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Tang H, Li YX, Lian JJ, Ng HY, Wang SSY. Personalized treatment using predictive biomarkers in solid organ malignancies: A review. TUMORI JOURNAL 2024:3008916241261484. [PMID: 39091157 DOI: 10.1177/03008916241261484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
In recent years, the influence of specific biomarkers in the diagnosis and prognosis of solid organ malignancies has been increasingly prominent. The relevance of the use of predictive biomarkers, which predict cancer response to specific forms of treatment provided, is playing a more significant role than ever before, as it affects diagnosis and initiation of treatment, monitoring for efficacy and side effects of treatment, and adjustment in treatment regimen in the long term. In the current review, we explored the use of predictive biomarkers in the treatment of solid organ malignancies, including common cancers such as colorectal cancer, breast cancer, lung cancer, prostate cancer, and cancers associated with high mortalities, such as pancreatic cancer, liver cancer, kidney cancer and cancers of the central nervous system. We additionally analyzed the goals and types of personalized treatment using predictive biomarkers, and the management of various types of solid organ malignancies using predictive biomarkers and their relative efficacies so far in the clinical settings.
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2
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Maldonado E, Rathmell WK, Shapiro GI, Takebe N, Rodon J, Mahalingam D, Trikalinos NA, Kalebasty AR, Parikh M, Boerner SA, Balido C, Krings G, Burns TF, Bergsland EK, Munster PN, Ashworth A, LoRusso P, Aggarwal RR. A Phase II Trial of the WEE1 Inhibitor Adavosertib in SETD2-Altered Advanced Solid Tumor Malignancies (NCI 10170). CANCER RESEARCH COMMUNICATIONS 2024; 4:1793-1801. [PMID: 38920407 PMCID: PMC11264598 DOI: 10.1158/2767-9764.crc-24-0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/16/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
We sought to evaluate the efficacy of WEE1 inhibitor adavosertib in patients with solid tumor malignancies (cohort A) and clear cell renal cell carcinoma (ccRCC; cohort B). NCT03284385 was a parallel cohort, Simon two-stage, phase II study of adavosertib (300 mg QDAY by mouth on days 1-5 and 8-12 of each 21-day cycle) in patients with solid tumor malignancies harboring a pathogenic SETD2 mutation. The primary endpoint was the objective response rate. Correlative assays evaluated the loss of H3K36me3 by IHC, a downstream consequence of SETD2 loss, in archival tumor tissue. Eighteen patients were enrolled (9/cohort). The median age was 60 years (range 45-74). The median duration of treatment was 1.28 months (range 0-24+). No objective responses were observed in either cohort; accrual was halted following stage 1. Minor tumor regressions were observed in 4/18 (22%) evaluable patients. Stable disease (SD) was the best overall response in 10/18 (56%) patients, including three patients with SD > 4 months. One patient with ccRCC remains on treatment for >24 months. The most common adverse events of any grade were nausea (59%), anemia (41%), diarrhea (41%), and neutropenia (41%). Nine patients (50%) experienced a Grade ≥3 adverse event. Of eight evaluable archival tissue samples, six (75%) had a loss of H3K36me3 by IHC. Adavosertib failed to exhibit objective responses in SETD2-altered ccRCC and other solid tumor malignancies although prolonged SD was observed in a subset of patients. Combination approaches may yield greater depth of tumor response. SIGNIFICANCE WEE1 inhibition with adavosertib monotherapy demonstrated limited clinical activity in patients with SETD2-altered solid tumors despite compelling preclinical data indicating a synthetic lethal effect, which did not translate into robust tumor regression. Loss of the H3K36me3 trimethylation mark caused by SETD2-deficiency was confirmed in the majority of evaluable tumors. A subset of patients derived clinical benefit as manifested by minor tumor regressions and prolonged SD.
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Affiliation(s)
- Edward Maldonado
- University of California, San Francisco, San Francisco, California.
| | | | | | | | - Jordi Rodon
- Investigational Cancer Therapeutics, MD Anderson Cancer Center, Houston, Texas.
| | | | | | | | - Mamta Parikh
- University of California, Davis, Davis, California.
| | | | - Celene Balido
- University of California, San Francisco, San Francisco, California.
| | - Gregor Krings
- University of California, San Francisco, San Francisco, California.
| | - Timothy F. Burns
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
| | | | | | - Alan Ashworth
- University of California, San Francisco, San Francisco, California.
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Bursch KL, Goetz CJ, Jiao G, Nuñez R, Olp MD, Dhiman A, Khurana M, Zimmermann MT, Urrutia RA, Dykhuizen EC, Smith BC. Cancer-associated polybromo-1 bromodomain 4 missense variants variably impact bromodomain ligand binding and cell growth suppression. J Biol Chem 2024; 300:107146. [PMID: 38460939 PMCID: PMC11002309 DOI: 10.1016/j.jbc.2024.107146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024] Open
Abstract
The polybromo, brahma-related gene 1-associated factors (PBAF) chromatin remodeling complex subunit polybromo-1 (PBRM1) contains six bromodomains that recognize and bind acetylated lysine residues on histone tails and other nuclear proteins. PBRM1 bromodomains thus provide a link between epigenetic posttranslational modifications and PBAF modulation of chromatin accessibility and transcription. As a putative tumor suppressor in several cancers, PBRM1 protein expression is often abrogated by truncations and deletions. However, ∼33% of PBRM1 mutations in cancer are missense and cluster within its bromodomains. Such mutations may generate full-length PBRM1 variant proteins with undetermined structural and functional characteristics. Here, we employed computational, biophysical, and cellular assays to interrogate the effects of PBRM1 bromodomain missense variants on bromodomain stability and function. Since mutations in the fourth bromodomain of PBRM1 (PBRM1-BD4) comprise nearly 20% of all cancer-associated PBRM1 missense mutations, we focused our analysis on PBRM1-BD4 missense protein variants. Selecting 16 potentially deleterious PBRM1-BD4 missense protein variants for further study based on high residue mutational frequency and/or conservation, we show that cancer-associated PBRM1-BD4 missense variants exhibit varied bromodomain stability and ability to bind acetylated histones. Our results demonstrate the effectiveness of identifying the unique impacts of individual PBRM1-BD4 missense variants on protein structure and function, based on affected residue location within the bromodomain. This knowledge provides a foundation for drawing correlations between specific cancer-associated PBRM1 missense variants and distinct alterations in PBRM1 function, informing future cancer personalized medicine approaches.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Christopher J Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Raymundo Nuñez
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Mallika Khurana
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael T Zimmermann
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Raul A Urrutia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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4
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de Miguel-Perez D, Pickering EM, Malapelle U, Grier W, Pepe F, Pisapia P, Russo G, Pinto JA, Russo A, Troncone G, Culligan MJ, Scilla KA, Mehra R, Mohindra P, Arrieta O, Cardona AF, Del Re M, Sachdeva A, Hirsch FR, Wolf A, Friedberg JS, Rolfo C. Genomic profiling of tissue and blood predicts survival outcomes in patients with resected pleural mesothelioma. Eur J Cancer 2024; 196:113457. [PMID: 38008032 DOI: 10.1016/j.ejca.2023.113457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
PURPOSE Pleural mesothelioma (PM) is an aggressive tumor still considered incurable, in part due to the lack of predictive biomarkers. Little is known about the clinical implications of molecular alterations in resectable PM tissues and blood. Here, we characterized genetic alterations to identify prognostic and predictive biomarkers in patients with resected PM. EXPERIMENTAL DESIGN Targeted next-generation sequencing was performed in retrospective pleural tumor tissue and paired plasma samples from stage IB-IIIB resected PM. Association between prognosis and presence of specific mutations was validated in silico. RESULTS Thirty PM tissues and paired blood samples from 12 patients were analyzed. High tissue tumor mutational burden (TMB) (>10 mutations/Mb), tissue median minor allele frequency (MAF) (>9 mutations/Mb), and blood TMB (>6 mutations/Mb), tissue KMT2C, PBRM1, PKHD1,EPHB1 and blood LIFR mutations correlated with longer disease-free survival and/or overall survival. High concordance (>80%) between tissue and blood was found for some mutations. CONCLUSIONS Tissue TMB and MAF, blood TMB, and specific mutations correlated with outcomes in patients with resected PM and should be further studied to validate their role as prognostic biomarkers and potentially predictive factors for combinations with immune-checkpoint inhibitors. This suggest that molecular profiling could identify longer survivors in patients with resected PM.
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Affiliation(s)
- Diego de Miguel-Perez
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Edward M Pickering
- Section of Interventional Pulmonology, Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - William Grier
- Division of Pulmonary and Critical Care Medicine, University of Maryland Medical Center, Baltimore, MD, USA
| | - Francesco Pepe
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Joseph A Pinto
- Centro de Investigación Básica y Traslacional, Auna Ideas, Lima, Peru
| | - Alessandro Russo
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Giancarlo Troncone
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Melissa J Culligan
- Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, USA
| | - Katherine A Scilla
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ranee Mehra
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Pranshu Mohindra
- Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Andres F Cardona
- Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC) / Foundation for Clinical and Applied Cancer Research (FICMAC) / Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Marzia Del Re
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashutosh Sachdeva
- Section of Interventional Pulmonology, Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Fred R Hirsch
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea Wolf
- Department of Thoracic Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph S Friedberg
- Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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Yan W, Hou N, Zheng J, Zhai W. Predictive genomic biomarkers of therapeutic effects in renal cell carcinoma. Cell Oncol (Dordr) 2023; 46:1559-1575. [PMID: 37223875 DOI: 10.1007/s13402-023-00827-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND In recent years, there have been great improvements in the therapy of renal cell carcinoma. Nevertheless, the therapeutic effect varies significantly from person to person. To discern the effective treatment for different populations, predictive molecular biomarkers in response to target, immunological, and combined therapies are widely studied. CONCLUSION This review summarized those studies from three perspectives (SNPs, mutation, and expression level) and listed the relationship between biomarkers and therapeutic effect, highlighting the great potential of predictive molecular biomarkers in metastatic RCC therapy. However, due to a series of reasons, most of these findings require further validation.
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Affiliation(s)
- Weijie Yan
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Naiqiao Hou
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junhua Zheng
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zhai
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Sellner F, Compérat E, Klimpfinger M. Genetic and Epigenetic Characteristics in Isolated Pancreatic Metastases of Clear-Cell Renal Cell Carcinoma. Int J Mol Sci 2023; 24:16292. [PMID: 38003482 PMCID: PMC10671160 DOI: 10.3390/ijms242216292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Isolated pancreatic metastases of renal cell carcinoma (IsPMRCC) are a rare manifestation of metastatic, clear-cell renal cell carcinoma (RCC) in which distant metastases occur exclusively in the pancreas. In addition to the main symptom of the isolated occurrence of pancreatic metastases, the entity surprises with additional clinical peculiarities: (a) the unusually long interval of about 9 years between the primary RCC and the onset of pancreatic metastases; (b) multiple pancreatic metastases occurring in 36% of cases; (c) favourable treatment outcomes with a 75% 5-year survival rate; and (d) volume and growth-rate dependent risk factors generally accepted to be relevant for overall survival in metastatic surgery are insignificant in isPMRCC. The genetic and epigenetic causes of exclusive pancreatic involvement have not yet been investigated and are currently unknown. Conversely, according to the few available data in the literature, the following genetic and epigenetic peculiarities can already be identified as the cause of the protracted course: 1. high genetic stability of the tumour cell clones in both the primary tumour and the pancreatic metastases; 2. a low frequency of copy number variants associated with aggressiveness, such as 9p, 14q and 4q loss; 3. in the chromatin-modifying genes, a decreased rate of PAB1 (3%) and an increased rate of PBRM1 (77%) defects are seen, a profile associated with a favourable course; 4. an increased incidence of KDM5C mutations, which, in common with increased PBRM1 alterations, is also associated with a favourable outcome; and 5. angiogenetic biomarkers are increased in tumour tissue, while inflammatory biomarkers are decreased, which explains the good response to TKI therapy and lack of sensitivity to IT.
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Affiliation(s)
- Franz Sellner
- Department of General, Visceral and Vascular Surgery, Clinic Favoriten Vienna, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
| | - Eva Compérat
- Clinical Institute of Pathology, Medical University Vienna, 1090 Vienna, Austria
| | - Martin Klimpfinger
- Clinical Institute of Pathology, Medical University Vienna, 1090 Vienna, Austria
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7
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Kapur P, Rajaram S, Brugarolas J. The expanding role of BAP1 in clear cell renal cell carcinoma. Hum Pathol 2023; 133:22-31. [PMID: 35932824 PMCID: PMC9898467 DOI: 10.1016/j.humpath.2022.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023]
Abstract
Mutations drive renal cell carcinoma biology and tumor growth. The BRCA1-associated protein-1 (BAP1) gene is frequently mutated in clear cell renal cell carcinoma (ccRCC) and has emerged as a prognostic and putative predictive biomarker. In this review, we discuss the role of BAP1 as a signature event of a subtype of ccRCC marked by aggressiveness, inflammation, and possibly a heightened response to immunotherapy.
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Affiliation(s)
- Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, Dallas, TX, 75390, USA.
| | - Satwik Rajaram
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, Dallas, TX, 75390, USA; Department of Internal Medicine (Hematology-Oncology), University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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Lou Y, Guo K, Zheng S. Case Report: Pancreatic metastasis of renal cell carcinoma 16 years after nephrectomy. Front Oncol 2023; 13:1091635. [PMID: 36845747 PMCID: PMC9948010 DOI: 10.3389/fonc.2023.1091635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Background Renal cell carcinoma (RCC) is the most common renal malignancy, and may metastasize to different sites in the body via hematogenous and lymphomatous routes. The pancreas is a rare metastatic site of metastatic RCC (mRCC) and isolated pancreatic metastasis of RCC (isPMRCC) is even rarer. Results The present report describes a case of isPMRCC that recurred 16 years after surgery. The patient responded well to the treatment with pancreaticoduodenectomy and systemic therapy, and no recurrence was recorded after 2 years. Conclusions isPMRCC is a distinct subgroup of RCC with unique clinical characteristics that may be explained by its underlying molecular mechanisms. Surgery and systemic therapy confer survival benefits to patients with isPMRCCs, although the recurrence problem has to be paid attention to.
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Affiliation(s)
- Yidan Lou
- Department of Oncology, Affilited Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Zhejiang University School of Medicine, Hangzhou, China
| | - Kaibo Guo
- Department of Oncology, Affilited Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Department of Oncology, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Song Zheng
- Department of Oncology, Affilited Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Department of Oncology, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China,Department of Oncology, Affiliated Hangzhou Cancer Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Song Zheng,
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9
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Sellner F, Thalhammer S, Klimpfinger M. Isolated Pancreatic Metastases of Renal Cell Carcinoma-Clinical Particularities and Seed and Soil Hypothesis. Cancers (Basel) 2023; 15:cancers15020339. [PMID: 36672289 PMCID: PMC9857376 DOI: 10.3390/cancers15020339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
A meta-analysis of 1470 isolated pancreatic metastases of renal cell carcinoma revealed, that, in addition to the unusual exclusive occurrence of pancreatic metastases and the favourable treatment results, the isPMRCC is characterised by further peculiarities of the clinical course: The lack of prognostic significance of volume and growth rate dependent risk factors and the independence of treatment results from standard or local resections. As an explanation for all these peculiarities, according to today's knowledge, a strong acting seed and soil mechanism can serve, which allows embolized tumour cells to grow to metastases only in the pancreas, and prevents them definitively or for years in all other organs. The good prognosis affects not only isolated PM, but also multi-organ metastases of the RCC, in which the additional occurrence of PM is also associated with a better prognosis. Genetic studies revealed specific changes in cases of PM of RCC: Lack of loss of 9p21.3 and 14q31.2, which are otherwise specific gene mutations at the onset of generalization, a low weight genome instability index, i.e., high genetic stability, and a low rate of PAB1 and a high rate of BPRM1 alterations, which signal a more favourable course. The cause of pancreatic organotropism in isPMRCC is still unclear, so only those factors that have been identified as promoting organotropism in other, more frequent tumour entities can be presented: Formation of the pre-metastatic niche, chemokine receptor-ligand mechanism, ability to metabolic adaptation, and immune surveillance.
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Affiliation(s)
- Franz Sellner
- Department of General, Visceral and Vascular Surgery, Clinic Favoriten, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
- Correspondence:
| | - Sabine Thalhammer
- Department of General, Visceral and Vascular Surgery, Clinic Favoriten, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
| | - Martin Klimpfinger
- Clinical Institute of Pathology, Medical University, 1090 Vienna, Austria
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10
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The RBPJ/DAPK3/UBE3A signaling axis induces PBRM1 degradation to modulate the sensitivity of renal cell carcinoma to CDK4/6 inhibitors. Cell Death Dis 2022; 13:295. [PMID: 35368029 PMCID: PMC8976838 DOI: 10.1038/s41419-022-04760-6] [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: 06/21/2021] [Revised: 03/03/2022] [Accepted: 03/16/2022] [Indexed: 11/09/2022]
Abstract
AbstractRenal cell carcinoma (RCC) is a kind of malignant tumor originating from the renal tubular epithelium. Approximately 30% of patients with renal cancer are found to have metastasis when first diagnosed. Exploring other effective treatment methods in addition to surgery is an urgent need in the research field of renal cell carcinoma. Polybromo 1 (PBRM1) is the second most mutated gene in RCC, with a mutation rate of ~40%. Notably, the posttranscriptional modification of PBRM1 in RCC is unclear. In this study, we performed unbiased mass spectrometry of PBRM1 and identified ubiquitin-protein ligase E3A (UBE3A), an extensively studied E3 ligase that can bind with PBRM1 and regulate the stability of PBRM1 in renal cancer cells. We further found that RBPJ/DAPK3 modulated the E3 ligase activity of UBE3A by interfering with the PKA phosphorylation of UBE3A. Finally, we demonstrated that the RBPJ/DAPK3/UBE3A/PBRM1/p21 axis contributed to the sensitivity of renal cancer cells to CDK4/6 inhibitors. In addition, in combination with RBPJ inhibitors, CDK4/6 inhibitors showed synergistically enhanced effects on renal cancer cells. In summary, we not only revealed a novel RBPJ/DAPK3/UBE3A/PBRM1/p21 signaling axis but also identified a combination strategy for overcoming the resistance of renal cancer cells to CDK4/6 inhibitors.
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11
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Sellner F, Thalhammer S, Klimpfinger M. Isolated Pancreatic Metastases of Renal Cell Cancer: Genetics and Epigenetics of an Unusual Tumour Entity. Cancers (Basel) 2022; 14:1539. [PMID: 35326690 PMCID: PMC8945920 DOI: 10.3390/cancers14061539] [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: 02/26/2022] [Accepted: 03/14/2022] [Indexed: 12/16/2022] Open
Abstract
Isolated pancreatic metastases of renal cell carcinoma (isPMRCC) are a rare manifestation of metastatic renal cell carcinoma (mRCC) characterized by two peculiarities: (1). The definite or at least long-term exclusive occurrence of metastases in the pancreas and (2). an unusual low tumour aggressiveness with slow tumour progression and consecutive, good treatment results. According to current knowledge, the exclusive occurrence of pancreatic metastases is due to a highly specific and highly selective seed and soil mechanism, which does not allow metastases settlement outside the pancreas, and whose detailed genetic/epigenetic causes are not yet elucidated. Recent studies have shed light on some of the pathways involved for the protracted course of the disease and highlighted a special genetic profile (lack of loss of 9p, lower weight genome instability index, low frequency of BAP1 alterations, and a high frequency of PBRM1 loss), which deviates from the conventional mRCC profile. Finally, the question of the reasons for the long-term relative genetic stability of the involved cell clones, which is an essential prerequisite for a favourable prognosis, remains unanswered.
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Affiliation(s)
- Franz Sellner
- Department of General-, Visceral- and Vascular Surgery, Clinic Favoriten—Kaiser Franz Josef Hospital, 1100 Vienna, Austria;
| | - Sabine Thalhammer
- Department of General-, Visceral- and Vascular Surgery, Clinic Favoriten—Kaiser Franz Josef Hospital, 1100 Vienna, Austria;
| | - Martin Klimpfinger
- Clinical Institute of Pathology, Medical University, 1090 Vienna, Austria;
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12
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Gudapati P, Abouamara M. Clear cell renal cell carcinoma with stage IV cavoatrial tumour thrombus extension and rapid metastatic reoccurrence postsurgical treatment with review of current treatment strategies. BMJ Case Rep 2022; 15:e248156. [PMID: 35296494 PMCID: PMC8928259 DOI: 10.1136/bcr-2021-248156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2022] [Indexed: 01/20/2023] Open
Abstract
Renal cell carcinoma (RCC) is the most aggressive urological malignancy, with a high recurrence rate. Despite the rapid evolution of the treatment of RCC from non-specific cytotoxic therapies to specific novel combination therapies, the general prognosis for advanced RCC remains poor because patients' responses to these therapies vary. Herein, we present the case of a male in early forties who was diagnosed with a right lower pole renal mass with a level IV tumour thrombus, which was later confirmed as stage IIIc clear cell RCC. About 19 months after radical nephrectomy (curative surgery), the patient was diagnosed with a biopsy-proven metastatic disease, which was not responsive to first-line treatment owing to insufficient data on the best treatment regimen. Herein, we also present a literature review on the pathological impact of genomic alterations in tumour suppressors and highlight emerging paradigm shifts in the treatment of RCC.
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Affiliation(s)
- Prathyusha Gudapati
- Internal Medicine, UNC Health Southeastern, Lumberton, North Carolina, USA
- Internal Medicine, Campbell University Jerry M Wallace School of Osteopathic Medicine, Buies Creek, North Carolina, USA
| | - Mouna Abouamara
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
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13
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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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14
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Dias Carneiro APC, Marques Monteiro FS, Soares A. PBRM1 Mutations as a Predictive Biomarker for Immunotherapy in Metastatic Renal Cell Carcinoma: A Systematic Review. KIDNEY CANCER 2021. [DOI: 10.3233/kca-210111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION: Genomic features linked to prediction of response to immunotherapy in metastatic renal cell carcinoma (mRCC) are still lacking. Protein polybromo-1 (PBRM1) mutations have been studied as a potential biomarker of clinical benefit, with conflicting published data so far. MATERIAL AND METHODS: This systematic review was guided by the standards of the PRISMA statement to identify studies involving mRCC, immunotherapy and mutations in PBRM1. The main objective was to assess the relationship between PBRM1 mutations and response to immune checkpoint inhibitors (ICI) in patients with mRCC. RESULTS: After an initial search that identified 422 studies, 8 studies met the eligibility criteria and were selected for the final analysis. Data are included from 2 trials in the first-line treatment setting, and 6 trials in second- or later treatment lines evaluating the relationship between the presence of PBRM1 mutations and clinical benefit (CB) with ICI treatment. Regarding the first-line treatment setting, the analysis of both studies failed to show any CB in patients with PBRM1 mutations treated with ICI. However, for the second- and later treatment lines, the results were mixed. CONCLUSIONS: PBRM1 mutations may be a potential genomic biomarker to predict response to ICI treatment in patients with mRCC, mainly in second- and later treatment lines, but the existence of conflicting data in the literature highlights an important bias in the studies and the need for additional clinical validation in large, prospective trials.
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Affiliation(s)
- André Paternò Castello Dias Carneiro
- Latin American Cooperative Oncology Group (LACOG), Porto Alegre, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
- Centro Paulista de Oncologia/Oncoclínicas, São Paulo, Brazil
| | - Fernando Sabino Marques Monteiro
- Latin American Cooperative Oncology Group (LACOG), Porto Alegre, Brazil
- Hospital Santa Lucia, Brasilia, Brazil
- Hospital Universitário de Brasília, Brasilia, Brazil
| | - Andrey Soares
- Latin American Cooperative Oncology Group (LACOG), Porto Alegre, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
- Centro Paulista de Oncologia/Oncoclínicas, São Paulo, Brazil
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15
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Liu L, Yi X, Lu C, Pang Y, Zu X, Chen M, Guan X. Background, applications and challenges of radiogenomics in genitourinary tumor. Am J Cancer Res 2021; 11:1936-1945. [PMID: 34094662 PMCID: PMC8167692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/03/2021] [Indexed: 06/12/2023] Open
Abstract
Genitourinary tumors are groups of tumors with high complexity and heterogeneity. For long-term monitoring, biomarkers that can be used in detection, grading and treatment response assessment are needed. With rapid development in imaging technology and cancer genomics, radiogenomics, the combination of "radiology" and "genomics", has emerged as a powerful tool in oncology practice in recent years because imaging can provide some information that genomic test cannot as gene expression and mutation status are usually evaluated on a small portion of the tumor and are usually not powerful enough to reflect tumor heterogeneity. Radiogenomics investigates the correlations between imaging features and gene expression of a disease, especially in oncologic diseases. It aims to detect the disease's mutation status and supplement genomic analysis based on imaging analysis, providing additional findings for diagnosis, treatment decisions, evaluation of treatment response and prognosis prediction of the disease. Recent years have seen an increase in the number of studies investigating the application of radiogenomics in genitourinary tumors. Many studies have shown promising results. However, there still exist limitations and challenges. In this review, we will summarize recent applications of radiogenomics in genitourinary tumors and discuss limitiations, challenges and future directions of radiogenomics.
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Affiliation(s)
- Longfei Liu
- Department of Urology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Xiaoping Yi
- Department of Radiology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Can Lu
- Department of Nephrology, The Second Xiangya Hospital of Central South UniversityChangsha 410000, Hunan, P. R. China
| | - Yingxian Pang
- Department of Urology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Minfeng Chen
- Department of Urology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Xiao Guan
- Department of Urology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
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16
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Chen XJ, Ren AQ, Zheng L, Zheng ED. Predictive Value of KDM5C Alterations for Immune Checkpoint Inhibitors Treatment Outcomes in Patients With Cancer. Front Immunol 2021; 12:664847. [PMID: 33953726 PMCID: PMC8089485 DOI: 10.3389/fimmu.2021.664847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022] Open
Abstract
Lysine (K)-specific demethylase 5C (KDM5C) plays a significant role in the tumor cell proliferation, invasion, drug resistance and the regulation of tumor-related gene expression. Here, we aimed to investigate its predictive value in patients with cancers received immune checkpoint inhibitors (ICIs). We explored the predictive value of KDM5C alterations and the association between KDM5C alteration and immune landscape by using published cohort with clinical outcome and sequenced data from online database. The frequency of KDM5C alterations was 2.1% across 48045 tumor samples with different cancers from 185 studies. KDM5C alterations were correlated with markedly inferior overall survival (OS, 53 vs. 102 months, P<0.0001) than those without. However, in ICI-treated group, patients with KDM5C alterations had a substantially prolonged OS than the wild-type group (not reached vs. 18 months, P=0.0041). The predictive value of KDM5C alterations for ICI treatment outcome was not observed in patients with microsatellite-stable tumors (P=0.2875). Intriguingly, patients with non-small-cell lung cancer and KDM5C alterations receiving ICI had the better progression-free survival than wild type group (13.2 vs. 3.2 months, P=0.0762). Mechanistically, KDM5C altered tumors had dramatically higher TMB level and was associated with significantly higher level of CD8+ T cell infiltration and T effector signature. In conclusion, KDM5C alterations was correlated with enhanced tumor immunogenicity and inflamed anti-tumor immunity, thus resulting in better treatment outcome in cancer patients receiving ICIs.
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Affiliation(s)
- Xiao-Juan Chen
- Department of Clinical Medicine, Graduate School, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Ai-Qun Ren
- Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Liang Zheng
- Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - En-Dian Zheng
- Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
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17
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Schmidt AL, Bain PA, McGregor BA. Tissue Based Biomarkers for Metastatic Clear Cell Renal Carcinoma: A Systematic Review. KIDNEY CANCER 2020. [DOI: 10.3233/kca-200103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: Treatments for metastatic clear cell renal carcinoma (mccRCC) are evolving with multiple targeted and immune therapy drugs currently approved by regulatory agencies as single agents or in combination. Developing predictive biomarkers to determine which patients derive a differential benefit from a particular treatment is an area of ongoing clinical research. Objective: We sought to systematically evaluate the role of tumour tissue-based biomarkers that assist in selection of therapy for mccRCC. Methods: Literature addressing the role of biomarkers in mccRCC was identified through a search of the electronic databases MEDLINE, Embase, and the Web of Science and a hand search of major conference abstracts (from Jan 2010 –Sep 2020). Abstracts were screened to identify papers meriting full-text review. Studies with a comparison arm were included to assess biomarker relevance. A narrative review of studies was performed. Results: The literature search yielded 6784 potentially relevant articles. 133 articles met criteria for full text review, and 10 articles were identified by scanning bibliographies of relevant studies. A total of 33 articles (involving 13 studies) were selected for data extraction and subsequent review. Conclusions: Predictive biomarkers for immediate use in the clinic are lacking, and embedding their evaluation and validation in future clinical trials is needed to refine practice and patient selection.
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Affiliation(s)
- Andrew L. Schmidt
- Lark Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul A. Bain
- Countway Library, Harvard Medical School, Boston, MA, USA
| | - Bradley A. McGregor
- Lark Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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18
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Motzer RJ, Banchereau R, Hamidi H, Powles T, McDermott D, Atkins MB, Escudier B, Liu LF, Leng N, Abbas AR, Fan J, Koeppen H, Lin J, Carroll S, Hashimoto K, Mariathasan S, Green M, Tayama D, Hegde PS, Schiff C, Huseni MA, Rini B. Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade. Cancer Cell 2020; 38:803-817.e4. [PMID: 33157048 PMCID: PMC8436590 DOI: 10.1016/j.ccell.2020.10.011] [Citation(s) in RCA: 268] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/21/2020] [Accepted: 10/07/2020] [Indexed: 12/28/2022]
Abstract
Integrated multi-omics evaluation of 823 tumors from advanced renal cell carcinoma (RCC) patients identifies molecular subsets associated with differential clinical outcomes to angiogenesis blockade alone or with a checkpoint inhibitor. Unsupervised transcriptomic analysis reveals seven molecular subsets with distinct angiogenesis, immune, cell-cycle, metabolism, and stromal programs. While sunitinib and atezolizumab + bevacizumab are effective in subsets with high angiogenesis, atezolizumab + bevacizumab improves clinical benefit in tumors with high T-effector and/or cell-cycle transcription. Somatic mutations in PBRM1 and KDM5C associate with high angiogenesis and AMPK/fatty acid oxidation gene expression, while CDKN2A/B and TP53 alterations associate with increased cell-cycle and anabolic metabolism. Sarcomatoid tumors exhibit lower prevalence of PBRM1 mutations and angiogenesis markers, frequent CDKN2A/B alterations, and increased PD-L1 expression. These findings can be applied to molecularly stratify patients, explain improved outcomes of sarcomatoid tumors to checkpoint blockade versus antiangiogenics alone, and develop personalized therapies in RCC and other indications.
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MESH Headings
- Angiogenesis Inhibitors/pharmacology
- Angiogenesis Inhibitors/therapeutic use
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Bevacizumab/pharmacology
- Bevacizumab/therapeutic use
- Biomarkers, Tumor/genetics
- Carcinoma, Renal Cell/drug therapy
- Carcinoma, Renal Cell/genetics
- Clinical Trials, Phase III as Topic
- Computational Biology/methods
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Immune Checkpoint Inhibitors/therapeutic use
- Kidney Neoplasms/drug therapy
- Kidney Neoplasms/genetics
- Prognosis
- Randomized Controlled Trials as Topic
- Sequence Analysis, RNA
- Sunitinib/pharmacology
- Sunitinib/therapeutic use
- Treatment Outcome
- Unsupervised Machine Learning
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Affiliation(s)
- Robert J Motzer
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Romain Banchereau
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Habib Hamidi
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Thomas Powles
- Barts Cancer Institute and the Royal Free Hospital, Queen Mary University of London, London, UK
| | | | - Michael B Atkins
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | | | - Li-Fen Liu
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Ning Leng
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Alexander R Abbas
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Jinzhen Fan
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Hartmut Koeppen
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Jennifer Lin
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | | | | | - Sanjeev Mariathasan
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Marjorie Green
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Darren Tayama
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | | | - Christina Schiff
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Mahrukh A Huseni
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA.
| | - Brian Rini
- Vanderbilt University Medical Center, Nashville, TN, USA
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19
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Kapur P, Christie A, Rajaram S, Brugarolas J. What morphology can teach us about renal cell carcinoma clonal evolution. KIDNEY CANCER JOURNAL : OFFICIAL JOURNAL OF THE KIDNEY CANCER ASSOCIATION 2020; 18:68-76. [PMID: 34178206 PMCID: PMC8232548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
While cancer is a clonal process, cumulative evidence suggest that tumors are rather heterogenous and are composed of multiple genetically-distinct subclones that arise at different times and either persist and co-exist, expand and evolve, or are eliminated. A paradigm of tumor heterogeneity is renal cell carcinoma (RCC). By exploiting morphological traits and building upon a framework around three axes (architecture, cytology and the microenvironment), we review recent advances in our understanding of RCC evolution leading to an integrated molecular genetic and morphologic evolutionary model with both prognostic and therapeutic implications. The ability to predict cancer evolution may have profound implications for clinical care and is central to oncology.
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Affiliation(s)
- Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Alana Christie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Satwik Rajaram
- Department of Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - James Brugarolas
- Department of Internal Medicine, Hematology-Oncology Division, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
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20
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A pan-cancer analysis of PBAF complex mutations and their association with immunotherapy response. Nat Commun 2020; 11:4168. [PMID: 32820162 PMCID: PMC7441387 DOI: 10.1038/s41467-020-17965-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/23/2020] [Indexed: 12/02/2022] Open
Abstract
There is conflicting data regarding the role of PBAF complex mutations and response to immune checkpoint blockade (ICB) therapy in clear cell renal cell carcinoma (ccRCC) and other solid tumors. We assess the prevalence of PBAF complex mutations from two large cohorts including the pan-cancer TCGA project (n = 10,359) and the MSK-IMPACT pan-cancer immunotherapy cohort (n = 3700). Across both cohorts, PBAF complex mutations, predominantly PBRM1 mutations, are most common in ccRCC. In multivariate models of ccRCC patients treated with ICB (n = 189), loss-of-function (LOF) mutations in PBRM1 are not associated with overall survival (OS) (HR = 1.24, p = 0.47) or time to treatment failure (HR = 0.85, p = 0.44). In a series of 11 solid tumors (n = 2936), LOF mutations are not associated with improved OS in a stratified multivariate model (HR = 0.9, p = 0.7). In a current series of solid tumors treated with ICB, we are unable to demonstrate favorable response to ICB in patients with PBAF complex mutations. The clinical benefit from immunotherapy response in patients with mutations of genes forming the chromatin remodelling complex PBAF remains controversial. Here the authors show that PBAF complex mutations are not associated with favourable response in pan-cancer cohorts of patients treated with immune-checkpoint blockade.
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21
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Attalla K, Weng S, Voss MH, Hakimi AA. Epidemiology, Risk Assessment, and Biomarkers for Patients with Advanced Renal Cell Carcinoma. Urol Clin North Am 2020; 47:293-303. [PMID: 32600532 DOI: 10.1016/j.ucl.2020.04.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the preceding two decades, several milestones have been reached in the management of patients with metastatic renal cell carcinoma (mRCC), including the development of novel targeted agents paralleling an increased understanding of the molecular biology of this disease process. Recently, a renewed enthusiasm for immunotherapy in the form of immune checkpoint blockade has resulted in significant strides in the treatment of mRCC. Despite these advances, treatment remains challenging for clinicians, and only modest survival benefits are observed with current treatment paradigms. The risk-stratification tools and investigated predictive and prognostic biomarkers in patients with mRCC are detailed in this review.
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Affiliation(s)
- Kyrollis Attalla
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, 353 East 68th Street, 5th Floor, New York, NY 10065, USA
| | - Stanley Weng
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, 353 East 68th Street, 5th Floor, New York, NY 10065, USA
| | - Martin H Voss
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, 353 East 68th Street, 5th Floor, New York, NY 10065, USA
| | - A Ari Hakimi
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, 353 East 68th Street, 5th Floor, New York, NY 10065, USA.
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22
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Kocak B, Durmaz ES, Kaya OK, Kilickesmez O. Machine learning-based unenhanced CT texture analysis for predicting BAP1 mutation status of clear cell renal cell carcinomas. Acta Radiol 2020; 61:856-864. [PMID: 31635476 DOI: 10.1177/0284185119881742] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND BRCA1-associated protein 1 (BAP1) mutation is an unfavorable factor for overall survival in patients with clear cell renal cell carcinoma (ccRCC). Radiomics literature about BAP1 mutation lacks papers that consider the reliability of texture features in their workflow. PURPOSE Using texture features with a high inter-observer agreement, we aimed to develop and internally validate a machine learning-based radiomic model for predicting the BAP1 mutation status of ccRCCs. MATERIAL AND METHODS For this retrospective study, 65 ccRCCs were included from a public database. Texture features were extracted from unenhanced computed tomography (CT) images, using two-dimensional manual segmentation. Dimension reduction was done in three steps: (i) inter-observer agreement analysis; (ii) collinearity analysis; and (iii) feature selection. The machine learning classifier was random forest. The model was validated using 10-fold nested cross-validation. The reference standard was the BAP1 mutation status. RESULTS Out of 744 features, 468 had an excellent inter-observer agreement. After the collinearity analysis, the number of features decreased to 17. Finally, the wrapper-based algorithm selected six features. Using selected features, the random forest correctly classified 84.6% of the labelled slices regarding BAP1 mutation status with an area under the receiver operating characteristic curve of 0.897. For predicting ccRCCs with BAP1 mutation, the sensitivity, specificity, and precision were 90.4%, 78.8%, and 81%, respectively. For predicting ccRCCs without BAP1 mutation, the sensitivity, specificity, and precision were 78.8%, 90.4%, and 89.1%, respectively. CONCLUSION Machine learning-based unenhanced CT texture analysis might be a potential method for predicting the BAP1 mutation status of ccRCCs.
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Affiliation(s)
- Burak Kocak
- Department of Radiology, Istanbul Training and Research Hospital, Istanbul, Turkey
| | - Emine Sebnem Durmaz
- Department of Radiology, Buyukcekmece Mimar Sinan State Hospital, Istanbul, Turkey
| | - Ozlem Korkmaz Kaya
- Department of Radiology, Koc University School of Medicine, Koc University Hospital, Istanbul, Turkey
| | - Ozgur Kilickesmez
- Department of Radiology, Istanbul Training and Research Hospital, Istanbul, Turkey
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23
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Abstract
The discovery of the von Hippel-Lindau (VHL) gene marked a milestone in our understanding of clear cell renal cell carcinoma (ccRCC) pathogenesis. VHL inactivation is not only a defining feature of ccRCC, but also the initiating event. Herein, we discuss canonical and noncanonical pVHL functions, as well as breakthroughs shaping our understanding of ccRCC evolution and evolutionary subtypes. We conclude by presenting evolving strategies to therapeutically exploit effector mechanisms downstream of pVHL.
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24
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Prognostic and Predictive Value of PBRM1 in Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2019; 12:cancers12010016. [PMID: 31861590 PMCID: PMC7016957 DOI: 10.3390/cancers12010016] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/27/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most frequent kidney solid tumor, the clear cell RCC (ccRCC) being the major histological subtype. The probability of recurrence and the clinical behavior of ccRCC will greatly depend on the different clinical and histopathological features, already incorporated to different scoring systems, and on the genomic landscape of the tumor. In this sense, ccRCC has for a long time been known to be associated to the biallelic inactivation of Von Hippel-Lindau (VHL) gene which causes aberrant hypoxia inducible factor (HIF) accumulation. Recently, next generation-sequencing technologies have provided the bases for an in-depth molecular characterization of ccRCC, identifying additional recurrently mutated genes, such as PBRM1 (≈40-50%), SETD2 (≈12%), or BAP1 (≈10%). PBRM1, the second most common mutated gene in ccRCC after VHL, is a component of the SWI/SNF chromatin remodeling complex. Different studies have investigated the biological consequences and the potential role of PBRM1 alterations in RCC prognosis and as a drug response modulator, although some results are contradictory. In the present article, we review the current evidence on PBRM1 as potential prognostic and predictive marker in both localized and metastatic RCC.
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25
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Chen P, Wang H, Zhang W, Chen Y, Lv Y, Wu D, Guo M, Deng H. Loss of BAP1 Results in Growth Inhibition and Enhances Mesenchymal-Epithelial Transition in Kidney Tumor Cells. Mol Cell Proteomics 2019; 18:1320-1329. [PMID: 30992312 PMCID: PMC6601205 DOI: 10.1074/mcp.ra119.001457] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
BRCA1-associated protein 1 (BAP1) is a member of the ubiquitin C-terminal hydrolase family of deubiquitinating enzymes and is implicated in transcriptional regulation. The BAP1 gene is mutated in about 10% of patients with ccRCC, the most common form of renal cancer, suggesting that BAP1 is a tumor suppressor. However, whether BAP1 influences the progression of ccRCC tumors expressing wild-type (WT) BAP1 is unclear. Here, we assessed the expression and function of BAP1 using human ccRCC specimens and cell lines. Analysis of datasets in The Cancer Genome Atlas revealed that lower BAP1 expression is correlated with longer overall survival of ccRCC patients. We established human ccRCC cell lines with stable BAP1 knockout and performed multiomic analysis of BAP1-mediated cellular processes. BAP1 knockout downregulated proteins associated with protein synthesis, resulting in decreased cell growth. Importantly, loss of BAP1 decreased the formation of stress fibers and membrane protrusions and induced migration and invasion defects. BAP1 knockout in ccRCC cells also downregulated the expression of transcriptional repressor protein Snail and decreased the activity of Rho family GTPases, promoting the cells to undergo mesenchymal-epithelial transition. Unexpectedly, quantitative proteomics also showed that BAP1 knockout increased expression of several amino acid transporters and multiple tyrosine kinases, including the epidermal growth factor receptor. Overall, our results suggest that BAP1 regulates multiple cellular processes, and we also uncover a new role for BAP1 in controlling mesenchymal-epithelial transition in ccRCC cells.
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Affiliation(s)
- Pengsheng Chen
- From the ‡MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences
| | - Huan Wang
- §MOE Key Laboratory for Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenhao Zhang
- From the ‡MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences
| | - Yuling Chen
- From the ‡MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences;; ¶Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Yang Lv
- ‖Department of Gastroenterology and Hepatology, and Center of Nephrology, Chinese PLA General Hospital, Beijing, China
| | - Di Wu
- ‖Department of Gastroenterology and Hepatology, and Center of Nephrology, Chinese PLA General Hospital, Beijing, China
| | - Mingzhou Guo
- ‖Department of Gastroenterology and Hepatology, and Center of Nephrology, Chinese PLA General Hospital, Beijing, China
| | - Haiteng Deng
- From the ‡MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences;.
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Dudani S, Savard MF, Heng DYC. An Update on Predictive Biomarkers in Metastatic Renal Cell Carcinoma. Eur Urol Focus 2019; 6:34-36. [PMID: 31010693 DOI: 10.1016/j.euf.2019.04.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/12/2019] [Accepted: 04/01/2019] [Indexed: 11/27/2022]
Abstract
One of the major challenges of personalized oncology lies in identifying predictive biomarkers of response to therapy that are practical in the clinical setting. Although many new targeted and immune-based treatments have emerged in recent years as effective systemic therapy options in metastatic renal cell carcinoma (mRCC), optimizing the selection and sequencing of treatments for any individual patient with this disease remains a significant challenge. The CheckMate-214 trial demonstrated that the International mRCC Database Consortium risk model is an effective predictive biomarker in the first-line treatment of mRCC. To date this remains the only prospectively validated predictive biomarker in mRCC. A number of other promising biomarker candidates are under active investigation but require prospective validation before widespread clinical adoption. PATIENT SUMMARY: The International Metastatic Renal Cell Carcinoma Database Consortium risk model is currently the only validated tool that can help clinicians in determining which patients should receive sunitinib versus a combination of nivolumab and ipilimumab as a first treatment for metastatic renal cell carcinoma. Other tools are being actively investigated.
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Affiliation(s)
- Shaan Dudani
- Division of Medical Oncology, Department of Oncology, Tom Baker Cancer Centre, University of Calgary, Calgary, Canada
| | - Marie-France Savard
- Division of Medical Oncology, Department of Oncology, Tom Baker Cancer Centre, University of Calgary, Calgary, Canada
| | - Daniel Y C Heng
- Division of Medical Oncology, Department of Oncology, Tom Baker Cancer Centre, University of Calgary, Calgary, Canada.
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Keenan TE, Burke KP, Van Allen EM. Genomic correlates of response to immune checkpoint blockade. Nat Med 2019; 25:389-402. [PMID: 30842677 PMCID: PMC6599710 DOI: 10.1038/s41591-019-0382-x] [Citation(s) in RCA: 315] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
Abstract
Despite impressive durable responses, immune checkpoint inhibitors do not provide a long-term benefit to the majority of patients with cancer. Understanding genomic correlates of response and resistance to checkpoint blockade may enhance benefits for patients with cancer by elucidating biomarkers for patient stratification and resistance mechanisms for therapeutic targeting. Here we review emerging genomic markers of checkpoint blockade response, including those related to neoantigens, antigen presentation, DNA repair, and oncogenic pathways. Compelling evidence also points to a role for T cell functionality, checkpoint regulators, chromatin modifiers, and copy-number alterations in mediating selective response to immune checkpoint blockade. Ultimately, efforts to contextualize genomic correlates of response into the larger understanding of tumor immune biology will build a foundation for the development of novel biomarkers and therapies to overcome resistance to checkpoint blockade.
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Affiliation(s)
- Tanya E Keenan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kelly P Burke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Immunology, Harvard Medical School, 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.
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Stenehjem DD, Hahn AW, Gill DM, Albertson D, Gowrishankar B, Merriman J, Agarwal AM, Thodima V, Harrington EB, Au TH, Maughan BL, Houldsworth J, Pal SK, Agarwal N. Predictive genomic markers of response to VEGF targeted therapy in metastatic renal cell carcinoma. PLoS One 2019; 14:e0210415. [PMID: 30682039 PMCID: PMC6347137 DOI: 10.1371/journal.pone.0210415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/21/2018] [Indexed: 11/18/2022] Open
Abstract
Background First-line treatment for metastatic renal cell carcinoma (mRCC) is rapidly changing. It currently includes VEGF targeted therapies (TT), multi-target tyrosine kinase inhibitors (TKIs), mTOR inhibitors, and immunotherapy. To optimize outcomes for individual patients, genomic markers of response to therapy are needed. Here, we aim to identify tumor-based genomic markers of response to VEGF TT to optimize treatment selection. Methods From an institutional database, primary tumor tissue was obtained from 79 patients with clear cell mRCC, and targeted sequencing was performed. Clinical outcomes were obtained retrospectively. Progression-free survival (PFS) on first-line VEGF TT was correlated to genomic alterations (GAs) using Kaplan-Meier methodology and Cox proportional hazard models. A composite model of significant GAs predicting PFS in the first-line setting was developed. Results Absence of VHL mutation was associated with inferior PFS on first-line VEGF TT. A trend for inferior PFS was observed with GAs in TP53 and FLT1 C/C variant. A composite model of these 3 GAs was associated with inferior PFS in a dose-dependent manner. Conclusion In mRCC, a composite model of TP53 mutation, wild type VHL, and FLT1 C/C variant strongly predicted PFS on first-line VEGF TT in a dose-dependent manner. These findings require external validation.
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Affiliation(s)
- David D. Stenehjem
- College of Pharmacy, University of Minnesota, Duluth, MN, United States of America
| | - Andrew W. Hahn
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
| | - David M. Gill
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
| | - Daniel Albertson
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, United States of America
| | | | - Joseph Merriman
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
| | - Archana M. Agarwal
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, United States of America
| | - Venkata Thodima
- Cancer Genetics Inc., Rutherford, NJ, United States of America
| | - Erik B. Harrington
- Pharmacotherapy Outcomes Research Center (PORC), College of Pharmacy, University of Utah, Salt Lake City, UT, United States of America
| | - Trang H. Au
- Pharmacotherapy Outcomes Research Center (PORC), College of Pharmacy, University of Utah, Salt Lake City, UT, United States of America
| | - Benjamin L. Maughan
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
| | - Jane Houldsworth
- Cancer Genetics Inc., Rutherford, NJ, United States of America
- Department of Pathology, Mount Sinai School of Medicine, New York City, NY, United States of America
| | - Sumanta K. Pal
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, United States of America
| | - Neeraj Agarwal
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
- * E-mail:
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Hakimi AA, Voss MH, Kuo F, Sanchez A, Liu M, Nixon BG, Vuong L, Ostrovnaya I, Chen YB, Reuter V, Riaz N, Cheng Y, Patel P, Marker M, Reising A, Li MO, Chan TA, Motzer RJ. Transcriptomic Profiling of the Tumor Microenvironment Reveals Distinct Subgroups of Clear Cell Renal Cell Cancer: Data from a Randomized Phase III Trial. Cancer Discov 2019; 9:510-525. [PMID: 30622105 DOI: 10.1158/2159-8290.cd-18-0957] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/09/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022]
Abstract
Metastasis remains the main reason for renal cell carcinoma (RCC)-associated mortality. Tyrosine kinase inhibitors (TKI) impart clinical benefit for most patients with RCC, but the determinants of response are poorly understood. We report an integrated genomic and transcriptomic analysis of patients with metastatic clear cell RCC (ccRCC) treated with TKI therapy and identify predictors of response. Patients in the COMPARZ phase III trial received first-line sunitinib or pazopanib with comparable efficacy. RNA-based analyses revealed four distinct molecular subgroups associated with response and survival. Characterization of these subgroups identified mutation profiles, angiogenesis, and macrophage infiltration programs to be powerful predictors of outcome with TKI therapy. Notably, predictors differed by the type of TKI received. Our study emphasizes the clinical significance of angiogenesis and immune tumor microenvironment and suggests that the critical effects its various aspects have on TKI efficacy vary by agent. This has broad implications for optimizing precision treatment of RCC. SIGNIFICANCE: The determinants of response to TKI therapy in metastatic ccRCC remain unknown. Our study demonstrates that key angiogenic and immune profiles of the tumor microenvironment may affect TKI response. These findings have the potential to inform treatment personalization in patients with RCC.This article is highlighted in the In This Issue feature, p. 453.
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Affiliation(s)
- A Ari Hakimi
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Martin H Voss
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alejandro Sanchez
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ming Liu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Briana G Nixon
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lynda Vuong
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ying-Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem Riaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy A Chan
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert J Motzer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Radiogenomics in Clear Cell Renal Cell Carcinoma: Machine Learning-Based High-Dimensional Quantitative CT Texture Analysis in Predicting PBRM1 Mutation Status. AJR Am J Roentgenol 2019; 212:W55-W63. [PMID: 30601030 DOI: 10.2214/ajr.18.20443] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE The purpose of this study is to evaluate the potential value of machine learning (ML)-based high-dimensional quantitative CT texture analysis in predicting the mutation status of the gene encoding the protein polybromo-1 (PBRM1) in patients with clear cell renal cell carcinoma (RCC). MATERIALS AND METHODS In this retrospective study, 45 patients with clear cell RCC (29 without the PBRM1 mutation and 16 with the PBRM1 mutation) were identified in The Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma database. To create stable ML models and balanced classes, the data were augmented to a total of 161 labeled segmentations (87 without the PBRM1 mutation and 74 with the PBRM1 mutation) by obtaining three to five different samples per patient. Texture features were extracted from corticomedullary phase contrast-enhanced CT images with the use of an open-source software package for the extraction of radiomic data from medical images. Reproducibility analysis (intraclass correlation) was performed by two radiologists. Attribute selection and model optimization were done using a wrapper-based classifier-specific algorithm with nested cross-validation. ML classifiers were an artificial neural network (ANN) algorithm and a random forest (RF) algorithm. The models were validated using 10-fold cross-validation. The reference standard was the PBRM1 mutation status. The main performance metric was the AUC value. RESULTS Of 828 extracted texture features, 759 had excellent reproducibility. Using 10 selected features, the ANN algorithm correctly classified 88.2% (142 of 161) of the clear cell RCCs in terms of PBRM1 mutation status (AUC value, 0.925). Using five selected features, the RF algorithm correctly classified 95.0% (153 of 161) of the clear cell RCCs (AUC value, 0.987). Overall, the RF algorithm performed better than the ANN algorithm (z score = -2.677; p = 0.007). CONCLUSION ML-based high-dimensional quantitative CT texture analysis might be a feasible and potential method for predicting PBRM1 mutation status in patients with clear cell RCC.
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31
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Elias R, Sharma A, Singla N, Brugarolas J. Next Generation Sequencing in Renal Cell Carcinoma: Towards Precision Medicine. KIDNEY CANCER JOURNAL : OFFICIAL JOURNAL OF THE KIDNEY CANCER ASSOCIATION 2019; 17:94-104. [PMID: 32206160 PMCID: PMC7089604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Roy Elias
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
- Department of Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
| | - Akanksha Sharma
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
| | - Nirmish Singla
- Department of Urology, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
| | - James Brugarolas
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
- Department of Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
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32
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Voss MH, Reising A, Cheng Y, Patel P, Marker M, Kuo F, Chan TA, Choueiri TK, Hsieh JJ, Hakimi AA, Motzer RJ. Genomically annotated risk model for advanced renal-cell carcinoma: a retrospective cohort study. Lancet Oncol 2018; 19:1688-1698. [PMID: 30416077 DOI: 10.1016/s1470-2045(18)30648-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND The Memorial Sloan Kettering Cancer Center (MSKCC) risk model is an established prognostic tool for metastatic renal-cell carcinoma that integrates clinical and laboratory data, but is agnostic to tumour genomics. Several mutations, including BAP1 and PBRM1, have prognostic value in renal-cell carcinoma. Using two independent clinical trial datasets of patients with metastatic renal-cell carcinoma, we aimed to study whether the addition of the mutation status for several candidate prognostic genes to the MSKCC model could improve the model's prognostic performance. METHODS In this retrospective cohort study, we used available formalin-fixed paraffin-embedded tumour tissue and clinical outcome data from patients with metastatic renal-cell carcinoma assigned to treatment with tyrosine kinase inhibitors in the COMPARZ trial (training cohort; n=357) and RECORD-3 trial (validation cohort; n=258). Eligible patients in both trials were treatment-naive; had histologically confirmed, advanced, or metastatic renal-cell carcinoma; and a Karnofsky performance status score of at least 70. For each cohort, data from patients in all treatment groups (sunitinib and pazopanib in the training cohort, and everolimus and sunitinib in the validation cohort) were pooled for this analysis. In the training cohort, tumour tissue was used to evaluate somatic mutations by next-generation sequencing, and the association between cancer-specific outcomes (overall survival, progression-free survival, and overall response) and the mutation status of six genes of interest (BAP1, PBRM1, TP53, TERT, KDM5C, and SETD2) was tested. Only those genes with prognostic value in this setting were added to the MSKCC risk model to create a genomically annotated version. The validation cohort was used to independently test the prognostic value of the annotated model compared with the original MSKCC risk model. FINDINGS 357 (32%) of 1110 patients assigned to protocol treatment in the COMPARZ study between August, 2008, and September, 2011, were evaluable for mutation status and clinical outcomes in the training cohort. The independent validation cohort included 258 (55%) of 471 evaluable patients, enrolled between October, 2009, and June, 2011, on the RECORD-3 study. In the training cohort, the presence of any mutation in BAP1 or TP53, or both, and absence of any mutation in PBRM1 were prognostic in terms of overall survival (TP53wt/BAP1mut, TP53mut/BAP1wt o TP53mut/BAP1mut vs TP53wt/BAP1wt hazard ratio [HR] 1·57, 95% CI 1·21-2·04; p=0·0008; PBRM1wt vs PBRMmut, HR 1·58, 1·16-2·14; p=0·0035). The mutation status for these three prognostic genes were added to the original MSKCC risk model to create a genomically annotated version. Distribution of participants in the training cohort into the three risk groups of the original MSKCC model changed from 87 (24%) of 357 patients deemed at favourable risk, 217 (61%) at intermediate risk, and 53 (15%) at poor risk, to distribution across four risk groups in the genomically annotated risk model, with 36 (10%) of 357 deemed at favourable risk, 77 (22%) at good risk, 108 (30%) at intermediate risk, and 136 (38%) at poor risk. Addition of genomic information improved model performance for predicting overall survival (C-index: original model, 0·595 [95% CI 0·557-0·634] vs new model, 0·637 [0·595-0·679]) and progression-free survival (0·567 [95% CI 0·529-0·604] vs 0·602 [0·560-0·643]) with adequate discrimination of the proportion of patients who achieved an objective response (Cochran-Armitage one-sided p=0·0014). Analyses in the validation cohort confirmed the superiority of the genomically annotated risk model over the original version. INTERPRETATION The mutation status of BAP1, PBRM1, and TP53 has independent prognostic value in patients with advanced or metastatic renal-cell carcinoma treated with first-line tyrosine kinase inhibitors. Improved stratification of patients across risk groups by use of a genomically annotated model including the mutational status of these three genes warrants further investigation in prospective trials and could be of use as a model to stratify patients with metastatic renal-cell carcinoma in clinical trials. FUNDING Novartis Pharmaceuticals Corporation, MSKCC Support Grant/Core Grant, and the J Randall & Kathleen L MacDonald Research Fund.
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Affiliation(s)
- Martin H Voss
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Albert Reising
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA
| | - Yuan Cheng
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA
| | - Parul Patel
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA
| | - Mahtab Marker
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA
| | - Fengshen Kuo
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Toni K Choueiri
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - James J Hsieh
- Washington University in St Louis, St Louis, MO, USA
| | - A Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Graham J, Dudani S, Heng DYC. Prognostication in Kidney Cancer: Recent Advances and Future Directions. J Clin Oncol 2018; 36:JCO2018790147. [PMID: 30372388 DOI: 10.1200/jco.2018.79.0147] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The most common type of cancer originating in the kidney is renal cell carcinoma (RCC). In both localized and advanced RCC, a number of clinical, pathologic, and molecular factors have been identified as having prognostic significance. In localized disease, risk stratification has traditionally involved the anatomic extent of disease, and several integrated scoring systems have been developed to help predict outcomes after definitive local therapy. In metastatic RCC, integrated prognostic models have also been established. These are used to stratify patients in contemporary clinical trials and to guide risk-directed treatment selection in clinical practice. Although many prognostic factors are common to both localized and advanced disease, there are some important distinctions. In both of these types of disease, the prognostic role of specific molecular and genomic alterations is an area of active investigation. In this review, we highlight the current staging systems and prognostic factors in localized and metastatic RCC. We also explore future directions in this area, including the expanding role of molecular biomarkers and their integration into the traditional prognostic models.
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Affiliation(s)
- Jeffrey Graham
- Jeffrey Graham and Daniel Y.C. Heng, University of Calgary, Calgary, Alberta; and Shaan Dudani, University of Ottawa, Ottawa, Ontario, Canada
| | - Shaan Dudani
- Jeffrey Graham and Daniel Y.C. Heng, University of Calgary, Calgary, Alberta; and Shaan Dudani, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Y C Heng
- Jeffrey Graham and Daniel Y.C. Heng, University of Calgary, Calgary, Alberta; and Shaan Dudani, University of Ottawa, Ottawa, Ontario, Canada
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34
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Miao D, Margolis CA, Gao W, Voss MH, Li W, Martini DJ, Norton C, Bossé D, Wankowicz SM, Cullen D, Horak C, Wind-Rotolo M, Tracy A, Giannakis M, Hodi FS, Drake CG, Ball MW, Allaf ME, Snyder A, Hellmann MD, Ho T, Motzer RJ, Signoretti S, Kaelin WG, Choueiri TK, Van Allen EM. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science 2018; 359:801-806. [PMID: 29301960 PMCID: PMC6035749 DOI: 10.1126/science.aan5951] [Citation(s) in RCA: 825] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/30/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Abstract
Immune checkpoint inhibitors targeting the programmed cell death 1 receptor (PD-1) improve survival in a subset of patients with clear cell renal cell carcinoma (ccRCC). To identify genomic alterations in ccRCC that correlate with response to anti-PD-1 monotherapy, we performed whole-exome sequencing of metastatic ccRCC from 35 patients. We found that clinical benefit was associated with loss-of-function mutations in the PBRM1 gene (P = 0.012), which encodes a subunit of the PBAF switch-sucrose nonfermentable (SWI/SNF) chromatin remodeling complex. We confirmed this finding in an independent validation cohort of 63 ccRCC patients treated with PD-1 or PD-L1 (PD-1 ligand) blockade therapy alone or in combination with anti-CTLA-4 (cytotoxic T lymphocyte-associated protein 4) therapies (P = 0.0071). Gene-expression analysis of PBAF-deficient ccRCC cell lines and PBRM1-deficient tumors revealed altered transcriptional output in JAK-STAT (Janus kinase-signal transducers and activators of transcription), hypoxia, and immune signaling pathways. PBRM1 loss in ccRCC may alter global tumor-cell expression profiles to influence responsiveness to immune checkpoint therapy.
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Affiliation(s)
- Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Claire A Margolis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Wenhua Gao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Martin H Voss
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Wei Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dylan J Martini
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Craig Norton
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dominick Bossé
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stephanie M Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Dana Cullen
- Bristol-Myers Squibb, New York, NY 10154, USA
| | | | | | - Adam Tracy
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Frank Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Mark W Ball
- James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mohamad E Allaf
- James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Matthew D Hellmann
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Thai Ho
- Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Robert J Motzer
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
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Hsieh JJ, Le V, Cao D, Cheng EH, Creighton CJ. Genomic classifications of renal cell carcinoma: a critical step towards the future application of personalized kidney cancer care with pan-omics precision. J Pathol 2018; 244:525-537. [PMID: 29266437 DOI: 10.1002/path.5022] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/10/2017] [Accepted: 12/13/2017] [Indexed: 12/17/2022]
Abstract
Over the past 20 years, classifications of kidney cancer have undergone major revisions based on morphological refinements and molecular characterizations. The 2016 WHO classification of renal tumors recognizes more than ten different renal cell carcinoma (RCC) subtypes. Furthermore, the marked inter- and intra-tumor heterogeneity of RCC is now well appreciated. Nevertheless, contemporary multi-omics studies of RCC, encompassing genomics, transcriptomics, proteomics, and metabolomics, not only highlight apparent diversity but also showcase and underline commonality. Here, we wish to provide an integrated perspective concerning the future 'functional' classification of renal cancer by bridging gaps among morphology, biology, multi-omics, and therapeutics. This review focuses on recent progress and elaborates the potential value of contemporary pan-omics approaches with a special emphasis on cancer genomics unveiled through next-generation sequencing technology, and how an integrated multi-omics approach might impact precision-based personalized kidney cancer care in the near future. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- James J Hsieh
- Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University, St Louis, MO, USA
| | - Valerie Le
- Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University, St Louis, MO, USA
| | - Dengfeng Cao
- Department of Pathology, Washington University, St Louis, MO, USA
| | - Emily H Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad J Creighton
- Human Genome Sequencing Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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