated by ETS1 and upregulated in clear cell renal cell carcinoma. Silencing MEX3A markedly reduced clear cell renal cell carcinoma cell proliferation in vitro and in vivo. Inhibiting MEX3A induced G1/S cell-cycle arrest. Gene set enrichment analysis revealed that E2F targets are the central downstream pathways of MEX3A. To identify MEX3A targets, systematic screening using enhanced cross-linking and immunoprecipitation sequencing, and RNA-immunoprecipitation sequencing assays were performed. A network of 4,000 genes was identified as potential targets of MEX3A. Gene ontology analysis of upregulated genes bound by MEX3A indicated that negative regulation of the cell proliferation pathway was highly enriched. Further assays indicated that MEX3A bound to the CDKN2B 3′ untranslated region, promoting its mRNA degradation. This leads to decreased levels of CDKN2B and an uncontrolled cell cycle in clear cell renal cell carcinoma, which was confirmed by rescue experiments. Our findings revealed that MEX3A acts as a post-transcriptional regulator of abnormal cell-cycle progression in clear cell renal cell carcinoma.
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207
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Kapur P, Gao M, Zhong H, Chintalapati S, Mitui M, Barnes S, Zhou Q, Miyata J, Carrillo D, Malladi V, Rakheja D, Pedrosa I, Xu L, Kinch L, Brugarolas J. Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney. Mod Pathol 2022; 35:333-343. [PMID: 34538873 PMCID: PMC9817016 DOI: 10.1038/s41379-021-00896-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 01/11/2023]
Abstract
Low-grade oncocytic tumor (LOT) of the kidney is a recently described entity with poorly understood pathogenesis. Using next-generation sequencing (NGS) and complementary approaches, we provide insight into its biology. We describe 22 LOT corresponding to 7 patients presenting with a median age of 75 years (range 63-86 years) and male to female ratio 2:5. All 22 tumors demonstrated prototypical microscopic features. Tumors were well-circumscribed and solid. They were composed of sheets of tumor cells in compact nests. Tumor cells had eosinophilic cytoplasm, round to oval nuclei (without nuclear membrane irregularities), focal subtle perinuclear halos, and occasional binucleation. Sharply delineated edematous stromal islands were often observed. Tumor cells were positive for PAX8, negative for CD117, and exhibited diffuse and strong cytokeratin-7 expression. Six patients presented with pT1 tumors. At a median follow-up of 29 months, four patients were alive without recurrence (three patients had died from unrelated causes). All tumors were originally classified as chromophobe renal cell carcinoma, eosinophilic variant (chRCC-eo). While none of the patients presented with known syndromic features, one patient with multiple bilateral LOTs was subsequently found to have a likely pathogenic germline TSC1 mutation. Somatic, likely activating, mutations in MTOR and RHEB were identified in all other evaluable LOTs. As assessed by phospho-S6 and phospho-4E-BP1, mTOR complex 1 (mTORC1) was activated across all cases but to different extent. MTOR mutant LOT exhibited lower levels of mTORC1 activation, possibly related to mTORC1 dimerization and the preservation of a wild-type MTOR copy (retained chromosome 1). Supporting its distinction from related entities, gene expression analyses showed that LOT clustered separately from classic chRCC, chRCC-eo, and RO. In summary, converging mTORC1 pathway mutations, mTORC1 complex activation, and a distinctive gene expression signature along with characteristic phenotypic features support LOT designation as a distinct entity with both syndromic and non-syndromic cases associated with an indolent course.
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Affiliation(s)
- Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Ming Gao
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Hua Zhong
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Suneetha Chintalapati
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Midori Mitui
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Spencer Barnes
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Qinbo Zhou
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Jeffrey Miyata
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Deyssy Carrillo
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Venkat Malladi
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Ivan Pedrosa
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Lin Xu
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Lisa Kinch
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - James Brugarolas
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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208
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Low-grade oncocytic renal tumor (LOT): mutations in mTOR pathway genes and low expression of FOXI1. Mod Pathol 2022; 35:352-360. [PMID: 34531523 DOI: 10.1038/s41379-021-00906-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 11/09/2022]
Abstract
Low-grade oncocytic renal tumor (LOT) is an emerging provisional entity, described as rare solid renal oncocytic/eosinophilic tumor sharing diffuse CK7 and negative CD117 immunoprofile. The links between LOT and other eosinophilic chromophobe like-renal cell carcinomas (RCC) are currently discussed. We sequenced tumoral DNA with a next generation sequencing panel for kidney cancer and carried out immunohistochemical analyses with CK7, CD117, SDHB, 4EBP1-P, S6K-P, and FOXI1 antibodies in a series of ten cases of LOT (9 females, 1 male; mean age at surgery: 66 years, 42.3 to 83.4) retrospectively diagnosed from a cohort of 272 tumors initially classified as chromophobe RCC (CHRCC). All LOT were single, without known hereditary predisposition, classified stage pT1 (70%), pT2 (20%) or pT3a (10%). Morphological features were similar to previous descriptions and clinical behavior was indolent for the six cases with available follow-up. We identified genetic variations in mTOR pathway related genes in 80% of cases, MTOR (7 cases) or TSC1 (1 case). Expression of FOXI1 was absent in all cases. In 9 LOT, 4EBP1-P and S6K-P were overexpressed, suggesting mTOR pathway activation.Our data highlights the major role of mTOR pathway in tumorigenesis of LOT mostly due to activating MTOR gene variations. Absence of FOXI1 expression is a strong argument to distinguish LOT from eosinophilic CHRCC and to bring them closer to other recently described FOXI1 negative eosinophilic-CHRCC like with MTOR/TSC mutations. Altogether, our data argue to consider LOT as a distinct entity with a favorable clinical outcome. However, in case of metastasis, an accurate diagnosis of LOT would be essential for the patient's management and could allow targeted therapy.
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209
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Wang B, Liu L, Wu J, Mao X, Fang Z, Chen Y, Li W. Construction and Verification of a Combined Hypoxia and Immune Index for Clear Cell Renal Cell Carcinoma. Front Genet 2022; 13:711142. [PMID: 35222525 PMCID: PMC8863964 DOI: 10.3389/fgene.2022.711142] [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: 05/18/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most aggressive malignancies in humans. Hypoxia-related genes are now recognized as a reflection of poor prognosis in cancer patients with cancer. Meanwhile, immune-related genes play an important role in the occurrence and progression of ccRCC. Nevertheless, reliable prognostic indicators based on hypoxia and immune status have not been well established in ccRCC. The aims of this study were to develop a new gene signature model using bioinformatics and open databases and to validate its prognostic value in ccRCC. The data used for the model structure can be accessed from The Cancer Genome Atlas database. Univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were used to identify the hypoxia- and immune-related genes associated with prognostic risk, which were used to develop a characteristic model of prognostic risk. Kaplan-Meier and receiver-operating characteristic curve analyses were performed as well as independent prognostic factor analyses and correlation analyses of clinical characteristics in both the training and validation cohorts. In addition, differences in tumor immune cell infiltrates were compared between the high and low risk groups. Overall, 30 hypoxia- and immune-related genes were identified, and five hypoxia- and immune-related genes (EPO, PLAUR, TEK, TGFA, TGFB1) were ultimately selected. Survival analysis showed that the high-risk score on the hypoxia- and immune-related gene signature was significantly associated with adverse survival outcomes. Furthermore, clinical ccRCC samples from our medical center were used to validate the differential expression of the five genes in tumor tissue compared to normal tissue through quantitative real-time polymerase chain reaction (qRT-PCR). However, more clinical trials are needed to confirm these results, and future experimental studies must verify the potential mechanism behind the predictive value of the hypoxia- and immune-related gene signature.
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Affiliation(s)
- Bin Wang
- Department of Medical Oncology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lixiao Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jinting Wu
- Department of Medical Oncology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaolu Mao
- Department of Medical Oncology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhen Fang
- Department of Medical Oncology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yingyu Chen
- Department of Neurosurgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenfeng Li
- Department of Medical Oncology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Wenfeng Li,
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210
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LiKidMiRs: A ddPCR-Based Panel of 4 Circulating miRNAs for Detection of Renal Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14040858. [PMID: 35205607 PMCID: PMC8869982 DOI: 10.3390/cancers14040858] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 01/26/2023] Open
Abstract
Simple Summary Early detection of renal cell carcinoma (RCC) significantly increases the likelihood of curative treatment, avoiding the need of adjuvant therapies, associated side effects and comorbidities. Thus, we aimed to discover circulating microRNAs that might aid in early, minimally invasive, RCC detection/diagnosis. Abstract Background: Decreased renal cell cancer-related mortality is an important societal goal, embodied by efforts to develop effective biomarkers enabling early detection and increasing the likelihood of curative treatment. Herein, we sought to develop a new biomarker for early and minimally invasive detection of renal cell carcinoma (RCC) based on a microRNA panel assessed by ddPCR. Methods: Plasma samples from patients with RCC (n = 124) or oncocytomas (n = 15), and 64 healthy donors, were selected. Hsa-miR-21-5p, hsa-miR-126-3p, hsa-miR-155-5p and hsa-miR-200b-3p levels were evaluated using a ddPCR protocol. Results: RCC patients disclosed significantly higher circulating levels of hsa-miR-155-5p compared to healthy donors, whereas the opposite was observed for hsa-miR-21-5p levels. Furthermore, hsa-miR-21-5p and hsa-miR-155-5p panels detected RCC with high sensitivity (82.66%) and accuracy (71.89%). The hsa-miR-126-3p/hsa-miR-200b-3p panel identified the most common RCC subtype (clear cell, ccRCC) with 74.78% sensitivity. Conclusion: Variable combinations of plasma miR levels assessed by ddPCR enable accurate detection of RCC in general, and of ccRCC. These findings, if confirmed in larger studies, provide evidence for a novel ancillary tool which might aid in early detection of RCC.
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The Next Paradigm Shift in the Management of Clear Cell Renal Cancer: Radiogenomics—Definition, Current Advances, and Future Directions. Cancers (Basel) 2022; 14:cancers14030793. [PMID: 35159060 PMCID: PMC8833879 DOI: 10.3390/cancers14030793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/28/2021] [Accepted: 01/28/2022] [Indexed: 02/01/2023] Open
Abstract
With improved molecular characterization of clear cell renal cancer and advances in texture analysis as well as machine learning, diagnostic radiology is primed to enter personalized medicine with radiogenomics: the identification of relationships between tumor image features and underlying genomic expression. By developing surrogate image biomarkers, clinicians can augment their ability to non-invasively characterize a tumor and predict clinically relevant outcomes (i.e., overall survival; metastasis-free survival; or complete/partial response to treatment). It is thus important for clinicians to have a basic understanding of this nascent field, which can be difficult due to the technical complexity of many of the studies. We conducted a review of the existing literature for radiogenomics in clear cell kidney cancer, including original full-text articles until September 2021. We provide a basic description of radiogenomics in diagnostic radiology; summarize existing literature on relationships between image features and gene expression patterns, either computationally or by radiologists; and propose future directions to facilitate integration of this field into the clinical setting.
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212
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Yates J, Boeva V. Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. Brief Bioinform 2022; 23:6520307. [PMID: 35134107 PMCID: PMC8921629 DOI: 10.1093/bib/bbab610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/06/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
Numerous cancer types have shown to present hypermethylation of CpG islands, also known as a CpG island methylator phenotype (CIMP), often associated with survival variation. Despite extensive research on CIMP, the etiology of this variability remains elusive, possibly due to lack of consistency in defining CIMP. In this work, we utilize a pan-cancer approach to further explore CIMP, focusing on 26 cancer types profiled in the Cancer Genome Atlas (TCGA). We defined CIMP systematically and agnostically, discarding any effects associated with age, gender or tumor purity. We then clustered samples based on their most variable DNA methylation values and analyzed resulting patient groups. Our results confirmed the existence of CIMP in 19 cancers, including gliomas and colorectal cancer. We further showed that CIMP was associated with survival differences in eight cancer types and, in five, represented a prognostic biomarker independent of clinical factors. By analyzing genetic and transcriptomic data, we further uncovered potential drivers of CIMP and classified them in four categories: mutations in genes directly involved in DNA demethylation; mutations in histone methyltransferases; mutations in genes not involved in methylation turnover, such as KRAS and BRAF; and microsatellite instability. Among the 19 CIMP-positive cancers, very few shared potential driver events, and those drivers were only IDH1 and SETD2 mutations. Finally, we found that CIMP was strongly correlated with tumor microenvironment characteristics, such as lymphocyte infiltration. Overall, our results indicate that CIMP does not exhibit a pan-cancer manifestation; rather, general dysregulation of CpG DNA methylation is caused by heterogeneous mechanisms.
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Affiliation(s)
- Josephine Yates
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland
| | - Valentina Boeva
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland.,Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland.,Cochin Institute, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, Paris 75014, France
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213
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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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214
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Establishing a Prognostic Model Based on Three Genomic Instability-related LncRNAs for Clear Cell Renal Cell Cancer. Clin Genitourin Cancer 2022; 20:e317-e329. [DOI: 10.1016/j.clgc.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/17/2022]
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215
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Ohe C, Yoshida T, Ikeda J, Tsuzuki T, Ohashi R, Ohsugi H, Atsumi N, Yamaka R, Saito R, Yasukochi Y, Higasa K, Kinoshita H, Tsuta K. Histologic-Based Tumor-Associated Immune Cells Status in Clear Cell Renal Cell Carcinoma Correlates with Gene Signatures Related to Cancer Immunity and Clinical Outcomes. Biomedicines 2022; 10:biomedicines10020323. [PMID: 35203532 PMCID: PMC8869140 DOI: 10.3390/biomedicines10020323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
The three-tier immunophenotype (desert, excluded, and inflamed) and the four-tier immunophenotype (cold, immunosuppressed, excluded, and hot) have been linked to prognosis and immunotherapy response. This study aims to evaluate whether immunophenotypes of clear cell renal cell carcinoma, identified on hematoxylin and eosin-stained slides, correlate with gene expression signatures related to cancer immunity, and clinical outcomes. We evaluated tumor-associated immune cells (TAICs) status using three methodologies: three-tier immunophenotype based on the location of TAICs, four-tier immunophenotype considering both the location and degree of TAICs and inflammation score focusing only on the degree of TAICs, using a localized clear cell renal cell carcinoma cohort (n = 436) and The Cancer Genome Atlas (TCGA)-KIRC cohort (n = 162). We evaluated the association of the TAICs status assessed by three methodologies with CD8 and PD-L1 immunohistochemistry and immune gene expression signatures by TCGA RNA-sequencing data. All three methodologies correlated with immunohistochemical and immune gene expression signatures. The inflammation score and the four-tier immunophenotype showed similarly higher accuracy in predicting recurrence-free survival and overall survival compared to the three-tier immunophenotype. In conclusion, a simple histologic assessment of TIACs may predict clinical outcomes and immunotherapy responses.
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Affiliation(s)
- Chisato Ohe
- Department of Pathology, Kansai Medical University, Hirakata 573-1191, Japan; (J.I.); (N.A.); (R.Y.); (K.T.)
- Correspondence:
| | - Takashi Yoshida
- Department of Urology and Andrology, Kansai Medical University, Hirakata 573-1191, Japan; (T.Y.); (H.O.); (R.S.); (H.K.)
| | - Junichi Ikeda
- Department of Pathology, Kansai Medical University, Hirakata 573-1191, Japan; (J.I.); (N.A.); (R.Y.); (K.T.)
- Department of Urology and Andrology, Kansai Medical University, Hirakata 573-1191, Japan; (T.Y.); (H.O.); (R.S.); (H.K.)
| | - Toyonori Tsuzuki
- Department of Surgical Pathology, Aichi Medical University Hospital, Nagakute 480-1195, Japan;
| | - Riuko Ohashi
- Histopathology Core Facility, Faculty of Medicine, Niigata University, Niigata 951-8510, Japan;
| | - Haruyuki Ohsugi
- Department of Urology and Andrology, Kansai Medical University, Hirakata 573-1191, Japan; (T.Y.); (H.O.); (R.S.); (H.K.)
| | - Naho Atsumi
- Department of Pathology, Kansai Medical University, Hirakata 573-1191, Japan; (J.I.); (N.A.); (R.Y.); (K.T.)
| | - Ryosuke Yamaka
- Department of Pathology, Kansai Medical University, Hirakata 573-1191, Japan; (J.I.); (N.A.); (R.Y.); (K.T.)
| | - Ryoichi Saito
- Department of Urology and Andrology, Kansai Medical University, Hirakata 573-1191, Japan; (T.Y.); (H.O.); (R.S.); (H.K.)
| | - Yoshiki Yasukochi
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1191, Japan; (Y.Y.); (K.H.)
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1191, Japan; (Y.Y.); (K.H.)
| | - Hidefumi Kinoshita
- Department of Urology and Andrology, Kansai Medical University, Hirakata 573-1191, Japan; (T.Y.); (H.O.); (R.S.); (H.K.)
| | - Koji Tsuta
- Department of Pathology, Kansai Medical University, Hirakata 573-1191, Japan; (J.I.); (N.A.); (R.Y.); (K.T.)
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Identification of Key Proteins from the Alternative Lengthening of Telomeres-Associated Promyelocytic Leukemia Nuclear Bodies Pathway. BIOLOGY 2022; 11:biology11020185. [PMID: 35205052 PMCID: PMC8868596 DOI: 10.3390/biology11020185] [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: 12/12/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/26/2022]
Abstract
Simple Summary The alternative lengthening of telomeres is a telomere maintenance mechanism used by some cancer types to elongate their telomeres without the aid of telomerase. This mechanism contributes to the proliferation and immortality of cancer cells. One of the hallmarks of this mechanism is the interaction with promyelocytic leukemia nuclear bodies, which are suspected to be the key places where telomere extension occurs. Despite the discovery of some mechanisms, elements, key genes, and proteins from the pathway, the alternative lengthening of telomeres mechanism is still poorly understood, and it is highly associated with a poor prognosis. In this study, we combined multiomics approaches with genomic, transcriptomic, and proteomic analyses of 71 genes/proteins related to promyelocytic leukemia nuclear bodies in more than 10,000 cancer samples from The Cancer Genome Atlas Consortium. As a result, 13 key proteins were proposed as candidates for future experimental studies that will validate these proteins as therapeutic markers, which will improve the understanding and treatment of these type of cancers. Abstract Alternative lengthening of telomeres-associated promyelocytic leukemia nuclear bodies (APBs) are a hallmark of telomere maintenance. In the last few years, APBs have been described as the main place where telomeric extension occurs in ALT-positive cancer cell lines. A different set of proteins have been associated with APBs function, however, the molecular mechanisms behind their assembly, colocalization, and clustering of telomeres, among others, remain unclear. To improve the understanding of APBs in the ALT pathway, we integrated multiomics analyses to evaluate genomic, transcriptomic and proteomic alterations, and functional interactions of 71 APBs-related genes/proteins in 32 Pan-Cancer Atlas studies from The Cancer Genome Atlas Consortium (TCGA). As a result, we identified 13 key proteins which showed distinctive mutations, interactions, and functional enrichment patterns across all the cancer types and proposed this set of proteins as candidates for future ex vivo and in vivo analyses that will validate these proteins to improve the understanding of the ALT pathway, fill the current research gap about APBs function and their role in ALT, and be considered as potential therapeutic targets for the diagnosis and treatment of ALT-positive cancers in the future.
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217
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Chen Q, Kuai Y, Wang S, Zhu X, Wang H, Liu W, Cheng L, Yang D. Deep Learning-Based Classification of Epithelial-Mesenchymal Transition for Predicting Response to Therapy in Clear Cell Renal Cell Carcinoma. Front Oncol 2022; 11:782515. [PMID: 35141144 PMCID: PMC8819137 DOI: 10.3389/fonc.2021.782515] [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: 09/24/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) profoundly impacts prognosis and immunotherapy of clear cell renal cell carcinoma (ccRCC). However, not every patient is tested for EMT status because this requires additional genetic studies. In this study, we developed an EMT gene signature to classify the H&E-stained slides from The Cancer Genome Atlas (TCGA) into epithelial and mesenchymal subtypes, then we trained a deep convolutional neural network to classify ccRCC which according to our EMT subtypes accurately and automatically and to further predict genomic data and prognosis. The clinical significance and multiomics analysis of the EMT signature was investigated. Patient cohorts from TCGA (n = 252) and whole slide images were used for training, testing, and validation using an algorithm to predict the EMT subtype. Our approach can robustly distinguish features predictive of the EMT subtype in H&E slides. Visualization techniques also detected EMT-associated histopathological features. Moreover, EMT subtypes were characterized by distinctive genomes, metabolic states, and immune components. Deep learning convolutional neural networks could be an extremely useful tool for predicting the EMT molecular classification of ccRCC tissue. The underlying multiomics information can be crucial in applying the appropriate and tailored targeted therapy to the patient.
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Affiliation(s)
- Qiwei Chen
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, China
- School of Information Science and Technology of Dalian Maritime University, Dalian, China
| | - Yue Kuai
- School of Information and Communication Engineering, Dalian University of Technology, Dalian, China
| | - Shujing Wang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
| | - Xinqing Zhu
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hongyu Wang
- School of Information and Communication Engineering, Dalian University of Technology, Dalian, China
| | - Wenlong Liu
- School of Information and Communication Engineering, Dalian University of Technology, Dalian, China
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Deyong Yang
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, China
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218
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Lee MH, Järvinen P, Nísen H, Brück O, Ilander M, Uski I, Theodoropoulos J, Kankainen M, Mirtti T, Mustjoki S, Kreutzman A. T and NK cell abundance defines two distinct subgroups of renal cell carcinoma. Oncoimmunology 2022; 11:1993042. [PMID: 35003893 PMCID: PMC8741293 DOI: 10.1080/2162402x.2021.1993042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Renal cell carcinoma (RCC) is considered as an immunogenic cancer. Because not all patients respond to current immunotherapies, we aimed to investigate the immunological heterogeneity of RCC tumors. We analyzedthe immunophenotype of the circulating, tumor, and matching adjacent healthy kidney immune cells from 52 nephrectomy patients with multi-parameter flow cytometry. Additionally, we studied the transcriptomic and mutation profiles of 20 clear cell RCC (ccRCC) tumors with bulk RNA sequencing and a customized pan-cancer gene panel. The tumor samples clustered into two distinct subgroups defined by the abundance of intratumoral CD3+ T cells (CD3high, 25/52) and NK cells (NKhigh, 27/52). CD3high tumors had an overall higher frequency of tumor infiltrating lymphocytes and PD-1 expression on the CD8+ T cells compared to NKhigh tumors. The tumor infiltrating T and NK cells had significantly elevated expression levels of LAG-3, PD-1, and HLA-DR compared to the circulating immune cells. Transcriptomic analysis revealed increased immune signaling (IFN-γ, TNF-α via NF-κB, and T cell receptor signaling) and kidney metabolism pathways in the CD3high subgroup. Genomic analysis confirmed the typical ccRCC mutation profile including VHL, PBRM1, and SETD2 mutations, and revealed PBRM1 as a uniquely mutated gene in the CD3high subgroup. Approximately half of the RCC tumors have a high infiltration of NK cells associated with a lower number of tumor infiltrating lymphocytes, lower PD-1 expression, a distinct transcriptomic and mutation profile, providing insights to the immunological heterogeneity of RCC which may impact treatment responses to immunological therapies.
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Affiliation(s)
- Moon Hee Lee
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Petrus Järvinen
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Harry Nísen
- Abdominal Center, Urology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Oscar Brück
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Mette Ilander
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Ilona Uski
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tuomas Mirtti
- Department of Pathology, Helsinki University Hospital and Research Program in Systems Oncology, University of Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Anna Kreutzman
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
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219
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Bakouny Z, Sadagopan A, Ravi P, Metaferia NY, Li J, AbuHammad S, Tang S, Denize T, Garner ER, Gao X, Braun DA, Hirsch L, Steinharter JA, Bouchard G, Walton E, West D, Labaki C, Dudani S, Gan CL, Sethunath V, Carvalho FLF, Imamovic A, Ricker C, Vokes NI, Nyman J, Berchuck JE, Park J, Hirsch MS, Haq R, Mary Lee GS, McGregor BA, Chang SL, Feldman AS, Wu CJ, McDermott DF, Heng DY, Signoretti S, Van Allen EM, Choueiri TK, Viswanathan SR. Integrative clinical and molecular characterization of translocation renal cell carcinoma. Cell Rep 2022; 38:110190. [PMID: 34986355 PMCID: PMC9127595 DOI: 10.1016/j.celrep.2021.110190] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/01/2021] [Accepted: 12/08/2021] [Indexed: 02/08/2023] Open
Abstract
Translocation renal cell carcinoma (tRCC) is a poorly characterized subtype of kidney cancer driven by MiT/TFE gene fusions. Here, we define the landmarks of tRCC through an integrative analysis of 152 patients with tRCC identified across genomic, clinical trial, and retrospective cohorts. Most tRCCs harbor few somatic alterations apart from MiT/TFE fusions and homozygous deletions at chromosome 9p21.3 (19.2% of cases). Transcriptionally, tRCCs display a heightened NRF2-driven antioxidant response that is associated with resistance to targeted therapies. Consistently, we find that outcomes for patients with tRCC treated with vascular endothelial growth factor receptor inhibitors (VEGFR-TKIs) are worse than those treated with immune checkpoint inhibitors (ICI). Using multiparametric immunofluorescence, we find that the tumors are infiltrated with CD8+ T cells, though the T cells harbor an exhaustion immunophenotype distinct from that of clear cell RCC. Our findings comprehensively define the clinical and molecular features of tRCC and may inspire new therapeutic hypotheses.
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Affiliation(s)
- Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Praful Ravi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shatha AbuHammad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Stephen Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas Denize
- Harvard Medical School, Boston, MA, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Emma R. Garner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xin Gao
- Harvard Medical School, Boston, MA, USA,Department of Internal Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - David A. Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Yale Cancer Center / Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Laure Hirsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - John A. Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Emily Walton
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Destiny West
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaan Dudani
- Division of Medical Oncology/Hematology, William Osler Health System, Brampton, ON, Canada
| | - Chun-Loo Gan
- Division of Medical Oncology, Tom Baker Cancer Centre, University of Calgary, AB, Canada
| | | | | | - Alma Imamovic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cora Ricker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Natalie I. Vokes
- Department of Thoracic/Head and Neck Medical Oncology; Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Jackson Nyman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E. Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle S. Hirsch
- Harvard Medical School, Boston, MA, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Rizwan Haq
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley A. McGregor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven L. Chang
- Harvard Medical School, Boston, MA, USA,Division of Urology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Adam S. Feldman
- Department of Urology, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Daniel Y.C. Heng
- Division of Medical Oncology, Tom Baker Cancer Centre, University of Calgary, AB, Canada
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Toni K. Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA,Corresponding authors: Toni K. Choueiri, MD, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts, 02215 (). Tel: +1 617-632-5456, Srinivas R. Viswanathan, MD, PhD, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts, 02215 (). Tel: +1 617-632-2429
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Corresponding authors: Toni K. Choueiri, MD, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts, 02215 (). Tel: +1 617-632-5456, Srinivas R. Viswanathan, MD, PhD, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts, 02215 (). Tel: +1 617-632-2429
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Jiang A, Bao Y, Wang A, Gong W, Gan X, Wang J, Bao Y, Wu Z, Liu B, Lu J, Wang L. Establishment of a Prognostic Prediction and Drug Selection Model for Patients with Clear Cell Renal Cell Carcinoma by Multiomics Data Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3617775. [PMID: 35028006 PMCID: PMC8752262 DOI: 10.1155/2022/3617775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/11/2021] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
METHODS This study was based on the multiomics data (including mRNA, lncRNA, miRNA, methylation, and WES) of 258 ccRCC patients from TCGA database. Firstly, we screened the feature values that had impact on the prognosis and obtained two subtypes. Then, we used 10 algorithms to achieve multiomics clustering and conducted pseudotiming analysis to further validate the robustness of our clustering method, based on which the two subtypes of ccRCC patients were further subtyped. Meanwhile, the immune infiltration was compared between the two subtypes, and drug sensitivity and potential drugs were analyzed. Furthermore, to analyze the heterogeneity of patients at the multiomics level, biological functions between two subtypes were compared. Finally, Boruta and PCA methods were used for dimensionality reduction and cluster analysis to construct a renal cancer risk model based on mRNA expression. RESULTS A prognosis predicting model of ccRCC was established by dividing patients into the high- and low-risk groups. It was found that overall survival (OS) and progression-free interval (PFI) were significantly different between the two groups (p < 0.01). The area under the OS time-dependent ROC curve for 1, 3, 5, and 10 years in the training set was 0.75, 0.72, 0.71, and 0.68, respectively. CONCLUSION The model could precisely predict the prognosis of ccRCC patients and may have implications for drug selection for ccRCC patients.
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Affiliation(s)
- Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yewei Bao
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Anbang Wang
- Department of Urology, Changzheng Hospital, Naval Medical University, (Second Military Medical University), Shanghai, China
| | - Wenliang Gong
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xinxin Gan
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Jie Wang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yi Bao
- Department of Urology, Changzheng Hospital, Naval Medical University, (Second Military Medical University), Shanghai, China
| | - Zhenjie Wu
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Bing Liu
- Department of Urology, The Third Affiliated Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Juan Lu
- Vocational Education Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
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Sobottka B, Nienhold R, Nowak M, Hench J, Haeuptle P, Frank A, Sachs M, Kahraman A, Moch H, Koelzer VH, Mertz KD. Integrated Analysis Of Immunotherapy Treated Clear Cell Renal Cell Carcinomas: An Exploratory Study. J Immunother 2022; 45:35-42. [PMID: 34406159 PMCID: PMC8654255 DOI: 10.1097/cji.0000000000000387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/15/2021] [Indexed: 11/25/2022]
Abstract
Molecular or immunological differences between responders and nonresponders to immune checkpoint inhibitors (ICIs) of clear cell renal cell carcinomas (ccRCCs) remain incompletely understood. To address this question, we performed next-generation sequencing, methylation analysis, genome wide copy number analysis, targeted RNA sequencing and T-cell receptor sequencing, and we studied frequencies of tumor-infiltrating CD8+ T cells, presence of tertiary lymphoid structures (TLS) and PD-L1 expression in 8 treatment-naive ccRCC patients subsequently treated with ICI (3 responders, 5 nonresponders). Unexpectedly, we identified decreased frequencies of CD8+ tumor-infiltrating T cells and TLS, and a decreased expression of PD-L1 in ICI responders when compared with nonresponders. However, neither tumor-specific genetic alterations nor gene expression profiles correlated with response to ICI or the observed immune features. Our results underline the challenge to stratify ccRCC patients for immunotherapy based on routinely available pathologic primary tumor material, even with advanced technologies. Our findings emphasize the analysis of pretreated metastatic tissue in line with recent observations describing treatment effects on the tumor microenvironment. In addition, our data call for further investigation of additional parameters in a larger ccRCC cohort to understand the mechanistic implications of the observed differences in tumor-infiltrating CD8+ T cells, TLS, and PD-L1 expression.
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Affiliation(s)
- Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich
| | | | - Marta Nowak
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich
| | | | | | | | | | - Abdullah Kahraman
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich
| | - Viktor H. Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich
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Gulati S, Labaki C, Karachaliou GS, Choueiri TK, Zhang T. OUP accepted manuscript. Oncologist 2022; 27:125-134. [PMID: 35641205 PMCID: PMC8895741 DOI: 10.1093/oncolo/oyab056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/03/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shuchi Gulati
- Division of Hematology and Oncology, Department of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Georgia Sofia Karachaliou
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC, USA
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tian Zhang
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC, USA
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC, USA
- Division of Hematology and Oncology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
- Corresponding author: Tian Zhang, Division of Hematology and Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.
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223
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Javier-DesLoges J, Derweesh I, McKay RR. Targeted Therapy for Renal Cell Carcinoma. Urol Oncol 2022. [DOI: 10.1007/978-3-030-89891-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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224
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Ricketts CJ, Vocke CD, Lang M, Chen X, Zhao Y, Tran B, Tandon M, Schmidt LS, Ball MW, Linehan WM. A germline 1;3 translocation disrupting the VHL gene: a novel genetic cause for von Hippel-Lindau. J Med Genet 2022; 59:18-22. [PMID: 33067352 PMCID: PMC8080673 DOI: 10.1136/jmedgenet-2020-107308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 12/27/2022]
Abstract
Von Hippel-Lindau (VHL) disease is an autosomal dominant hereditary tumour susceptibility disease caused by germline pathogenic variation of the VHL tumour suppressor gene. Affected individuals are at risk of developing multiple malignant and benign tumours in a number of organs.In this report, a male patient in his 20s who presented to the Urologic Oncology Branch at the National Cancer Institute with a clinical diagnosis of VHL was found to have multiple cerebellar haemangioblastomas, bilateral epididymal cysts, multiple pancreatic cysts, and multiple, bilateral renal tumours and cysts. The patient had no family history of VHL and was negative for germline VHL mutation by standard genetic testing. Further genetic analysis demonstrated a germline balanced translocation between chromosomes 1 and 3, t(1;3)(p36.3;p25) with a breakpoint on chromosome 3 within the second intron of the VHL gene. This created a pathogenic germline alteration in VHL by a novel mechanism that was not detectable by standard genetic testing.Karyotype analysis is not commonly performed in existing genetic screening protocols for patients with VHL. Based on this case, protocols should be updated to include karyotype analysis in patients who are clinically diagnosed with VHL but demonstrate no detectable mutation by existing genetic testing.
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Affiliation(s)
- Christopher J Ricketts
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Cathy D Vocke
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Martin Lang
- Urologic Oncology Branch, National Cancer Institue, Bethesda, Maryland, USA
| | - Xiongfong Chen
- CCR Sequencing Facility, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Yongmei Zhao
- CCR Sequencing Facility, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bao Tran
- CCR Sequencing Facility, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, Bethesda, Maryland, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Mark W Ball
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - W Marston Linehan
- Urologic Oncology Branch, National Cancer Institue, Bethesda, Maryland, USA
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The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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226
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Bassanelli M, Borro M, Roberto M, Giannarelli D, Giacinti S, Di Martino S, Ceribelli A, Russo A, Aschelter A, Scarpino S, Montori A, Pescarmona E, Tomao S, Simmaco M, Cognetti F, Milella M, Marchetti P. A 17-Gene Expression Signature for Early Identification of Poor Prognosis in Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2021; 14:178. [PMID: 35008342 PMCID: PMC8750239 DOI: 10.3390/cancers14010178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/13/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
The Identification of reliable Biomarkers able to predict the outcome after nephrectomy of patients with clear cell renal cell carcinoma (ccRCC) is an unmet need. The gene expression analysis in tumor tissues represents a promising tool for better stratification of ccRCC subtypes and patients' evaluation. METHODS In our study we retrospectively analyzed using Next-Generation expression analysis (NanoString), the expression of a gene panel in tumor tissue from 46 consecutive patients treated with nephrectomy for non-metastatic ccRCC at two Italian Oncological Centres. Significant differences in expression levels of selected genes was sought. Additionally, we performed a univariate and a multivariate analysis on overall survival according to Cox regression model. RESULTS A 17-gene expression signature of patients with a recurrence-free survival (RFS) < 1 year (unfavorable genomic signature (UGS)) and of patients with a RFS > 5 years (favorable genomic signature (FGS)) was identified and resulted in being significantly correlated with overall survival of the patients included in this analysis (HR 51.37, p < 0.0001). CONCLUSIONS The identified Genomic Signatures may serve as potential biomarkers for prognosis prediction of non-metastatic RCC and could drive both follow-up and treatment personalization in RCC management.
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Affiliation(s)
- Maria Bassanelli
- Department of Medical and Surgical Sciences and Translational Medicine, Faculty of Medicine and Psychology, Sapienza University of Rome, 00100 Rome, Italy;
| | - Marina Borro
- (DIMA) Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00187 Rome, Italy;
| | - Michela Roberto
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Medical Oncology Unit, Umberto I University Hospital, Sapienza University of Rome, 00185 Rome, Italy;
| | - Diana Giannarelli
- Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy;
| | - Silvana Giacinti
- Department of Oncology, Sant’Andrea Hospital, 00187 Rome, Italy; (S.G.); (A.A.)
| | - Simona Di Martino
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy; (S.D.M.); (A.R.); (E.P.)
| | - Anna Ceribelli
- Department of Oncology, San Camillo de Lellis Hospital, Viale Kennedy, 12100 Rieti, Italy;
| | - Andrea Russo
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy; (S.D.M.); (A.R.); (E.P.)
| | - Annamaria Aschelter
- Department of Oncology, Sant’Andrea Hospital, 00187 Rome, Italy; (S.G.); (A.A.)
| | - Stefania Scarpino
- Department of Clinical and Molecular Medicine, Pathology Unit, St. Andrea University Hospital, University of Rome La Sapienza, 00187 Rome, Italy; (S.S.); (A.M.)
| | - Andrea Montori
- Department of Clinical and Molecular Medicine, Pathology Unit, St. Andrea University Hospital, University of Rome La Sapienza, 00187 Rome, Italy; (S.S.); (A.M.)
| | - Edoardo Pescarmona
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy; (S.D.M.); (A.R.); (E.P.)
| | - Silverio Tomao
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Medical Oncology Unit, Umberto I University Hospital, Sapienza University of Rome, 00185 Rome, Italy;
| | - Maurizio Simmaco
- Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Advanced Molecular Diagnostic Unit (Dima), Sapienza University, Sant’Andrea Hospital, 00187 Rome, Italy;
| | - Francesco Cognetti
- Medical Oncology 1, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy;
| | - Michele Milella
- Division of Oncology, Integrated University Hospital of Verona, Via S. Francesco 22, 37129 Verona, Italy;
| | - Paolo Marchetti
- Department of Clinical and Molecular Medicine, Oncology Unit, Sant’ Andrea Hospital, Sapienza University of Rome, 00187 Rome, Italy;
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Katzendorn O, Peters I, Dubrowinskaja N, Moog JM, Reese C, Tezval H, Faraj Tabrizi P, Hennenlotter J, Lafos M, Kuczyk MA, Serth J. DNA Methylation in INA, NHLH2, and THBS4 Is Associated with Metastatic Disease in Renal Cell Carcinoma. Cancers (Basel) 2021; 14:cancers14010039. [PMID: 35008203 PMCID: PMC8750163 DOI: 10.3390/cancers14010039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
The detection of DNA methylation in primary tumor tissues could be relevant for early stratification of aggressive renal cell carcinomas (RCCs) as a basis for future personalized adjuvant therapy. Methylated TCGA KIRC based candidate CpG loci in INA, NHLH2, and THBS4 that are possibly associated with RCC metastasis were evaluated by pyrosequencing in 154 paired normal adjacent and primary tumor tissues, as well as in 202 metastatic tissues. Statistical analysis was carried out by bivariate logistic regression for group comparisons, log rank survival analysis, and unsupervised and supervised analysis for the classification of tumors. Increased methylation of INA, NHLH2, and THBS4 loci were significantly associated with distant metastasis in primary tumors (p < 0.05), tissue-specific hypermethylation in metastatic (p = 7.88 × 10-8, 5.57 × 10-10, 2.06 × 10-7) and tumor tissues (p = 3.72 × 10-24, 3.17 × 10-13, 1.58 × 10-19), and shortened progression free survival in patients (p = 0.03). Combined use of CpG site-specific methylation permits the discrimination of tissues with metastatic disease and reveals a significant contribution of CpG sites in all genes to the statistical classification model. Thus, metastasis in RCC is significantly associated with methylation alterations in INA, NHLH2, and THBS4 loci, providing independent information for the potential early detection of aggressive renal cancers as a rationale for stratifying patients to adjuvant therapies.
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Affiliation(s)
- Olga Katzendorn
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Natalia Dubrowinskaja
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Joana M. Moog
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Christel Reese
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Pouriya Faraj Tabrizi
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Jörg Hennenlotter
- Department of Urology, Eberhard Karls University of Tuebingen, 72076 Tuebingen, Germany;
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, 30625 Hannover, Germany;
| | - Markus A. Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
- Correspondence: ; Tel.: +49-511-532-6673
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Park KY, Hefti HO, Liu P, Lugo-Cintrón KM, Kerr SC, Beebe DJ. Immune cell mediated cabozantinib resistance for patients with renal cell carcinoma. Integr Biol (Camb) 2021; 13:259-268. [PMID: 34931665 PMCID: PMC8730366 DOI: 10.1093/intbio/zyab018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/15/2021] [Accepted: 10/29/2021] [Indexed: 01/05/2023]
Abstract
Renal cell carcinoma (RCC) is the third most common genitourinary cancer in the USA. Despite recent advances in the treatment for advanced and metastatic clear cell RCC (ccRCC), the 5-year relative survival rate for the distant disease remains at 12%. Cabozantinib, a tyrosine kinase inhibitor (TKI), which is one of the first-line therapies approved to treat advanced ccRCC as a single agent, is now being investigated as a combination therapy with newer immunotherapeutic agents. However, not much is known about how cabozantinib modulates the immune system. Here, we present a high throughput tri-culture model that incorporates cancer cells, endothelial cells, and patient-derived immune cells to study the effect of immune cells from patients with ccRCC on angiogenesis and cabozantinib resistance. We show that circulating immune cells from patients with ccRCC induce cabozantinib resistance via increased secretion of a set of pro-angiogenic factors. Using multivariate partial least square regression modeling, we identified CD4+ T cell subsets that are correlated with cabozantinib resistance and report the changes in the frequency of these populations in ccRCC patients who are undergoing cabozantinib therapy. These findings provide a potential set of biomarkers that should be further investigated in the current TKI-immunotherapy combination clinical trials to improve personalized treatments for patients with ccRCC.
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Affiliation(s)
- Keon Young Park
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Hunter O Hefti
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA
| | - Peng Liu
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | | | - Sheena C Kerr
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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Roldán FL, Lozano JJ, Ingelmo-Torres M, Carrasco R, Díaz E, Ramirez-Backhaus M, Rubio J, Reig O, Alcaraz A, Mengual L, Izquierdo L. Clinicopathological and Molecular Prognostic Classifier for Intermediate/High-Risk Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13246338. [PMID: 34944958 PMCID: PMC8699125 DOI: 10.3390/cancers13246338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary In this report, we identified biomarkers for tumor progression from tissue samples of intermediate/high-risk ccRCC. Using the molecular findings and the clinical data, we developed an improved prognostic model which could help to provide better individualized management recommendations. Abstract The probability of tumor progression in intermediate/high-risk clear cell renal cell carcinoma (ccRCC) is highly variable, underlining the lack of predictive accuracy of the current clinicopathological factors. To develop an accurate prognostic classifier for these patients, we analyzed global gene expression patterns in 13 tissue samples from progressive and non-progressive ccRCC using Illumina Hi-seq 4000. Expression levels of 22 selected differentially expressed genes (DEG) were assessed by nCounter analysis in an independent series of 71 ccRCCs. A clinicopathological-molecular model for predicting tumor progression was developed and in silico validated in a total of 202 ccRCC patients using the TCGA cohort. A total of 1202 DEGs were found between progressive and non-progressive intermediate/high-risk ccRCC in RNAseq analysis, and seven of the 22 DEGs selected were validated by nCounter. Expression of HS6ST2, pT stage, tumor size, and ISUP grade were found to be independent prognostic factors for tumor progression. A risk score generated using these variables was able to distinguish patients at higher risk of tumor progression (HR 7.27; p < 0.001), consistent with the results obtained from the TCGA cohort (HR 2.74; p < 0.002). In summary, a combined prognostic algorithm was successfully developed and validated. This model may aid physicians to select high-risk patients for adjuvant therapy.
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Affiliation(s)
- Fiorella L. Roldán
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Juan J. Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clinic, 08036 Barcelona, Spain;
| | - Mercedes Ingelmo-Torres
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Raquel Carrasco
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Esther Díaz
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Miguel Ramirez-Backhaus
- Department of Urology, Oncologic Institute of Valencia, 46009 Valencia, Spain; (M.R.-B.); (J.R.)
| | - José Rubio
- Department of Urology, Oncologic Institute of Valencia, 46009 Valencia, Spain; (M.R.-B.); (J.R.)
| | - Oscar Reig
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS) and Medical Oncology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain;
| | - Antonio Alcaraz
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Lourdes Mengual
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-93-227-54-00 (ext. 4820)
| | - Laura Izquierdo
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
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Zhang L, Zhang M, Wang L, Li J, Yang T, Shao Q, Liang X, Ma M, Zhang N, Jing M, Song R, Fan J. Identification of CCL4 as an Immune-Related Prognostic Biomarker Associated With Tumor Proliferation and the Tumor Microenvironment in Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:694664. [PMID: 34900664 PMCID: PMC8652234 DOI: 10.3389/fonc.2021.694664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/05/2021] [Indexed: 12/29/2022] Open
Abstract
The last decade has witnessed revolutionary advances taken in immunotherapy for various malignant tumors. However, immune-related molecules and their characteristics in the prediction of clinical outcomes and immunotherapy response in clear cell renal cell carcinoma (ccRCC) remain largely unclear. C-C Motif Chemokine Ligand 4 (CCL4) was extracted from the intersection analysis of common differentially expressed genes (DEGs) of four microarray datasets from the Gene Expression Omnibus database and immune-related gene lists in the ImmPort database using Cytoscape plug-ins and univariate Cox regression analysis. Subsequential analysis revealed that CCL4 was highly expressed in ccRCC patients, and positively correlated with multiple clinicopathological characteristics, such as grade, stage and metastasis, while negatively with overall survival (OS). We performed gene set enrichment analysis (GSEA) and gene set variant analysis (GSVA) with gene sets coexpressed with CCL4, and observed that gene sets positively related to CCL4 were enriched in tumor proliferation and immune-related pathways while metabolic activities in the negatively one. To further explore the correlation between CCL4 and immune-related biological process, the CIBERSORT algorithm, ESTIMATE method, and tumor mutational burden (TMB) score were employed to evaluate the tumor microenvironment (TME) characteristics of each sample and confirmed that high CCL4 expression might give rise to high immune cell infiltration. Moreover, correlation analysis revealed that CCL4 was positively correlated with common immune checkpoint genes, such as programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA4), and lymphocyte activating 3 (LAG3). Overall, this study demonstrated that CCL4 might serve as a potential immune-related prognostic biomarker to predict clinical outcomes and immunotherapy response in ccRCC. Moreover, CCL4 might contribute to TME modulation, indicating the mechanism CCL4 involved in tumor proliferation and metastasis, which could provide novel therapeutic perceptions for ccRCC patients.
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Affiliation(s)
- Lu Zhang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mengzhao Zhang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lu Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jianlong Li
- Department of Urology, Xi'an NO.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
| | - Tao Yang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qiuya Shao
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Liang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Minghai Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Nan Zhang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Minxuan Jing
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rundong Song
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jinhai Fan
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Oncology Research Lab, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, China
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Gulati S, Previtera M, Lara PN. BRCA1-Associated Protein 1 (BAP-1) as a Prognostic and Predictive Biomarker in Clear Cell Renal Cell Carcinoma: A Systematic Review. KIDNEY CANCER 2021. [DOI: 10.3233/kca-210006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: The gene that encodes BRCA1-associated protein 1 (BAP1) has been reported to be dysregulated in several human cancers such as uveal melanoma, malignant pleural mesothelioma, hepatocellular carcinoma, thymic epithelial tumors, and clear-cell renal cell carcinoma (ccRCC). The gene is located on the human chromosome 3p21.3, encoding a deubiquitinase and acts as a classic two-hit tumor suppressor gene. BAP1 predominantly resides in the nucleus, where it interacts with several chromatin-associated factors, as well as regulates calcium signaling in the cytoplasm. As newer therapies continue to evolve for the management of RCC, it is important to understand the role of BAP1 mutation as a prognostic and predictive biomarker. OBJECTIVE: We aimed to systematically evaluate the role of BAP1 mutations in patients with RCC in terms of its impact on prognosis and its role as a predictive biomarker. METHODS: Following PRISMA guidelines, we performed a systematic literature search using PubMed and Embase through March 2021. Titles and abstracts were screened to identify articles for full-text and then a descriptive review was performed. RESULTS: A total of 490 articles were initially identified. Ultimately 71 articles that met our inclusion criteria published between 2012–2021 were included in the analysis. Data were extracted and organized to reflect the role of BAP1 alterations as a marker of prognosis as well as a marker of response to treatments, such as mTOR inhibitors, VEGF tyrosine kinase inhibitors, and immune checkpoint inhibitors. CONCLUSIONS: Alterations in BAP1 appear to be uniformly associated with poor prognosis in patients with RCC. Knowledge gaps remain with regard to the predictive relevance of BAP1 alterations, especially in the context of immunotherapy. Prospective studies are required to more precisely ascertain the predictive value of BAP1 alterations in RCC.
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Affiliation(s)
- Shuchi Gulati
- Department of Medicine, Division of Hematology and Oncology, University of Cincinnati, Cincinnati, OH, USA
| | - Melissa Previtera
- Academic & Research Services Specialist, Donald C. Harrison Health Sciences Library, University of Cincinnati Libraries, Cincinnati, OH, USA
| | - Primo N. Lara
- Department of Internal Medicine, Division of Hematology and Oncology, UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
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Ged Y, Voss MH. Novel emerging biomarkers to immunotherapy in kidney cancer. Ther Adv Med Oncol 2021; 13:17588359211059367. [PMID: 34868351 PMCID: PMC8640284 DOI: 10.1177/17588359211059367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
The treatment of metastatic renal cell carcinoma has significantly evolved in recent years, particularly with the advent of novel immune checkpoint inhibitors (ICI). Despite the striking benefits observed on a population level, outcomes vary and some patients do not respond to ICI-based regimens, ultimately require salvage therapies. An ever deeper understanding of the disease biology mediated by the development of multiple high-throughput molecular omics has led to significant progress in biomarkers discovery. But despite growing insights into the molecular underpinnings of the tumor microenvironment, biomarkers have not been integrated successfully into clinical practice. In this review, we discuss some of the novel emerging predictive biomarkers to ICIs in metastatic renal cell carcinoma.
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Affiliation(s)
- Yasser Ged
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Martin H Voss
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, New York, NY 10065, USA
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233
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Popławski P, Bogusławska J, Hanusek K, Piekiełko-Witkowska A. Nucleolar Proteins and Non-Coding RNAs: Roles in Renal Cancer. Int J Mol Sci 2021; 22:ijms222313126. [PMID: 34884928 PMCID: PMC8658237 DOI: 10.3390/ijms222313126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Renal cell cancer is the most frequent kidney malignancy. Most RCC cases are classified as clear cell renal cell carcinoma (ccRCC), characterized by high aggressiveness and poor prognosis for patients. ccRCC aggressiveness is defined by classification systems based on changes in morphology of nucleoli, the membraneless substructures of nuclei. The latter act as the sites of ribosome biogenesis as well as the hubs that trap and immobilize proteins, preventing their action in other cellular compartments. Thereby, nucleoli control cellular functioning and homeostasis. Nucleoli are also the sites of activity of multiple noncoding RNAs, including snoRNAs, IGS RNA, and miRNAs. Recent years have brought several remarkable discoveries regarding the role of nucleolar non-coding RNAs, in particular snoRNAs, in ccRCC. The expression of snoRNAs is largely dysregulated in ccRCC tumors. snoRNAs, such as SNHG1, SNHG4 and SNHG12, act as miRNA sponges, leading to aberrant expression of oncogenes and tumor suppressors, and directly contributing to ccRCC development and progression. snoRNAs can also act without affecting miRNA functioning, by altering the expression of key oncogenic proteins such as HIF1A. snoRNAs are also potentially useful biomarkers of ccRCC progression. Here, we comprehensively discuss the role of nucleolar proteins and non-coding RNAs in ccRCC.
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234
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Khare S, Kim LC, Lobel G, Doulias PT, Ischiropoulos H, Nissim I, Keith B, Simon MC. ASS1 and ASL suppress growth in clear cell renal cell carcinoma via altered nitrogen metabolism. Cancer Metab 2021; 9:40. [PMID: 34861885 PMCID: PMC8642968 DOI: 10.1186/s40170-021-00271-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Kidney cancer is a common adult malignancy in the USA. Clear cell renal cell carcinoma (ccRCC), the predominant subtype of kidney cancer, is characterized by widespread metabolic changes. Urea metabolism is one such altered pathway in ccRCC. The aim of this study was to elucidate the contributions of urea cycle enzymes, argininosuccinate synthase 1 (ASS1), and argininosuccinate lyase (ASL) towards ccRCC progression. METHODS We employed a combination of computational, genetic, and metabolomic tools along with in vivo animal models to establish a tumor-suppressive role for ASS1 and ASL in ccRCC. RESULTS We show that the mRNA and protein expression of urea cycle enzymes ASS1 and ASL are reduced in ccRCC tumors when compared to the normal kidney. Furthermore, the loss of ASL in HK-2 cells (immortalized renal epithelial cells) promotes growth in 2D and 3D growth assays, while combined re-expression of ASS1 and ASL in ccRCC cell lines suppresses growth in 2D, 3D, and in vivo xenograft models. We establish that this suppression is dependent on their enzymatic activity. Finally, we demonstrate that conservation of cellular aspartate, regulation of nitric oxide synthesis, and pyrimidine production play pivotal roles in ASS1+ASL-mediated growth suppression in ccRCC. CONCLUSIONS ccRCC tumors downregulate the components of the urea cycle including the enzymes argininosuccinate synthase 1 (ASS1) and argininosuccinate lyase (ASL). These cytosolic enzymes lie at a critical metabolic hub in the cell and are involved in aspartate catabolism and arginine and nitric oxide biosynthesis. Loss of ASS1 and ASL helps cells redirect aspartate towards pyrimidine synthesis and support enhanced proliferation. Additionally, reduced levels of ASS1 and ASL might help regulate nitric oxide (NO) generation and mitigate its cytotoxic effects. Overall, our work adds to the understanding of urea cycle enzymes in a context-independent of ureagenesis, their role in ccRCC progression, and uncovers novel potential metabolic vulnerabilities in ccRCC.
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Affiliation(s)
- Sanika Khare
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Laura C Kim
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Graham Lobel
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paschalis-Thomas Doulias
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Pharmacology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Pharmacology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Itzhak Nissim
- Division of Genetics and Metabolism, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Biochemistry, and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brian Keith
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Han D, Yu Z, Zhang H, Liu H, Wang B, Qian D. Microenvironment-associated gene HSD11B1 may serve as a prognostic biomarker in clear cell renal cell carcinoma: a study based on TCGA, RT‑qPCR, Western blotting, and immunohistochemistry. Bioengineered 2021; 12:10891-10904. [PMID: 34845968 PMCID: PMC8810109 DOI: 10.1080/21655979.2021.1994908] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common malignant tumors worldwide. The clinical treatment of ccRCC is strongly associated with the tumor microenvironment (TME). Identifying potential markers of ccRCC is important to improve prognosis. Therefore, in the present study, the levels of immune/stromal components and the proportion of tumor-infiltrating immune cells (TIICs) were determined in 611 ccRCC samples using the ESTIMATE and CIBERSORT analytical tools. Subsequently, hydroxysteroid 11-beta dehydrogenase-1 (HSD11B1) was identified by univariate Cox regression analysis, protein-protein interaction (PPI) networks and clinical survival analysis to be associated with ccRCC prognosis. At the same time, the abundance of HSD11B1 increased significantly in ccRCC was verified by western blotting, RT‑qPCR and immunostaining analysis. Furthermore, Gene Set Enrichment Analysis (GSEA) and TME suggested that HSD11B1 was involved in TME immune-related status. Taken together, the results of the present study demonstrated that HSD11B1 is a potential prognostic biomarker associated with immune cell infiltration in ccRCC.
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Affiliation(s)
- Di Han
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, P. R. China
| | - Zhongjie Yu
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, P. R. China
| | - Hong Zhang
- School of Public Health, Qingdao University, Qingdao, Shandong, P. R. China
| | - Haipeng Liu
- Oral Research Center, Qingdao Municipal Hospital, Qingdao, Shandong, P. R. China
| | - Bin Wang
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, P. R. China
| | - Donmeng Qian
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, P. R. China
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Alaghehbandan R, Przybycin CG, Verkarre V, Mehra R. Chromophobe renal cell carcinoma: Novel molecular insights and clinicopathologic updates. Asian J Urol 2021; 9:1-11. [PMID: 35198391 PMCID: PMC8841285 DOI: 10.1016/j.ajur.2021.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 01/12/2023] Open
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Cost-Effectiveness Analysis of First-Line Nivolumab Plus Cabozantinib for Advanced Renal Cell Carcinoma in the United States. Adv Ther 2021; 38:5662-5670. [PMID: 34664194 DOI: 10.1007/s12325-021-01926-0] [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: 08/12/2021] [Accepted: 09/16/2021] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Nivolumab plus cabozantinib improved progression-free survival and overall survival compared with sunitinib in the first-line treatment of advanced renal cell carcinoma (RCC) according to CheckMate 9ER study. METHODS A Markov model was developed to compare the costs and effectiveness of nivolumab plus cabozantinib with those of sunitinib in the first-line treatment of advanced RCC. Primary outcomes were costs, quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratio (ICER). Model uncertainty was assessed in univariable and probabilistic sensitivity analyses. RESULTS The total cost per patient was $681,425 for nivolumab plus cabozantinib and $256,302 for sunitinib. The incremental QALY for nivolumab plus cabozantinib was 0.49 compared with sunitinib. The ICER for nivolumab plus cabozantinib was $863,720 per QALY gained versus sunitinib. The results remained robust in univariable and probabilistic sensitivity analyses. CONCLUSIONS On the basis of a willingness-to-pay threshold of $150,000, nivolumab plus cabozantinib was not cost-effective under current drug pricing in the first-line treatment of advanced RCC from a US payer's perspective.
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Molecular Mechanisms of Resistance to Immunotherapy and Antiangiogenic Treatments in Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13235981. [PMID: 34885091 PMCID: PMC8656474 DOI: 10.3390/cancers13235981] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype arising from renal cell carcinomas. This tumor is characterized by a predominant angiogenic and immunogenic microenvironment that interplay with stromal, immune cells, and tumoral cells. Despite the obscure prognosis traditionally related to this entity, strategies including angiogenesis inhibition with tyrosine kinase inhibitors (TKIs), as well as the enhancement of the immune system with the inhibition of immune checkpoint proteins, such as PD-1/PDL-1 and CTLA-4, have revolutionized the treatment landscape. This approach has achieved a substantial improvement in life expectancy and quality of life from patients with advanced ccRCC. Unfortunately, not all patients benefit from this success as most patients will finally progress to these therapies and, even worse, approximately 5 to 30% of patients will primarily progress. In the last few years, preclinical and clinical research have been conducted to decode the biological basis underlying the resistance mechanisms regarding angiogenic and immune-based therapy. In this review, we summarize the insights of these molecular alterations to understand the resistance pathways related to the treatment with TKI and immune checkpoint inhibitors (ICIs). Moreover, we include additional information on novel approaches that are currently under research to overcome these resistance alterations in preclinical studies and early phase clinical trials.
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239
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Prochazkova K, Ptakova N, Alaghehbandan R, Williamson SR, Vaněček T, Vodicka J, Treska V, Rogala J, Pivovarcikova K, Michalova K, Slisarenko M, Hora M, Michal M, Hes O. Mutation Profile Variability in the Primary Tumor and Multiple Pulmonary Metastases of Clear Cell Renal Cell Carcinoma. A Review of the Literature and Analysis of Four Metastatic Cases. Cancers (Basel) 2021; 13:5906. [PMID: 34885018 PMCID: PMC8656868 DOI: 10.3390/cancers13235906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/13/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
(1) Background: There are limited data concerning inter-tumoral and inter-metastatic heterogeneity in clear cell renal cell carcinoma (CCRCC). The aim of our study was to review published data and to examine mutation profile variability in primary and multiple pulmonary metastases (PMs) in our cohort of four patients with metastatic CCRCC. (2) Methods: Four patients were enrolled in this study. The clinical characteristics, types of surgeries, histopathologic results, immunohistochemical and genetic evaluations of corresponding primary tumor and PMs, and follow-up data were recorded. (3) Results: In our series, the most commonly mutated genes were those in the canonically dysregulated VHL pathway, which were detected in both primary tumors and corresponding metastasis. There were genetic profile differences between primary and metastatic tumors, as well as among particular metastases in one patient. (4) Conclusions: CCRCC shows heterogeneity between the primary tumor and its metastasis. Such mutational changes may be responsible for suboptimal treatment outcomes in targeted therapy settings.
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Affiliation(s)
- Kristyna Prochazkova
- Department of Surgery, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 304 60 Pilsen, Czech Republic; (K.P.); (J.V.); (V.T.)
| | - Nikola Ptakova
- Second Faculty of Medicine, Charles University, 150 06 Prague, Czech Republic;
| | - Reza Alaghehbandan
- Department of Pathology, University of British Columbia, Vancouver, BC 2329, Canada;
| | - Sean R. Williamson
- Robert J. Tomsich Pathology and Laboratory Medicine Institute and Glickman Urological Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Tomáš Vaněček
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 305 99 Pilsen, Czech Republic; (T.V.); (J.R.); (K.P.); (K.M.); (M.S.); (M.M.)
| | - Josef Vodicka
- Department of Surgery, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 304 60 Pilsen, Czech Republic; (K.P.); (J.V.); (V.T.)
| | - Vladislav Treska
- Department of Surgery, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 304 60 Pilsen, Czech Republic; (K.P.); (J.V.); (V.T.)
| | - Joanna Rogala
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 305 99 Pilsen, Czech Republic; (T.V.); (J.R.); (K.P.); (K.M.); (M.S.); (M.M.)
| | - Kristyna Pivovarcikova
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 305 99 Pilsen, Czech Republic; (T.V.); (J.R.); (K.P.); (K.M.); (M.S.); (M.M.)
| | - Kvetoslava Michalova
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 305 99 Pilsen, Czech Republic; (T.V.); (J.R.); (K.P.); (K.M.); (M.S.); (M.M.)
| | - Maryna Slisarenko
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 305 99 Pilsen, Czech Republic; (T.V.); (J.R.); (K.P.); (K.M.); (M.S.); (M.M.)
| | - Milan Hora
- Department of Urology, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 305 99 Pilsen, Czech Republic;
| | - Michal Michal
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 305 99 Pilsen, Czech Republic; (T.V.); (J.R.); (K.P.); (K.M.); (M.S.); (M.M.)
| | - Ondrej Hes
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital Pilsen, Charles University, 305 99 Pilsen, Czech Republic; (T.V.); (J.R.); (K.P.); (K.M.); (M.S.); (M.M.)
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Elias R, Tcheuyap VT, Kaushik AK, Singla N, Gao M, Reig Torras O, Christie A, Mulgaonkar A, Woolford L, Stevens C, Kettimuthu KP, Pavia-Jimenez A, Boroughs LK, Joyce A, Dakanali M, Notgrass H, Margulis V, Cadeddu JA, Pedrosa I, Williams NS, Sun X, DeBerardinis RJ, Öz OK, Zhong H, Seshagiri S, Modrusan Z, Cantarel BL, Kapur P, Brugarolas J. A renal cell carcinoma tumorgraft platform to advance precision medicine. Cell Rep 2021; 37:110055. [PMID: 34818533 PMCID: PMC8762721 DOI: 10.1016/j.celrep.2021.110055] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/10/2021] [Accepted: 11/03/2021] [Indexed: 12/30/2022] Open
Abstract
Renal cell carcinoma (RCC) encompasses a heterogenous group of tumors, but representative preclinical models are lacking. We previously showed that patient-derived tumorgraft (TG) models recapitulate the biology and treatment responsiveness. Through systematic orthotopic implantation of tumor samples from 926 ethnically diverse individuals into non-obese diabetic (NOD)/severe combined immunodeficiency (SCID) mice, we generate a resource comprising 172 independently derived, stably engrafted TG lines from 148 individuals. TG lines are characterized histologically and genomically (whole-exome [n = 97] and RNA [n = 102] sequencing). The platform features a variety of histological and oncogenotypes, including TCGA clades further corroborated through orthogonal metabolomic analyses. We illustrate how it enables a deeper understanding of RCC biology; enables the development of tissue- and imaging-based molecular probes; and supports advances in drug development.
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Affiliation(s)
- Roy Elias
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vanina T Tcheuyap
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Akash K Kaushik
- Howard Hughes Medical Institute and Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nirmish Singla
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ming Gao
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Oscar Reig Torras
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alana Christie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Division of Biostatistics, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aditi Mulgaonkar
- Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Layton Woolford
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Christina Stevens
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kavitha Priya Kettimuthu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrea Pavia-Jimenez
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lindsey K Boroughs
- Howard Hughes Medical Institute and Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Allison Joyce
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marianna Dakanali
- Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hollis Notgrass
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vitaly Margulis
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey A Cadeddu
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ivan Pedrosa
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Noelle S Williams
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiankai Sun
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralph J DeBerardinis
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute and Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Orhan K Öz
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Zhong
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Somasekar Seshagiri
- Department of Microchemistry, Proteomics, Lipidomics and NGS, Genentech, Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and NGS, Genentech, Inc., South San Francisco, CA, USA
| | - Brandi L Cantarel
- Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Wang Z, Chen Z, Zhao H, Lin H, Wang J, Wang N, Li X, Ding D. ISPRF: a machine learning model to predict the immune subtype of kidney cancer samples by four genes. Transl Androl Urol 2021; 10:3773-3786. [PMID: 34804821 PMCID: PMC8575581 DOI: 10.21037/tau-21-650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cell carcinoma (RCC). Immunotherapy, especially anti-PD-1, is becoming a pillar of ccRCC treatment. However, precise biomarkers and robust models are needed to select the proper patients for immunotherapy. Methods A total of 831 ccRCC transcriptomic profiles were obtained from 6 datasets. Unsupervised clustering was performed to identify the immune subtypes among ccRCC samples based on immune cell enrichment scores. Weighted correlation network analysis (WGCNA) was used to identify hub genes distinguishing subtypes and related to prognosis. A machine learning model was established by a random forest (RF) algorithm and used on an open and free online website to predict the immune subtype. Results In the identified immune subtypes, subtype2 was enriched in immune cell enrichment scores and immunotherapy biomarkers. WGCNA analysis identified four hub genes related to immune subtypes, CTLA4, FOXP3, IFNG, and CD19. The RF model was constructed by mRNA expression of these four hub genes, and the value of area under the receiver operating characteristic curve (AUC) was 0.78. Subtype2 patients in the independent validation cohort had a better drug response and prognosis for immunotherapy treatment. Moreover, an open and free website was developed by the RF model (https://immunotype.shinyapps.io/ISPRF/). Conclusions The current study constructs a model and provides a free online website that could identify suitable ccRCC patients for immunotherapy, and it is an important step forward to personalized treatment.
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Affiliation(s)
- Zhifeng Wang
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Zihao Chen
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongfan Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Lin
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Junjie Wang
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Ning Wang
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Xiqing Li
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Degang Ding
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
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242
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Xu Y, Huang D, Zhang K, Tang Z, Ma J, Zhu M, Xiong H. Overexpressing IFITM family genes predict poor prognosis in kidney renal clear cell carcinoma. Transl Androl Urol 2021; 10:3837-3851. [PMID: 34804826 PMCID: PMC8575577 DOI: 10.21037/tau-21-848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/21/2021] [Indexed: 11/09/2022] Open
Abstract
Background The interferon-inducible transmembrane (IFITM) proteins are localized in the endolysosomal and plasma membranes, conferring cellular immunity to various infections. However, the relationship with carcinogenesis remains poorly elucidated. In the present study, we investigated the role of IFITM in kidney renal clear cell carcinoma (KIRC). Methods We utilized the online databases of Oncomine, UALCAN and Human Protein Atlas to analyze the expression of IFITMs and validate their levels in human KIRC cells by qPCR and western blot. Furthermore, we evaluated prognostic significance with the Gene Expression Profiling Interactive Analysis tool (Kaplan-Meier (KM) Plotter) and delineated the immune cell infiltration profile related to IFITMs with the TIMER2.0 database. Results IFITMs were overexpressed in KIRC and varied in subtypes and tumor grades. High expression of IFITMs indicated a poor prognosis and more immune cell infiltration, especially endothelial cells and cancer-associated fibroblasts. IFITMs were associated with immune genes, which correlated with poor prognosis of renal clear cell carcinoma. We also explored the enriched network of IFITMs co-occurrence genes and their targeted transcription factors and miRNA. The expression of IFITMs correlated with hub mutated genes of KIRC. Conclusions IFITMs play a crucial role in the oncogenesis of KIRC and could be a potential surrogate marker for treatment response to targeted therapies.
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Affiliation(s)
- Ying Xu
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Danqi Huang
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kun Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zengqi Tang
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianchi Ma
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mansheng Zhu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hui Xiong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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243
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Kim MC, Jin Z, Kolb R, Borcherding N, Chatzkel JA, Falzarano SM, Zhang W. Updates on Immunotherapy and Immune Landscape in Renal Clear Cell Carcinoma. Cancers (Basel) 2021; 13:5856. [PMID: 34831009 PMCID: PMC8616149 DOI: 10.3390/cancers13225856] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/24/2022] Open
Abstract
Several clinicopathological features of clear cell renal cell carcinomas (ccRCC) contribute to make an "atypical" cancer, including resistance to chemotherapy, sensitivity to anti-angiogenesis therapy and ICIs despite a low mutational burden, and CD8+ T cell infiltration being the predictor for poor prognosis-normally CD8+ T cell infiltration is a good prognostic factor in cancer patients. These "atypical" features have brought researchers to investigate the molecular and immunological mechanisms that lead to the increased T cell infiltrates despite relatively low molecular burdens, as well as to decipher the immune landscape that leads to better response to ICIs. In the present study, we summarize the past and ongoing pivotal clinical trials of immunotherapies for ccRCC, emphasizing the potential molecular and cellular mechanisms that lead to the success or failure of ICI therapy. Single-cell analysis of ccRCC has provided a more thorough and detailed understanding of the tumor immune microenvironment and has facilitated the discovery of molecular biomarkers from the tumor-infiltrating immune cells. We herein will focus on the discussion of some major immune cells, including T cells and tumor-associated macrophages (TAM) in ccRCC. We will further provide some perspectives of using molecular and cellular biomarkers derived from these immune cell types to potentially improve the response rate to ICIs in ccRCC patients.
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Affiliation(s)
- Myung-Chul Kim
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (M.-C.K.); (Z.J.); (R.K.); (S.M.F.)
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Zeng Jin
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (M.-C.K.); (Z.J.); (R.K.); (S.M.F.)
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Ryan Kolb
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (M.-C.K.); (Z.J.); (R.K.); (S.M.F.)
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA;
| | | | - Sara Moscovita Falzarano
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (M.-C.K.); (Z.J.); (R.K.); (S.M.F.)
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (M.-C.K.); (Z.J.); (R.K.); (S.M.F.)
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
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Glennon KI, Maralani M, Abdian N, Paccard A, Montermini L, Nam AJ, Arseneault M, Staffa A, Jandaghi P, Meehan B, Brimo F, Tanguay S, Rak J, Riazalhosseini Y. Rational Development of Liquid Biopsy Analysis in Renal Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13225825. [PMID: 34830979 PMCID: PMC8616270 DOI: 10.3390/cancers13225825] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Among patients affected by renal cell carcinoma (RCC), the most common type of kidney cancer, it remains difficult to identify those who are at high risk for relapse or metastasis. This is in part due to the absence of reliable clinical biomarkers and robust methods to capture them. The aim of our study was to develop an improved assay to capture prognostic genomic biomarkers in circulating tumor DNA (ctDNA) in RCC. For this purpose, we first established a next generation sequencing (NGS) assay, targeting genes that are tailored for RCC and that are largely excluded from commercially available assays. Next, we showed the reliable performance of this assay to detect prognostic gene mutations in tumor DNA isolated from plasma, and from extracellular vesicles. Thus, our study provides a resource to facilitate ctDNA analysis for precision medicine in RCC. Abstract Renal cell carcinoma (RCC) is known for its variable clinical behavior and outcome, including heterogeneity in developing relapse or metastasis. Recent data highlighted the potential of somatic mutations as promising biomarkers for risk stratification in RCC. Likewise, the analysis of circulating tumor DNA (ctDNA) for such informative somatic mutations (liquid biopsy) is considered an important advance for precision oncology in RCC, allowing to monitor molecular disease evolution in real time. However, our knowledge about the utility of ctDNA analysis in RCC is limited, in part due to the lack of RCC-appropriate assays for ctDNA analysis. Here, by interrogating different blood compartments in xenograft models, we identified plasma cell-free (cf) DNA and extracellular vesicles (ev) DNA enriched for RCC-associated ctDNA. Additionally, we developed sensitive targeted sequencing and bioinformatics workflows capable of detecting somatic mutations in RCC-relevant genes with allele frequencies ≥ 0.5%. Applying this assay to patient-matched tumor and liquid biopsies, we captured tumor mutations in cf- and ev-DNA fractions isolated from the blood, highlighting the potentials of both fractions for ctDNA analysis. Overall, our study presents an RCC-appropriate sequencing assay and workflow for ctDNA analysis and provides a proof of principle as to the feasibility of detecting tumor-specific mutations in liquid biopsy in RCC patients.
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Affiliation(s)
- Kate I. Glennon
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
- Department of Human Genetics, McGill University, 1205 Doctor Penfield Avenue, Montreal, QC H3A 1B1, Canada
| | - Mahafarin Maralani
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
- Department of Human Genetics, McGill University, 1205 Doctor Penfield Avenue, Montreal, QC H3A 1B1, Canada
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Narges Abdian
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Antoine Paccard
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
| | - Laura Montermini
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Alice Jisoo Nam
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
| | - Madeleine Arseneault
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
| | - Alfredo Staffa
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
| | - Pouria Jandaghi
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
- Department of Human Genetics, McGill University, 1205 Doctor Penfield Avenue, Montreal, QC H3A 1B1, Canada
| | - Brian Meehan
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Fadi Brimo
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada;
| | - Simon Tanguay
- Division of Urology, McGill University, Montreal, QC H4A 3J1, Canada;
| | - Janusz Rak
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Yasser Riazalhosseini
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
- Department of Human Genetics, McGill University, 1205 Doctor Penfield Avenue, Montreal, QC H3A 1B1, Canada
- Correspondence:
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Anker J, Miller J, Taylor N, Kyprianou N, Tsao CK. From Bench to Bedside: How the Tumor Microenvironment Is Impacting the Future of Immunotherapy for Renal Cell Carcinoma. Cells 2021; 10:3231. [PMID: 34831452 PMCID: PMC8619121 DOI: 10.3390/cells10113231] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
Immunotherapy has revolutionized the treatment landscape for many cancer types. The treatment for renal cell carcinoma (RCC) has especially evolved in recent years, from cytokine-based immunotherapies to immune checkpoint inhibitors. Although clinical benefit from immunotherapy is limited to a subset of patients, many combination-based approaches have led to improved outcomes. The success of such approaches is a direct result of the tumor immunology knowledge accrued regarding the RCC microenvironment, which, while highly immunogenic, demonstrates many unique characteristics. Ongoing translational work has elucidated some of the mechanisms of response, as well as primary and secondary resistance, to immunotherapy. Here, we provide a comprehensive review of the RCC immunophenotype with a specific focus on how preclinical and clinical data are shaping the future of immunotherapy.
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Affiliation(s)
- Jonathan Anker
- Division of Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Justin Miller
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.M.); (N.T.)
| | - Nicole Taylor
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.M.); (N.T.)
| | - Natasha Kyprianou
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Department of Pathology and Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Che-Kai Tsao
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.M.); (N.T.)
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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Chen CV, Croom NA, Simko JP, Stohr BA, Chan E. Differential Immunohistochemical and Molecular Profiling of Conventional and Aggressive Components of Chromophobe Renal Cell Carcinoma: Pitfalls for Diagnosis. Hum Pathol 2021; 119:85-93. [PMID: 34800526 DOI: 10.1016/j.humpath.2021.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 11/19/2022]
Abstract
Chromophobe renal cell carcinoma (ChRCC) is a relatively rare subtype of RCC with a characteristic histologic appearance. Most ChRCC are slow growing, but sarcomatoid differentiation and metastases can occur, indicative of aggressive behavior and poor prognosis. Herein, we characterize ten ChRCC with aggressive components, defined as sarcomatoid change and/or metastasis. Immunohistochemistry and next-generation sequencing was performed on available formalin-fixed paraffin-embedded tissue, with differential profiling of conventional and aggressive components. All ten cases showed a conventional component of renal tumor morphologically consistent with ChRCC: three had sarcomatoid change, four had metastases, and three had both sarcomatoid change and metastases. In the primary conventional components, a typical ChRCC IHC pattern (CK7+, CD117+ and CAIX-) was observed in 8/10 cases; 2 cases had rare CK7 staining. In the aggressive components, CD117 and/or CK7 was lost in 7/10 cases; 3 cases showed loss of both. Two of 10 cases showed significant CAIX staining in the aggressive component. All 7 cases that had molecular profiling performed showed characteristic chromosomal losses reported for ChRCC, though two cases showed additional complex copy number alterations in the aggressive component only. Recurrent TP53 mutations (TP53m) were also seen; however surprisingly, the conventional and aggressive components had no shared TP53m: a TP53m was private to aggressive components in 2 cases; to the conventional component in 1 case; and in 4 cases, components demonstrated different TP53m. Of the 21 pathogenic alterations identified in 7 tumors, only a PTEN splicing alteration was shared between both components in one case. In conclusion, ChRCC can have IHC staining patterns and molecular profile that differ between conventional and aggressive components. Interpretation of stains on metastases or small biopsies to determine histologic subtype can be misleading. The lack of shared pathogenic mutations between the two components supports a model in which aggressive ChRCC can have convergent subclones with different TP53m.
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Affiliation(s)
- Constance V Chen
- Department of Pathology, University of California-San Francisco, San Francisco, CA, 94143, USA
| | - Nicole A Croom
- Department of Pathology, University of California-San Francisco, San Francisco, CA, 94143, USA
| | - Jeffry P Simko
- Department of Pathology, University of California-San Francisco, San Francisco, CA, 94143, USA
| | - Bradley A Stohr
- Department of Pathology, University of California-San Francisco, San Francisco, CA, 94143, USA
| | - Emily Chan
- Department of Pathology, University of California-San Francisco, San Francisco, CA, 94143, USA.
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Ding L, Yang Y, Ge Y, Lu Q, Yan Z, Chen X, Du J, Hafizi S, Xu X, Yao J, Liu J, Cao Z, Weygant N. Inhibition of DCLK1 with DCLK1-IN-1 Suppresses Renal Cell Carcinoma Invasion and Stemness and Promotes Cytotoxic T-Cell-Mediated Anti-Tumor Immunity. Cancers (Basel) 2021; 13:cancers13225729. [PMID: 34830884 PMCID: PMC8616267 DOI: 10.3390/cancers13225729] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary In this study, we found that the novel small molecule kinase inhibitor DCLK1-IN-1 not only inhibited DCLK1 phosphorylation, stemness, and EMT-related properties of RCC cells but also revealed its potential as an immunotherapy agent and potential combination therapy with anti-PD1 against RCC in immune co-culture experiments. Abstract The approval of immune checkpoint inhibitors has expanded treatment options for renal cell carcinoma (RCC), but new therapies that target RCC stemness and promote anti-tumor immunity are needed. Previous findings demonstrate that doublecortin-like kinase 1 (DCLK1) regulates stemness and is associated with RCC disease progression. Herein, we demonstrate that small-molecule kinase inhibitor DCLK1-IN-1 strongly inhibits DCLK1 phosphorylation and downregulates pluripotency factors and cancer stem cell (CSC) or epithelial-mesenchymal transition (EMT)-associated markers including c-MET, c-MYC, and N-Cadherin in RCC cell lines. Functionally, DCLK1-IN-1 treatment resulted in significantly reduced colony formation, migration, and invasion. Additionally, assays using floating or Matrigel spheroid protocols demonstrated potent inhibition of stemness. An analysis of clinical populations showed that DCLK1 predicts RCC survival and that its expression is correlated with reduced CD8+ cytotoxic T-cell infiltration and increases in M2 immunosuppressive macrophage populations. The treatment of RCC cells with DCLK1-IN-1 significantly reduced the expression of immune checkpoint ligand PD-L1, and co-culture assays using peripheral blood monocytes (PBMCs) or T-cell expanded PBMCs demonstrated a significant increase in immune-mediated cytotoxicity alone or in combination with anti-PD1 therapy. Together, these findings demonstrate broad susceptibility to DCLK1 kinase inhibition in RCC using DCLK1-IN-1 and provide the first direct evidence for DCLK1-IN-1 as an immuno-oncology agent.
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Affiliation(s)
- Ling Ding
- Department of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; (L.D.); (Y.Y.); (Q.L.); (X.C.); (J.D.)
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Key Laboratory of Integrative Medicine, Fujian Province University, Fuzhou 350122, China
| | - Yuning Yang
- Department of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; (L.D.); (Y.Y.); (Q.L.); (X.C.); (J.D.)
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Key Laboratory of Integrative Medicine, Fujian Province University, Fuzhou 350122, China
| | - Yang Ge
- Department of Oncology, Capital Medical University, Beijing Chao-Yang Hospital, Beijing 100020, China; (Y.G.); (J.Y.); (J.L.)
| | - Qin Lu
- Department of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; (L.D.); (Y.Y.); (Q.L.); (X.C.); (J.D.)
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Key Laboratory of Integrative Medicine, Fujian Province University, Fuzhou 350122, China
| | - Zixing Yan
- Affiliated Fuzhou Hospital of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350001, China;
| | - Xuzheng Chen
- Department of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; (L.D.); (Y.Y.); (Q.L.); (X.C.); (J.D.)
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Key Laboratory of Integrative Medicine, Fujian Province University, Fuzhou 350122, China
| | - Jian Du
- Department of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; (L.D.); (Y.Y.); (Q.L.); (X.C.); (J.D.)
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Key Laboratory of Integrative Medicine, Fujian Province University, Fuzhou 350122, China
| | - Sassan Hafizi
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK;
| | - Xiaohui Xu
- Department of General Surgery, The First People’s Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Suzhou 215400, China;
| | - Jiannan Yao
- Department of Oncology, Capital Medical University, Beijing Chao-Yang Hospital, Beijing 100020, China; (Y.G.); (J.Y.); (J.L.)
| | - Jian Liu
- Department of Oncology, Capital Medical University, Beijing Chao-Yang Hospital, Beijing 100020, China; (Y.G.); (J.Y.); (J.L.)
| | - Zhiyun Cao
- Department of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; (L.D.); (Y.Y.); (Q.L.); (X.C.); (J.D.)
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Key Laboratory of Integrative Medicine, Fujian Province University, Fuzhou 350122, China
- Correspondence: (Z.C.); (N.W.)
| | - Nathaniel Weygant
- Department of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; (L.D.); (Y.Y.); (Q.L.); (X.C.); (J.D.)
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Key Laboratory of Integrative Medicine, Fujian Province University, Fuzhou 350122, China
- Correspondence: (Z.C.); (N.W.)
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Targeted Quantification of Carbon Metabolites Identifies Metabolic Progression Markers and an Undiagnosed Case of SDH-Deficient Clear Cell Renal Cell Carcinoma in a German Cohort. Metabolites 2021; 11:metabo11110764. [PMID: 34822422 PMCID: PMC8624007 DOI: 10.3390/metabo11110764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/22/2021] [Accepted: 11/03/2021] [Indexed: 12/18/2022] Open
Abstract
Renal cell carcinoma (RCC) is among the 10 most common cancer entities and can be categorised into distinct subtypes by differential expression of Krebs cycle genes. We investigated the predictive value of several targeted metabolites with regards to tumour stages and patient survival in an unselected cohort of 420 RCCs. Unsupervised hierarchical clustering of metabolite ratios identified two main clusters separated by α-ketoglutarate (α-KG) levels and sub-clusters with differential levels of the oncometabolite 2-hydroxyglutarate (2HG). Sub-clusters characterised by high 2HG were enriched in higher tumour stages, suggesting metabolite profiles might be suitable predictors of tumour stage or survival. Bootstrap forest models based on single metabolite signatures showed that lactate, 2HG, citrate, aspartate, asparagine, and glutamine better predicted the cancer-specific survival (CSS) of clear cell RCC patients, whereas succinate and α-ketoglutarate were better CSS predictors for papillary RCC patients. Additionally, this assay identifies rare cases of tumours with SDHx mutations, which are caused predominantly by germline mutations and which predispose to development of different neoplasms. Hence, analysis of selected metabolites should be further evaluated for potential utility in liquid biopsies, which can be obtained using less invasive methods and potentially facilitate disease monitoring for both patients and caregivers.
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249
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Au L, Hatipoglu E, Robert de Massy M, Litchfield K, Beattie G, Rowan A, Schnidrig D, Thompson R, Byrne F, Horswell S, Fotiadis N, Hazell S, Nicol D, Shepherd STC, Fendler A, Mason R, Del Rosario L, Edmonds K, Lingard K, Sarker S, Mangwende M, Carlyle E, Attig J, Joshi K, Uddin I, Becker PD, Sunderland MW, Akarca A, Puccio I, Yang WW, Lund T, Dhillon K, Vasquez MD, Ghorani E, Xu H, Spencer C, López JI, Green A, Mahadeva U, Borg E, Mitchison M, Moore DA, Proctor I, Falzon M, Pickering L, Furness AJS, Reading JL, Salgado R, Marafioti T, Jamal-Hanjani M, Kassiotis G, Chain B, Larkin J, Swanton C, Quezada SA, Turajlic S. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma. Cancer Cell 2021; 39:1497-1518.e11. [PMID: 34715028 PMCID: PMC8599450 DOI: 10.1016/j.ccell.2021.10.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.
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Affiliation(s)
- Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Emine Hatipoglu
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Gordon Beattie
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Desiree Schnidrig
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicos Fotiadis
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London SW3 6JJ, UK
| | - Steve Hazell
- Department of Pathology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - David Nicol
- Department of Urology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Robert Mason
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lyra Del Rosario
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kim Edmonds
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Karla Lingard
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sarah Sarker
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mary Mangwende
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Eleanor Carlyle
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Imran Uddin
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Pablo D Becker
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ayse Akarca
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Ignazio Puccio
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - William W Yang
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Tom Lund
- Translational Immune Oncology Lab, Centre for Molecular Pathology, The Royal Marsden Hospital, Sutton SM2 5PT, UK
| | - Kim Dhillon
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Marcos Duran Vasquez
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Hang Xu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charlotte Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - José I López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Anna Green
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London SE1 7EH, UK
| | - Ula Mahadeva
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London SE1 7EH, UK
| | - Elaine Borg
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Miriam Mitchison
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Ian Proctor
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Mary Falzon
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Lisa Pickering
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Andrew J S Furness
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne VIC 300, Australia; Department of Pathology, GZA-ZNA Hospitals, Wilrijk, Antwerp, Belgium
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - James Larkin
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK.
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
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Papanicolau-Sengos A, Aldape K. DNA Methylation Profiling: An Emerging Paradigm for Cancer Diagnosis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:295-321. [PMID: 34736341 DOI: 10.1146/annurev-pathol-042220-022304] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Histomorphology has been a mainstay of cancer diagnosis in anatomic pathology for many years. DNA methylation profiling is an additional emerging tool that will serve as an adjunct to increase accuracy of pathological diagnosis. Genome-wide interrogation of DNA methylation signatures, in conjunction with machine learning methods, has allowed for the creation of clinical-grade classifiers, most prominently in central nervous system and soft tissue tumors. Tumor DNA methylation profiling has led to the identification of new entities and the consolidation of morphologically disparate cancers into biologically coherent entities, and it will progressively become mainstream in the future. In addition, DNA methylation patterns in circulating tumor DNA hold great promise for minimally invasive cancer detection and classification. Despite practical challenges that accompany any new technology, methylation profiling is here to stay and will become increasingly utilized as a cancer diagnostic tool across a range of tumor types. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland 20892, USA; ,
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