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Bailey CN, Martin BJ, Petkov VI, Schussler NC, Stevens JL, Bentler S, Cress RD, Doherty JA, Durbin EB, Gomez SL, Gonsalves L, Hernandez BY, Liu L, Morawski BM, Schymura MJ, Schwartz SM, Ward KC, Wiggins C, Wu XC, Goldberg MS, Siegel JJ, Cook RW, Covington KR, Kurley SJ. 31-Gene Expression Profile Testing in Cutaneous Melanoma and Survival Outcomes in a Population-Based Analysis: A SEER Collaboration. JCO Precis Oncol 2023; 7:e2300044. [PMID: 37384864 PMCID: PMC10530886 DOI: 10.1200/po.23.00044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 07/01/2023] Open
Abstract
PURPOSE The DecisionDx-Melanoma 31-gene expression profile (31-GEP) test is validated to classify cutaneous malignant melanoma (CM) patient risk of recurrence, metastasis, or death as low (class 1A), intermediate (class 1B/2A), or high (class 2B). This study aimed to examine the effect of 31-GEP testing on survival outcomes and confirm the prognostic ability of the 31-GEP at the population level. METHODS Patients with stage I-III CM with a clinical 31-GEP result between 2016 and 2018 were linked to data from 17 SEER registries (n = 4,687) following registries' operation procedures for linkages. Melanoma-specific survival (MSS) and overall survival (OS) differences by 31-GEP risk category were examined using Kaplan-Meier analysis and the log-rank test. Crude and adjusted hazard ratios (HRs) were calculated using Cox regression model to evaluate variables associated with survival. 31-GEP tested patients were propensity score-matched to a cohort of non-31-GEP tested patients from the SEER database. Robustness of the effect of 31-GEP testing was assessed using resampling. RESULTS Patients with a 31-GEP class 1A result had higher 3-year MSS and OS than patients with a class 1B/2A or class 2B result (MSS: 99.7% v 97.1% v 89.6%, P < .001; OS: 96.6% v 90.2% v 79.4%, P < .001). A class 2B result was an independent predictor of MSS (HR, 7.00; 95% CI, 2.70 to 18.00) and OS (HR, 2.39; 95% CI, 1.54 to 3.70). 31-GEP testing was associated with a 29% lower MSS mortality (HR, 0.71; 95% CI, 0.53 to 0.94) and 17% lower overall mortality (HR, 0.83; 95% CI, 0.70 to 0.99) relative to untested patients. CONCLUSION In a population-based, clinically tested melanoma cohort, the 31-GEP stratified patients by their risk of dying from melanoma.
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Affiliation(s)
| | | | - Valentina I. Petkov
- Surveillance Research Program, Division of Cancer Control & Population Sciences, National Cancer Institute, Bethesda, MD
| | | | | | | | - Rosemary D. Cress
- Public Health Institute, Cancer Registry of Greater California, Sacramento, CA
| | - Jennifer A. Doherty
- Hunstman Cancer Institute, University of Utah, Salt Lake City, UT
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | - Eric B. Durbin
- Cancer Research Informatics Shared Resource Facility, Markey Cancer Center, Kentucky Cancer Registry, University of Kentucky, KY
| | - Scarlett L. Gomez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Lou Gonsalves
- Connecticut Tumor Registry, Connecticut Department of Public Health, Hartford, CT
| | | | - Lihua Liu
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Maria J. Schymura
- Bureau of Cancer Epidemiology, New York State Department of Health, Albany, NY
- School of Public Health Epidemiology & Biostatistics, University at Albany, State University of New York, New York, NY
| | - Stephen M. Schwartz
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | | | - Charles Wiggins
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM
| | - Xiao-Cheng Wu
- Louisiana State University, School of Medicine, New Orleans, LA
| | - Matthew S. Goldberg
- Castle Biosciences, Inc, Friendswood, TX
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY
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Jarell A, Gastman BR, Dillon LD, Hsueh EC, Podlipnik S, Covington KR, Cook RW, Bailey CN, Quick AP, Martin BJ, Kurley SJ, Goldberg MS, Puig S. Optimizing treatment approaches for patients with cutaneous melanoma by integrating clinical and pathologic features with the 31-gene expression profile test. J Am Acad Dermatol 2022; 87:1312-1320. [PMID: 35810840 DOI: 10.1016/j.jaad.2022.06.1202] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Many patients with low-stage cutaneous melanoma will experience tumor recurrence, metastasis, or death, and many higher staged patients will not. OBJECTIVE To develop an algorithm by integrating the 31-gene expression profile test with clinicopathologic data for an optimized, personalized risk of recurrence (integrated 31 risk of recurrence [i31-ROR]) or death and use i31-ROR in conjunction with a previously validated algorithm for precise sentinel lymph node positivity risk estimates (i31-SLNB) for optimized treatment plan decisions. METHODS Cox regression models for ROR were developed (n = 1581) and independently validated (n = 523) on a cohort with stage I-III melanoma. Using National Comprehensive Cancer Network cut points, i31-ROR performance was evaluated using the midpoint survival rates between patients with stage IIA and stage IIB disease as a risk threshold. RESULTS Patients with a low-risk i31-ROR result had significantly higher 5-year recurrence-free survival (91% vs 45%, P < .001), distant metastasis-free survival (95% vs 53%, P < .001), and melanoma-specific survival (98% vs 73%, P < .001) than patients with a high-risk i31-ROR result. A combined i31-SLNB/ROR analysis identified 44% of patients who could forego sentinel lymph node biopsy while maintaining high survival rates (>98%) or were restratified as being at a higher or lower risk of recurrence or death. LIMITATIONS Multicenter, retrospective study. CONCLUSION Integrating clinicopathologic features with the 31-GEP optimizes patient risk stratification compared to clinicopathologic features alone.
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Affiliation(s)
- Abel Jarell
- Northeast Dermatology Associates, PC, Portsmouth, New Hampshire
| | | | - Larry D Dillon
- Surgical Oncology & General Surgery, Colorado Springs, Colorado
| | - Eddy C Hsueh
- Department of Surgery, St Louis University, St Louis, Missouri
| | - Sebastian Podlipnik
- Dermatology Department, Hospital Clínic Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain. & Centro de investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Kyle R Covington
- Research and Development, Castle Biosciences, Inc, Friendswood, Texas
| | - Robert W Cook
- Research and Development, Castle Biosciences, Inc, Friendswood, Texas.
| | | | - Ann P Quick
- Research and Development, Castle Biosciences, Inc, Friendswood, Texas
| | - Brian J Martin
- Research and Development, Castle Biosciences, Inc, Friendswood, Texas
| | - Sarah J Kurley
- Research and Development, Castle Biosciences, Inc, Friendswood, Texas
| | | | - Susana Puig
- Dermatology Department, Hospital Clínic Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain. & Centro de investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
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Dillon LD, McPhee M, Davidson RS, Quick AP, Martin B, Covington KR, Zolochevska O, Cook RW, Vetto JT, Jarell AD, Fleming MD. Expanded evidence that the 31-gene expression profile test provides clinical utility for melanoma management in a multicenter study. Curr Med Res Opin 2022; 38:1267-1274. [PMID: 35081854 DOI: 10.1080/03007995.2022.2033560] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVE National Comprehensive Cancer Network (NCCN) guidelines for cutaneous melanoma (CM) recommend physicians consider increased surveillance for patients who typically have lower melanoma survival rates (stages IIB-IV as determined by the American Joint Committee on Cancer (AJCC), 8th edition). However, up to 15% of patients identified as having a low recurrence risk (stages I-IIA) experience disease recurrence, and some patients identified as having a high recurrence risk will not experience any recurrence. The 31-gene expression profile test (31-GEP) stratifies patient recurrence risk into low (Class 1) and high (Class 2) and has demonstrated risk-appropriate impact on disease management and clinical decisions. METHODS Five-year plans for lab work, frequency of clinical visits, and imaging pre- and post-31-GEP test results were assessed for a cohort of 509 stage I-III patients following an interim subset analysis of 247 patients. RESULTS After receiving 31-GEP results, 50.6% of patients had a change in management plans in at least one of the following categories-clinical visits, lab work, or surveillance imaging. The changes aligned with the risk predicted by the 31-GEP for 76.1% of patients with a Class 1 result and 78.7% of patients with a Class 2 result. A Class 1 31-GEP result was associated with changes toward low-intensity management recommendations, while a Class 2 result was associated with changes toward high-intensity management recommendations. CONCLUSION The 31-GEP can stratify patient recurrence risk in patients with CM, and clinicians understand and apply the prognostic ability of the 31-GEP test to alter patient management in risk-appropriate directions.
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Affiliation(s)
- Larry D Dillon
- Larry D. Dillon Surgical Oncology and General Surgery, Colorado Springs, CO, USA
| | - Michael McPhee
- Breast Cancer Program, Advent Health Cancer Institute, Orlando, FL, USA
| | - Robert S Davidson
- Department of Surgical Oncology, Morton Plant Mease Healthcare, FL, USA
| | - Ann P Quick
- Castle Biosciences, Inc, Friendswood, TX, USA
| | | | | | | | | | - John T Vetto
- Department of Neurology, Surgical Oncology, Oregon Health & Science University, Portland, OR, USA
| | - Abel D Jarell
- Department of Dermatology, Northeast Dermatology Associates, P.C., Portsmouth, NH, USA
| | - Martin D Fleming
- Department of Surgical Oncology, The University of Tennessee Health Science Center, Memphis, TN, USA
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Hong Y, Kurley SJ, Bailey CN, Martin B, Goldberg MS, Petkov VI, Covington KR, Zakharia Y. Validation of the 31-gene expression profile test to stratify melanoma-specific survival in an unselected, prospectively tested cohort of patients with stage IIB-III cutaneous melanoma. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e21538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e21538 Background: Given recent FDA extended approval of Pembrolizumab for stage IIB-IIC cutaneous melanoma (CM) patients, it is critical to risk-stratify patients to balance potential benefits versus toxicities of adjuvant therapy. The 31-gene expression profile (31-GEP) is a validated test for CM for risk of recurrence or metastasis prognosis in patients with stage I-III CM. A low-risk (Class 1A) 31-GEP result is associated with lower recurrence risk and higher melanoma-specific survival than an intermediate (Class 1B/2A) or high-risk (Class 2B) result. To validate the 31-GEP’s ability to stratify patients’ risk in an unselected, prospectively tested cohort of therapy-eligible CM patients, we collaborated with the National Cancer Institute and the Surveillance, Epidemiology, and End Results (SEER) program. Methods: A linkage was conducted between SEER registries’ CM cases diagnosed 2012-2018, and 31-GEP tested patients between 2013-2020. A de-identified dataset was used for the analysis. Kaplan-Meier analysis with log-rank test was used to analyze patient melanoma-specific survival (MSS) in the overall cohort and the subset of patients with potential adjuvant therapy access: stage IIB-III melanoma (n = 615). Results: In the overall cohort of patients (N = 5,225), those with a 31-GEP Class 1A result had higher 3-year MSS than patients with a Class 2B result (99.7% vs. 90.4%, p < 0.001). In multivariable Cox regression analysis, a Class 2B result was an independent significant predictor of MSS (HR = 5.71, p = 0.01), as were age (HR = 1.05, p < 0.001), SLN positivity (HR = 2.42, p = 0.02), and T2b (HR = 8.29, p = 0.025) and T4b (HR = 11.99, p = 0.009) tumors. In the subset of patients with stage IIB-III melanoma, those with a 31-GEP Class 1A result had higher 3-year MSS (98.8% vs. 82.4%, p = 0.02) than patients with a Class 2B result. Patients with a Class 2B result had a five and a half times higher event rate than those with a Class 1A result for MSS (5.5% [21/382] vs. 1.0% [1/105]). Conclusions: In a large, unselected, prospectively tested cohort of patients with stage I-III CM, the 31-GEP stratified patient risk of dying from melanoma, validating previous studies. While the 31-GEP identified a subgroup (Class 1A) of traditionally high-risk patients (stage IIB-III CM) who had a > 98% MSS over three years, it can also facilitate identifying patients who could warrant earlier adjuvant therapy with a higher 31-GEP class designation.
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Thorpe RB, Covington KR, Caruso HG, Quick AP, Zolochevska O, Bricca GM, Campoli M, DeBloom JR, Fazio MJ, Greenhaw BN, Kirkland EB, Machan ML, Brodland DG, Zitelli JA. Development and validation of a nomogram incorporating gene expression profiling and clinical factors for accurate prediction of metastasis in patients with cutaneous melanoma following Mohs micrographic surgery. J Am Acad Dermatol 2022; 86:846-853. [PMID: 34808324 DOI: 10.1016/j.jaad.2021.10.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 09/23/2021] [Accepted: 10/30/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND There is a need to improve prognostic accuracy for patients with cutaneous melanoma. A 31-gene expression profile (31-GEP) test uses the molecular biology of primary tumors to identify individual patient metastatic risk. OBJECTIVE Develop a nomogram incorporating 31-GEP with relevant clinical factors to improve prognostic accuracy. METHODS In an IRB-approved study, 1124 patients from 9 Mohs micrographic surgery centers were prospectively enrolled, treated with Mohs micrographic surgery, and underwent 31-GEP testing. Data from 684 of those patients with at least 1-year follow-up or a metastatic event were included in nomogram development to predict metastatic risk. RESULTS Logistic regression modeling of 31-GEP results and T stage provided the simplest nomogram with the lowest Bayesian information criteria score. Validation in an archival cohort (n = 901) demonstrated a significant linear correlation between observed and nomogram-predicted risk of metastasis. The resulting nomogram more accurately predicts the risk for cutaneous melanoma metastasis than T stage or 31-GEP alone. LIMITATIONS The patient population is representative of Mohs micrographic surgery centers. Sentinel lymph node biopsy was not performed for most patients and could not be used in the nomogram. CONCLUSIONS Integration of 31-GEP and T stage can gain clinically useful prognostic information from data obtained noninvasively.
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Affiliation(s)
| | | | | | | | | | | | | | - James R DeBloom
- South Carolina Skin Cancer Center, Greenville, South Carolina
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Wisco OJ, Marson JW, Litchman GH, Brownstone N, Covington KR, Martin BJ, Quick AP, Siegel JJ, Caruso HG, Cook RW, Winkelmann RR, Rigel DS. Improved cutaneous melanoma survival stratification through integration of 31-gene expression profile testing with the American Joint Committee on Cancer 8th Edition Staging. Melanoma Res 2022; 32:98-102. [PMID: 35254332 PMCID: PMC8893124 DOI: 10.1097/cmr.0000000000000804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/14/2021] [Indexed: 11/26/2022]
Abstract
Cutaneous melanoma (CM) survival is assessed using averaged data from the American Joint Committee on Cancer 8th edition (AJCC8). However, subsets of AJCC8 stages I-III have better or worse survival than the predicted average value. The objective of this study was to determine if the 31-gene expression profile (31-GEP) test for CM can further risk-stratify melanoma-specific mortality within each AJCC8 stage. This retrospective multicenter study of 901 archival CM samples obtained from patients with stages I-III CM assessed 31-GEP test predictions of 5-year melanoma-specific survival (MSS) using Kaplan-Meier and Cox proportional hazards. In stage I-III CM population, patients with a Class 2B result had a lower 5-year MSS (77.8%) than patients with a Class 1A result (98.7%) and log-rank testing demonstrated significant stratification of MSS [χ2 (2df, n = 901) = 99.7, P < 0.001). Within each stage, 31-GEP data provided additional risk stratification, including in stage I [χ2 (2df, n = 415) = 11.3, P = 0.004]. Cox regression multivariable analysis showed that the 31-GEP test was a significant predictor of melanoma-specific mortality (MSM) in patients with stage I-III CM [hazard ratio: 6.44 (95% confidence interval: 2.61-15.85), P < 0.001]. This retrospective study focuses on Class 1A versus Class 2B results. Intermediate results (Class 1B/2A) comprised 21.6% of cases with survival rates between Class 1A and 2B, and similar to 5-year MSS AJCC stage values. Data from the 31-GEP test significantly differentiates MSM into lower (Class 1A) and higher risk (Class 2B) groups within each AJCC8 stage. Incorporating 31-GEP results into AJCC8 survival calculations has the potential to more precisely assess survival and enhance management guidance.
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Affiliation(s)
| | | | - Graham H. Litchman
- Department of Dermatology, St. John’s Episcopal Hospital, Far Rockaway, New York
| | | | - Kyle R. Covington
- Research and Development, Castle Biosciences, Inc., Friendswood, Texas
| | - Brian J. Martin
- Research and Development, Castle Biosciences, Inc., Friendswood, Texas
| | - Ann P. Quick
- Research and Development, Castle Biosciences, Inc., Friendswood, Texas
| | | | - Hillary G. Caruso
- Research and Development, Castle Biosciences, Inc., Friendswood, Texas
| | - Robert W. Cook
- Research and Development, Castle Biosciences, Inc., Friendswood, Texas
| | | | - Darrell S. Rigel
- Department of Dermatology, Mount Sinai Ichan School of Medicine, New York, New York, USA
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Borman S, Wilkinson J, Meldi-Sholl L, Johnson C, Carter K, Covington KR, Fitzgerald AL, Kurley SJ, Farberg AS, Goldberg MS, Monzon FA, Oelschlager K, Cook RW. Analytical validity of DecisionDx-SCC, a gene expression profile test to identify risk of metastasis in cutaneous squamous cell carcinoma (SCC) patients. Diagn Pathol 2022; 17:32. [PMID: 35216597 PMCID: PMC8876832 DOI: 10.1186/s13000-022-01211-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/25/2022] [Indexed: 12/30/2022] Open
Abstract
Background To improve identification of patients with cutaneous squamous cell carcinoma (SCC) at high risk for metastatic disease, the DecisionDx-SCC assay, a prognostic 40-gene expression profile (40-GEP) test, was developed and validated. The 40-GEP assay utilizes RT-PCR gene expression analysis on primary tumor biopsy tissue to evaluate the expression of 34 signature gene targets and 6 normalization genes. The test provides classifications of low risk (Class 1), moderate risk (Class 2A), and high risk (Class 2B) of metastasis within 3 years of diagnosis. The primary objective of this study was to validate the analytical performance of the 40-gene expression signature. Methods The repeatability and reproducibility of the 40-GEP test was evaluated by performance of inter-assay, intra-assay, and inter-operator precision experiments along with monitoring the reliability of sample and reagent stability for class call concordance. The technical performance of clinical orders from September 2020 through July 2021 for the 40-GEP test was assessed. Results Patient hematoxylin and eosin (H&E) stained slides were reviewed by a board-certified pathologist to assess minimum acceptable tumor content. Class specific controls (Class 1 and Class 2B) were evaluated with Levey-Jennings analysis and demonstrated consistent and reproducible results. Inter-assay, inter-operator and intra-assay concordance were all ≥90%, with short-term and long-term RNA stability also meeting minimum concordance requirements. Of the 2586 orders received, 93.5% remained eligible for testing, with 97.1% of all tested samples demonstrating actionable class call results. Conclusion DecisionDx-SCC demonstrates a high degree of analytical precision, yielding high concordance rates across multiple performance experiments, along with exhibiting robust technical reliability on clinical samples.
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Affiliation(s)
| | | | | | | | | | - Kyle R Covington
- Castle Biosciences, Inc, 505 S. Friendswood Dr., Ste 400, Friendswood, TX, 77546, USA
| | - Alison L Fitzgerald
- Castle Biosciences, Inc, 505 S. Friendswood Dr., Ste 400, Friendswood, TX, 77546, USA
| | - Sarah J Kurley
- Castle Biosciences, Inc, 505 S. Friendswood Dr., Ste 400, Friendswood, TX, 77546, USA
| | | | - Matthew S Goldberg
- Castle Biosciences, Inc, 505 S. Friendswood Dr., Ste 400, Friendswood, TX, 77546, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Federico A Monzon
- Castle Biosciences, Inc, 505 S. Friendswood Dr., Ste 400, Friendswood, TX, 77546, USA
| | | | - Robert W Cook
- Castle Biosciences, Inc, 505 S. Friendswood Dr., Ste 400, Friendswood, TX, 77546, USA.
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Arron ST, Wysong A, Hall MA, Bailey CN, Covington KR, Kurley SJ, Goldberg MS, Kasprzak JM, Somani A, Ibrahim SF, Brodland DG, Cleaver NJ, Maher IA, Xia Y, Koyfman SA, Newman JG. Gene expression profiling for metastatic risk in head and neck cutaneous squamous cell carcinoma. Laryngoscope Investig Otolaryngol 2022; 7:135-144. [PMID: 35155791 PMCID: PMC8823155 DOI: 10.1002/lio2.724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/19/2021] [Accepted: 12/21/2021] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE Over 50% of newly diagnosed cutaneous squamous cell carcinoma (cSCC) lesions occur in the head and neck (cSCC-HN), and metastasis to nodal basins in this region further complicates surgical and adjuvant treatment. The current study addressed whether the 40-gene expression profile (40-GEP) test can predict metastatic risk in cSCC-HN with improved accuracy and provide independent prognostic value to complement current risk assessment methods. STUDY DESIGN Multicenter, retrospective cohort study. METHODS Formalin-fixed paraffin-embedded primary tumor tissue and associated clinical data from patients with cSCC-HN (n = 278) were collected from 33 independent centers. Samples were analyzed via the 40-GEP test. Cases were staged per American Joint Committee on Cancer, Eighth Edition (AJCC8) and Brigham and Women's Hospital (BWH) criteria after comprehensive medical record and pathology report review. Metastasis-free survival (MFS) rates were determined, and risk factors were analyzed via Cox regression. RESULTS The 40-GEP test classified the cohort into low (Class 1, n = 126; 45.3%), moderate (Class 2A, n = 134; 48.2%), and high (Class 2B, n = 18; 6.5%) metastatic risk at 3 years postdiagnosis. Regional/distant metastasis occurred in 54 patients (19.4%). MFS rates were 92.1% (Class 1), 76.1% (Class 2A), and 44.4% (Class 2B; p < .0001). Multivariate analysis of 40-GEP results with AJCC8 or BWH tumor stage, or clinicopathologic risk factors, demonstrated independent prognostic value of the 40-GEP test (p < .03). Accuracy of predicting metastatic risk was also improved using 40-GEP classification (p < .02). CONCLUSIONS Improved metastatic risk stratification through the 40-GEP test could complement cSCC-HN risk assessment for better-informed decision-making for treatment and surveillance and ultimately improve patient outcomes. LEVEL OF EVIDENCE 3.
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Affiliation(s)
| | - Ashley Wysong
- Department of DermatologyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Mary A. Hall
- Research and Development, Castle Biosciences, Inc.FriendswoodTexasUSA
| | | | - Kyle R. Covington
- Research and Development, Castle Biosciences, Inc.FriendswoodTexasUSA
| | - Sarah J. Kurley
- Research and Development, Castle Biosciences, Inc.FriendswoodTexasUSA
| | - Matthew S. Goldberg
- Research and Development, Castle Biosciences, Inc.FriendswoodTexasUSA
- Department of DermatologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Julia M. Kasprzak
- Department of DermatologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Ally‐Khan Somani
- Department of DermatologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Sherrif F. Ibrahim
- Department of DermatologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Rochester Dermatologic SurgeryVictorNew YorkUSA
| | - David G. Brodland
- Zitelli and Brodland, P.C., Z&B Skin Cancer CenterPittsburghPennsylvaniaUSA
| | | | | | - Yang Xia
- Brooke Army Medical CenterSan AntonioTexasUSA
| | | | - Jason G. Newman
- Department of Otorhinolaryngology, Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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Alsina KM, Sholl LM, Covington KR, Arnal SM, Durante MA, Decatur CL, Stone JF, Oelschlager KM, Harbour JW, Monzon FA, Cook RW, Borman S. Analytical Validation and Performance of a 7-Gene Next-Generation Sequencing Panel in Uveal Melanoma. Ocul Oncol Pathol 2021; 7:428-436. [PMID: 35083209 PMCID: PMC8739387 DOI: 10.1159/000518829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/31/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Gene expression profiling (GEP) is widely used for prognostication in patients with uveal melanoma (UM). Because biopsy tissue is limited, it is critical to obtain as much genomic information as possible from each sample. Combined application of both GEP and next-generation sequencing (NGS) allows for analysis of RNA and DNA from a single biopsy sample, offers additional prognostic information, and can potentially inform therapy selection. This study evaluated the analytical performance of a targeted custom NGS panel for mutational profiling of 7 genes commonly mutated in UM. METHODS One hundred five primary UM tumors were analyzed, including 37 formalin-fixed paraffin-embedded (FFPE) and 68 fine-needle aspiration biopsy specimens. Sequencing was performed on the Ion GeneStudio S5 platform to an average read depth of >500X per region of interest. RESULTS The 7-gene panel achieved a positive percent agreement of 100% for detection of both single-nucleotide variants and insertions/deletions, with a technical positive predictive value of 98.8% and 100%, respectively. Intra-assay and inter-assay concordance studies confirmed the assay's reproducibility and repeatability. DISCUSSION/CONCLUSION The 7-gene panel is a robust, highly accurate NGS test that can be successfully performed, along with GEP, from a single small-gauge needle biopsy sample or FFPE specimen.
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Affiliation(s)
- Katherina M. Alsina
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
| | - Lauren M. Sholl
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
| | - Kyle R. Covington
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
| | - Suzzette M. Arnal
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
| | - Michael A. Durante
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Christina L. Decatur
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - John F. Stone
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
| | - Kristen M. Oelschlager
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
| | - J. William Harbour
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Federico A. Monzon
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
| | - Robert W. Cook
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
| | - Sherri Borman
- Castle Biosciences, Inc., Friendswood, TX (Headquarters) and (Laboratory), Phoenix, Arizona, USA
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10
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Ibrahim SF, Kasprzak JM, Hall MA, Fitzgerald AL, Siegel JJ, Kurley SJ, Covington KR, Goldberg MS, Farberg AS, Trotter SC, Reed K, Brodland DG, Koyfman SA, Somani AK, Arron ST, Wysong A. Enhanced metastatic risk assessment in cutaneous squamous cell carcinoma with the 40-gene expression profile test. Future Oncol 2021; 18:833-847. [PMID: 34821148 DOI: 10.2217/fon-2021-1277] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: To clinically validate the 40-gene expression profile (40-GEP) test for cutaneous squamous cell carcinoma patients and evaluate coupling the test with individual clinicopathologic risk factor-based assessment methods. Patients & methods: In a 33-site study, primary tumors with known patient outcomes were assessed under clinical testing conditions (n = 420). The 40-GEP results were integrated with clinicopathologic risk factors. Kaplan-Meier and Cox regression analyses were performed for metastasis. Results: The 40-GEP test demonstrated significant prognostic value. Risk classification was improved via integration of 40-GEP results with clinicopathologic risk factor-based assessment, with metastasis rates near the general cutaneous squamous cell carcinoma population for Class 1 and ≥50% for Class 2B. Conclusion: Combining molecular profiling with clinicopathologic risk factor assessment enhances stratification of cutaneous squamous cell carcinoma patients and may inform decision-making for risk-appropriate management strategies.
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Affiliation(s)
- Sherrif F Ibrahim
- Rochester Dermatologic Surgery, Victor, NY 14564, USA.,Department of Dermatology, University of Rochester Medical Center, Rochester, NY 14620, USA
| | - Julia M Kasprzak
- Department of Dermatology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary A Hall
- Castle Biosciences, Inc., Friendswood, TX 77546, USA
| | | | | | | | | | - Matthew S Goldberg
- Castle Biosciences, Inc., Friendswood, TX 77546, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10025, USA
| | - Aaron S Farberg
- Department of Dermatology, Baylor University Medical Center, Dallas, TX 75246, USA
| | | | | | | | - Shlomo A Koyfman
- Department of Radiation Oncology, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Ally-Khan Somani
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Ashley Wysong
- Department of Dermatology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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11
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Whitman ED, Koshenkov VP, Gastman BR, Lewis D, Hsueh EC, Pak H, Trezona TP, Davidson RS, McPhee M, Guenther JM, Toomey P, Smith FO, Beitsch PD, Lewis JM, Ward A, Young SE, Shah PK, Quick AP, Martin BJ, Zolochevska O, Covington KR, Monzon FA, Goldberg MS, Cook RW, Fleming MD, Hyams DM, Vetto JT. Integrating 31-Gene Expression Profiling With Clinicopathologic Features to Optimize Cutaneous Melanoma Sentinel Lymph Node Metastasis Prediction. JCO Precis Oncol 2021; 5:PO.21.00162. [PMID: 34568719 PMCID: PMC8457832 DOI: 10.1200/po.21.00162] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/22/2021] [Accepted: 08/04/2021] [Indexed: 11/30/2022] Open
Abstract
National guidelines recommend sentinel lymph node biopsy (SLNB) be offered to patients with > 10% likelihood of sentinel lymph node (SLN) positivity. On the other hand, guidelines do not recommend SLNB for patients with T1a tumors without high-risk features who have < 5% likelihood of a positive SLN. However, the decision to perform SLNB is less certain for patients with higher-risk T1 melanomas in which a positive node is expected 5%-10% of the time. We hypothesized that integrating clinicopathologic features with the 31-gene expression profile (31-GEP) score using advanced artificial intelligence techniques would provide more precise SLN risk prediction.
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Affiliation(s)
- Eric D Whitman
- Carol G. Simon Cancer at Morristown Medical Center, Atlantic Health System, Morristown, NJ
| | | | | | - Deri Lewis
- Medical City Dallas Hospital, Dallas, TX
| | - Eddy C Hsueh
- Department of Surgery, St Louis University, St Louis, MO
| | - Ho Pak
- General Surgery Abington Memorial Hospital, Abington, PA
| | | | | | | | | | - Paul Toomey
- Florida State University College of Medicine, Bradenton, FL
| | | | | | - James M Lewis
- University of Tennessee Graduate School of Medicine, Knoxville, TN
| | - Andrew Ward
- University of Tennessee Graduate School of Medicine, Knoxville, TN
| | | | | | | | | | | | | | | | | | | | - Martin D Fleming
- Division of Surgical Oncology, The University of Tennessee Health Science Center, Memphis, TN
| | | | - John T Vetto
- Oregon Health & Science University, Portland, OR
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12
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Martin BJ, Covington KR, Quick AP, Cook RW. Risk Stratification of Patients with Stage I Cutaneous Melanoma Using 31-Gene Expression Profiling. J Clin Aesthet Dermatol 2021; 14:E61-E63. [PMID: 34980974 PMCID: PMC8675338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND While patients with localized cutaneous melanoma (CM) generally have good five-year melanoma-specific survival rates, identifying patients with localized disease at a high risk of recurrence could allow them access to additional follow-up or surveillance. OBJECTIVE We sought to examine the prognostic value of the 31-gene expression profile (31-GEP) test for the risk of recurrence in stage I CM patients according to 31-GEP main class (low risk: Class 1 vs. high-risk: Class 2) and the lowest and highest risk 31-GEP subclasses (Class 1A vs. Class 2B). METHODS Data from a previously described meta-analysis detailing the 31-GEP results for patients with stage I CM (N = 623) were re-analyzed to determine 31-GEP accuracy. RESULTS Patients with stage I CM and a Class 1 31-GEP result were less likely to have a recurrence (15/556; 2.7% vs. 6/67; 9.0%; p=0.018) than patients with a Class 2 result and had a higher five-year recurrence-free survival (RFS) (96% vs. 85%). Patients with a Class 2 result were 2.8 times as likely to experience a recurrence (positive likelihood ratio: 2.82; 95% confidence interval: 1.38-5.77). In a subset of patients with stage I CM stratified further into 31-GEP subclasses (n = 206), patients with a Class 1A result had a higher five-year RFS than those with a Class 2B result (98% vs. 73%). Patients with a Class 2B result were also 6.5 times as likely to experience a recurrence (positive likelihood ratio: 6.45; 95% confidence interval: 2.44-17.00) than those with a Class 1A result, and the 31-GEP had a negative predictive value of 96.3% (95% confidence interval: 92.3%-98.4%). CONCLUSION The 31-GEP test significantly differentiates between low and high recurrence risk in patients with stage I CM.
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Affiliation(s)
- Brian J Martin
- All authors are employees with Castle Biosciences, Inc. in Friendswood, Texas
| | - Kyle R Covington
- All authors are employees with Castle Biosciences, Inc. in Friendswood, Texas
| | - Ann P Quick
- All authors are employees with Castle Biosciences, Inc. in Friendswood, Texas
| | - Robert W Cook
- All authors are employees with Castle Biosciences, Inc. in Friendswood, Texas
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13
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Ibrahim SF, Arron ST, Somani AK, Kurley SJ, Covington KR, Fitzgerald AL, Schmults CD, Wysong A. 25726 Prospective adjuvant therapy trial design using a prognostic 40-gene expression profile (40-GEP) test for high-risk cutaneous squamous cell carcinoma (cSCC) and BWH staging-based risk assessment. J Am Acad Dermatol 2021. [DOI: 10.1016/j.jaad.2021.06.294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Hsueh EC, DeBloom JR, Lee JH, Sussman JJ, Covington KR, Caruso HG, Quick AP, Cook RW, Slingluff CL, McMasters KM. Long-Term Outcomes in a Multicenter, Prospective Cohort Evaluating the Prognostic 31-Gene Expression Profile for Cutaneous Melanoma. JCO Precis Oncol 2021; 5:PO.20.00119. [PMID: 34036233 PMCID: PMC8140806 DOI: 10.1200/po.20.00119] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 01/23/2021] [Accepted: 02/02/2021] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Current guidelines for postoperative management of patients with stage I-IIA cutaneous melanoma (CM) do not recommend routine cross-sectional imaging, yet many of these patients develop metastases. Methods that complement American Joint Committee on Cancer (AJCC) staging are needed to improve identification and treatment of these patients. A 31-gene expression profile (31-GEP) test predicts metastatic risk as low (class 1) or high (class 2). Prospective analysis of CM outcomes was performed to test the hypotheses that the 31-GEP provides prognostic value for patients with stage I-III CM, and that patients with stage I-IIA melanoma and class 2 31-GEP results have metastatic risk similar to patients for whom surveillance is recommended. MATERIALS AND METHODS Two multicenter registry studies, INTEGRATE (ClinicalTrials.gov identifier:NCT02355574) and EXPAND (ClinicalTrials.gov identifier:NCT02355587), were initiated under institutional review board approval, and 323 patients with stage I-III CM and median follow-up time of 3.2 years met inclusion criteria. Primary end points were 3-year recurrence-free survival (RFS), distant metastasis-free survival (DMFS), and overall survival (OS). RESULTS The 31-GEP was significant for RFS, DMFS, and OS in a univariate analysis and was a significant, independent predictor of RFS, DMFS, and OS in a multivariable analysis. GEP class 2 results were significantly associated with lower 3-year RFS, DMFS, and OS in all patients and those with stage I-IIA disease. Patients with stage I-IIA CM and a class 2 result had recurrence, distant metastasis, and death rates similar to patients with stage IIB-III CM. Combining 31-GEP results and AJCC staging enhanced sensitivity over each approach alone. CONCLUSION These data provide a rationale for using the 31-GEP along with AJCC staging, and suggest that patients with stage I-IIA CM and a class 2 31-GEP signature may be candidates for more intense follow-up.
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Affiliation(s)
- Eddy C Hsueh
- Department of Surgery, St Louis University, St Louis, MO
| | | | - Jonathan H Lee
- Allegheny Health Network Cancer Institute, Pittsburgh, PA
| | | | | | | | | | | | - Craig L Slingluff
- Department of Surgery and Cancer Center, University of Virginia School of Medicine, Charlottesville, VA
| | - Kelly M McMasters
- Department of Surgical Oncology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY
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15
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Wysong A, Covington KR, Kurley SJ, Johnson C, Cook RW, Newman JG, Schmults CD, Arron ST. 13813 Development and validation of a multigene signature for identification of cutaneous squamous cell carcinoma patients at high risk for regional or distant metastases. J Am Acad Dermatol 2020. [DOI: 10.1016/j.jaad.2020.06.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Aaberg TM, Covington KR, Tsai T, Shildkrot Y, Plasseraud KM, Alsina KM, Oelschlager KM, Monzon FA. Gene Expression Profiling in Uveal Melanoma: Five-Year Prospective Outcomes and Meta-Analysis. Ocul Oncol Pathol 2020; 6:360-367. [PMID: 33123530 DOI: 10.1159/000508382] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/30/2020] [Indexed: 01/09/2023] Open
Abstract
Introduction The prognostic 15-gene expression profile (15-GEP) test for uveal melanoma (UM) predicts metastatic risk based on primary tumor biology. Here we report outcomes from a prospective registry of 15-GEP-tested patients, and a meta-analysis with published cohorts. Objectives Management and 5-year clinical outcomes following 15-GEP testing were evaluated. Methods Eighty-nine patients with 15-GEP results were prospectively enrolled at four centers. Physician-recommended management plans were collected, and clinical outcomes tracked every 6 months. Results Eighty percent of Class 1 (low-risk) patients underwent low-intensity management; all Class 2 (high-risk) patients underwent high-intensity management (p < 0.0001). Median follow-up for event-free patients was 4.9 years. Five Class 1 (10%) and 23 Class 2 (58%) tumors metastasized (p < 0.0001). Five-year Class 1 and 2 metastasis-free survival rates were 90% (81-100%) and 41% (27-62%; p < 0.0001), and melanoma-specific survival rates were 94% (87-100%) and 63% (49-82%; p = 0.0007). Class 2 was the only independent predictor of metastasis and was associated with increased risk for metastasis and mortality by meta-analysis. Conclusions UM patient management is guided by 15-GEP testing. Class 2 patients were managed more intensely, in accordance with an observed metastatic rate of >50%; Class 1 patients were safely spared intensive surveillance, resulting in appropriate utilization of healthcare resources.
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Affiliation(s)
- Thomas M Aaberg
- Retina Specialists of Michigan, Michigan State University, Grand Rapids, Michigan, USA
| | | | - Tony Tsai
- Retinal Consultants, Sacramento, California, USA
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17
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Hyams DM, Covington KR, Johnson CE, Plasseraud KM, Cook RW. Integrating the melanoma 31-gene expression profile test with surgical oncology practice within national guideline and staging recommendations. Future Oncol 2020; 17:517-527. [PMID: 33021104 DOI: 10.2217/fon-2020-0827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Define changes in clinical management resulting from the use of the prognostic 31-gene expression profile (31-GEP) test for cutaneous melanoma in a surgical oncology practice. Patients & methods: Management plans for 112 consecutively tested patients with stage I-III melanoma were evaluated for duration and number of clinical visits, blood work and imaging. Results: 31-GEP high-risk (class 2; n = 46) patients received increased management compared with low-risk (class 1; n = 66) patients. Test results were most closely associated with follow-up and imaging. Of class 1 patients, 65% received surveillance intensity within guidelines for stage I-IIA patients; 98% of class 2 patients received surveillance intensity equal to stage IIB-IV patients. Conclusion: We suggest clinical follow-up and metastatic screening be adjusted according to 31-GEP test results.
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Affiliation(s)
- David M Hyams
- Desert Surgical Oncology, Rancho Mirage, CA 92270, USA
| | | | | | | | - Robert W Cook
- Castle Biosciences, Inc., Friendswood, TX 77546, USA
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18
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Farberg AS, Hall MA, Douglas L, Covington KR, Kurley SJ, Cook RW, Dinehart SM. Integrating gene expression profiling into NCCN high-risk cutaneous squamous cell carcinoma management recommendations: impact on patient management. Curr Med Res Opin 2020; 36:1301-1307. [PMID: 32351136 DOI: 10.1080/03007995.2020.1763284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Objective: To integrate gene expression profiling into the management of high-risk cutaneous squamous cell carcinoma (cSCC) within the National Comprehensive Cancer Network (NCCN) guidelines to improve risk-aligned management recommendations.Methods: A cohort of 300 NCCN-defined high-risk cSCC patients, along with the American Joint Committee on Cancer (AJCC) T stage, Brigham and Women's Hospital (BWH) T stage, and known patient outcomes were analyzed. Risk classifications using a validated 40-gene expression profile (40-GEP) test and T stage were applied to NCCN patient management guidelines. Risk-directed patient management recommendations within the NCCN guidelines framework were aligned based on risk for metastasis.Results: Of the 300 NCCN high-risk cSCC patients, 159 (53.0%) were 40-GEP Class 1 and AJCC T1-T2, and 173 (57.7%) were Class 1 and BWH T1-2a, indicating low risk for metastasis and, thereby, suggesting low management intensity. The 40-GEP integration suggested high intensity management for only 24 (8.0%) patients (all Class 2B), and moderate intensity management for the remainder of the cohort.Conclusions: The 40-GEP test can be integrated within existing NCCN guideline recommendations for managing cSCC patients to help refine risk-directed management decisions. Integration of the 40-GEP test would allow >50% of this NCCN-defined high-risk cohort to be managed with the lowest intensity recommendations within the broad NCCN guidelines. High intensity management was deemed risk-appropriate for a small subpopulation (8.0%). This study demonstrates that the 40-GEP test, in combination with T stage, has clinical utility to impact patient management decisions in NCCN high-risk cSCC for improving risk-aligned management within the NCCN guidelines framework.
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Affiliation(s)
- Aaron S Farberg
- Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Dermatology, Arkansas Dermatology Skin Cancer Center, Little Rock, AR, USA
| | - Mary A Hall
- Research and Development, Castle Biosciences, Inc, Friendswood, TX, USA
| | - Leah Douglas
- Dermatology, Baylor College of Medicine, Houston, TX, USA
| | - Kyle R Covington
- Research and Development, Castle Biosciences, Inc, Friendswood, TX, USA
| | - Sarah J Kurley
- Research and Development, Castle Biosciences, Inc, Friendswood, TX, USA
| | - Robert W Cook
- Research and Development, Castle Biosciences, Inc, Friendswood, TX, USA
| | - Scott M Dinehart
- Dermatology, Arkansas Dermatology Skin Cancer Center, Little Rock, AR, USA
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19
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Midorikawa Y, Yamamoto S, Tatsuno K, Renard-Guillet C, Tsuji S, Hayashi A, Ueda H, Fukuda S, Fujita T, Katoh H, Ishikawa S, Covington KR, Creighton CJ, Sugitani M, Wheeler DA, Shibata T, Nagae G, Takayama T, Aburatani H. Accumulation of Molecular Aberrations Distinctive to Hepatocellular Carcinoma Progression. Cancer Res 2020; 80:3810-3819. [DOI: 10.1158/0008-5472.can-20-0225] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/01/2020] [Accepted: 07/02/2020] [Indexed: 11/16/2022]
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20
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Greenhaw BN, Covington KR, Kurley SJ, Yeniay Y, Cao NA, Plasseraud KM, Cook RW, Hsueh EC, Gastman BR, Wei ML. Reply to Problematic methodology in a systematic review and meta-analysis of DecisionDx-Melanoma. J Am Acad Dermatol 2020; 83:e359-e360. [PMID: 32526325 DOI: 10.1016/j.jaad.2020.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 11/18/2022]
Affiliation(s)
| | | | | | | | - Nhat Anh Cao
- Veterans Affairs Medical Center, San Francisco, California
| | | | | | | | | | - Maria L Wei
- University of California, San Francisco, California; Veterans Affairs Medical Center, San Francisco, California
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21
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Gerami P, Covington KR, Zolochevska O, Quick AP, Cook RW, Wayne JD. Performance of a prognostic 31-gene expression profile test in patients with node-negative cutaneous melanoma. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e22071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e22071 Background: The National Comprehensive Cancer Network guidelines recommend considering sentinel lymph node biopsy (SLNB) for cutaneous melanoma (CM) patients with a 5-10% risk of SLN positivity and offering it to those with > 10% risk. However, SLNB limitations include identification of only 1/3 of patients who end up with distant metastasis and a regional metastasis false negative rate ranging from 5-21% indicating a need to detect the risk of metastasis in patients with a negative SLNB. The 31 gene expression profile (31GEP) test uses the molecular biology of the primary tumor to predict 5-year recurrence-free (RFS), distant metastasis-free (DMFS), melanoma-specific (MSS), and overall survival (OS). Therefore, the objective of this study is to determine whether the 31GEP can stratify risk for patients with SLN-negative results to help guide CM management. Methods: 607 primary CM tumors were collected from patients with SLN-negative status who were enrolled in multi-center IRB-approved studies. Tumors were staged according to the AJCC 8th edition and analyzed by 31GEP testing to differentiate low-risk (Class 1A), intermediate-risk (Class 1B/2A), and high-risk (Class 2B) tumor biology. Clinical data were recorded and Kaplan-Meier (KM) and Cox regression analyses were performed to assess the relationship between 31GEP class and patient outcomes including RFS, DMFS, MSS, and OS. Results: KM analysis for 5yr RFS, DMFS, MSS, and OS stratified by 31GEP class are listed in Table. Multivariate Cox regression analysis demonstrated that the 31GEP Class 2B status was an independent predictor of RFS, DMFS, MSS, and OS with hazard ratios of 4.4 (95% CI, 2.7-7.2; p < 0.001), 4.4 (95% CI, 2.3-8.5; p < 0.001), 15.6 (95% CI, 3.4-71.2; p < 0.001), and 5.4 (95% CI, 2.6-10.9; p < 0.001), respectively. Conclusions: The results indicate that the 31GEP can stratify risk for a subset of patients with SLNB-negative results with the highest 5-year survival rates being associated with a Class 1A result. Moreover, GEP Class 2B is a significant independent predictor of metastatic risk in patients who are node negative. [Table: see text]
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Affiliation(s)
- Pedram Gerami
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | | | | | | | - Jeffrey D. Wayne
- Northwestern University Feinberg School of Medicine, Chicago, IL
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22
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Schmults C, Covington KR, Kurley SJ, Cook RW. Implications of a prognostic 40-gene expression profile (40-GEP) test for high-risk cutaneous squamous cell carcinoma (cSCC) on staging-based risk assessment and adjuvant therapy trial design. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e22091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e22091 Background: Deaths due to cSCC are expected to exceed melanoma-specific deaths. With the demonstration of effective therapies for advanced cSCC, and as treatment of patients in the adjuvant setting is considered, accurate prognosis is critical. For improved identification of ‘high-risk’ patients, with biologically aggressive disease capable of metastasis, a prognostic 40-gene expression profile (40-GEP) test was validated using an independent cohort of patients with high-risk cSCC and known clinical outcomes. The test identified three groups with increasing metastasis risk profiles: Class 1 (low risk), Class 2A (high risk), and Class 2B (highest risk) having metastasis rates of 8.9%, 20.4%, and 60%, respectively. Multivariable analysis demonstrated prognostic efficacy of the 40-GEP test alone and in combination with clinicopathological staging systems. This study evaluated risk stratification with concurrent consideration of the 40-GEP result and the Brigham and Women’s Hospital (BWH) stage. The primary objective was evaluation of the potential impact of the 40-GEP on adjuvant clinical trial design. Methods: To determine if a 40-GEP Class 2B result could optimize clinical trial accrual, metastasis rates of BWH high-risk T stage patients (T2b-T3) alone and in combination with 40-GEP results from the validation cohort were used for two-arm trial sample size calculations. Results: Metastasis rates for cases with T2b-T3 tumors increased from 35.1% to 71.4% when selecting for T2b-T3 cases with a 40-GEP Class 2B result. To provide 80% power to detect hazard ratio of 0.6 with 3 years of follow-up (alpha = 0.05), in line with improvement rates by addition of radiation to surgery, 434 T2b-T3 patients are required for randomization. However, sample size could be reduced by 51% to 214 patients by focusing enrollment on T2b-T3 patients with a 40-GEP Class 2B result. Conclusions: These results support the incorporation of the 40-GEP test into selection processes for patients with T2b-T3 tumors who are at the highest risk for metastasis and appropriate for adjuvant clinical trials.
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23
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Wysong A, Newman JG, Covington KR, Kurley SJ, Ibrahim SF, Farberg AS, Bar A, Cleaver NJ, Somani AK, Panther D, Brodland DG, Zitelli J, Toyohara J, Maher IA, Xia Y, Bibee K, Griego R, Rigel DS, Meldi Plasseraud K, Estrada S, Sholl LM, Johnson C, Cook RW, Schmults CD, Arron ST. Validation of a 40-gene expression profile test to predict metastatic risk in localized high-risk cutaneous squamous cell carcinoma. J Am Acad Dermatol 2020; 84:361-369. [PMID: 32344066 DOI: 10.1016/j.jaad.2020.04.088] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/22/2020] [Accepted: 04/15/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Current staging systems for cutaneous squamous cell carcinoma (cSCC) have limited positive predictive value for identifying patients who will experience metastasis. OBJECTIVE To develop and validate a gene expression profile (GEP) test for predicting risk for metastasis in localized, high-risk cSCC with the goal of improving risk-directed patient management. METHODS Archival formalin-fixed paraffin-embedded primary cSCC tissue and clinicopathologic data (n = 586) were collected from 23 independent centers in a prospectively designed study. A GEP signature was developed using a discovery cohort (n = 202) and validated in a separate, nonoverlapping, independent cohort (n = 324). RESULTS A prognostic 40-GEP test was developed and validated, stratifying patients with high-risk cSCC into classes based on metastasis risk: class 1 (low risk), class 2A (high risk), and class 2B (highest risk). For the validation cohort, 3-year metastasis-free survival rates were 91.4%, 80.6%, and 44.0%, respectively. A positive predictive value of 60% was achieved for the highest-risk group (class 2B), an improvement over staging systems, and negative predictive value, sensitivity, and specificity were comparable to staging systems. LIMITATIONS Potential understaging of cases could affect metastasis rate accuracy. CONCLUSION The 40-GEP test is an independent predictor of metastatic risk that can complement current staging systems for patients with high-risk cSCC.
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Affiliation(s)
- Ashley Wysong
- University of Nebraska Medical Center, Omaha, Nebraska
| | | | | | | | | | - Aaron S Farberg
- Icahn School of Medicine at Mount Sinai, New York, New York; Arkansas Dermatology Skin Cancer Center, Little Rock, Arkansas
| | - Anna Bar
- Oregon Health & Science University, Portland, Oregon
| | | | | | - David Panther
- Zitelli and Brodland, P.C. Skin Cancer Center, Pittsburgh, Pennsylvania
| | - David G Brodland
- Zitelli and Brodland, P.C. Skin Cancer Center, Pittsburgh, Pennsylvania
| | - John Zitelli
- Zitelli and Brodland, P.C. Skin Cancer Center, Pittsburgh, Pennsylvania
| | | | - Ian A Maher
- University of Minnesota, Minneapolis, Minnesota
| | - Yang Xia
- Brooke Army Medical Center, San Antonio, Texas
| | - Kristin Bibee
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | | | - Sarah Estrada
- Castle Biosciences, Inc, Phoenix, Arizona; Affiliated Dermatology, Scottsdale, Arizona
| | | | | | | | | | - Sarah T Arron
- University of California San Francisco, San Francisco, California.
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24
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Greenhaw BN, Covington KR, Kurley SJ, Yeniay Y, Cao NA, Plasseraud KM, Cook RW, Hsueh EC, Gastman BR, Wei ML. Molecular risk prediction in cutaneous melanoma: A meta-analysis of the 31-gene expression profile prognostic test in 1,479 patients. J Am Acad Dermatol 2020; 83:745-753. [PMID: 32229276 DOI: 10.1016/j.jaad.2020.03.053] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/07/2020] [Accepted: 03/16/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND Multiple studies have reported on the accuracy of the prognostic 31-gene expression profile test for cutaneous melanoma. Consistency of the test results across studies has not been systematically evaluated. OBJECTIVE To assess the robustness of the prognostic value of the 31-gene expression profile. METHODS Raw data were obtained from studies identified from systematic review. A meta-analysis was performed to determine overall effect of the 31-gene expression profile. Clinical outcome metrics for the 31-gene expression profile were compared with American Joint Committee on Cancer staging. RESULTS Three studies met inclusion criteria; data from a novel cohort of 211 patients were included (n = 1,479). Five-year recurrence-free and distant metastasis-free survival rates were 91.4% and 94.1% for Class 1A patients and 43.6% and 55.5% for Class 2B patients (P < .0001). Meta-analysis results showed that Class 2 was significantly associated with recurrence (hazard ratio 2.90; P < .0001) and distant metastasis (hazard ratio 2.75; P < .0001). The 31-gene expression profile identified American Joint Committee on Cancer stage I to III patient subsets with high likelihood for recurrence and distant metastasis. Sensitivity was 76% (95% confidence interval 71%-80%) and 76% (95% confidence interval 70%-82%) for each end point, respectively. When 31-gene expression profile and sentinel lymph node biopsy results were considered together, sensitivity and negative predictive value for distant metastasis-free survival were both improved. CONCLUSION The 31-gene expression profile test consistently and accurately identifies melanoma patients at increased risk of metastasis, is independent of other clinicopathologic covariates, and augments current risk stratification by reclassifying patients for heightened surveillance who were previously designated as being at low risk.
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Affiliation(s)
| | | | | | - Yildiray Yeniay
- University of California-San Francisco, San Francisco, California
| | - Nhat Anh Cao
- San Francisco Veterans Affairs Medical Center, San Francisco, California
| | | | | | | | | | - Maria L Wei
- University of California-San Francisco, San Francisco, California; San Francisco Veterans Affairs Medical Center, San Francisco, California.
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25
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Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V, Getz G, Rozen SG, Stratton MR. The repertoire of mutational signatures in human cancer. Nature 2020; 578:94-101. [PMID: 32025018 PMCID: PMC7054213 DOI: 10.1038/s41586-020-1943-3] [Citation(s) in RCA: 1724] [Impact Index Per Article: 431.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/18/2019] [Indexed: 01/27/2023]
Abstract
Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses3-15, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.
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Affiliation(s)
- Ludmil B. Alexandrov
- 0000 0001 2107 4242grid.266100.3Department of Cellular and Molecular Medicine, Department of Bioengineering, Moores Cancer Center, University of California, San Diego, CA USA
| | - Jaegil Kim
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Nicholas J. Haradhvala
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Center for Cancer Research, Massachusetts General Hospital, Boston, MA USA
| | - Mi Ni Huang
- 0000 0004 0385 0924grid.428397.3Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore ,0000 0004 0385 0924grid.428397.3Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Alvin Wei Tian Ng
- 0000 0004 0385 0924grid.428397.3Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore ,0000 0004 0385 0924grid.428397.3Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Yang Wu
- 0000 0004 0385 0924grid.428397.3Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore ,0000 0004 0385 0924grid.428397.3Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Arnoud Boot
- 0000 0004 0385 0924grid.428397.3Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore ,0000 0004 0385 0924grid.428397.3Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Kyle R. Covington
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA ,0000 0001 2160 926Xgrid.39382.33Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX USA
| | - Dmitry A. Gordenin
- 0000 0001 2110 5790grid.280664.eGenome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Durham, NC USA
| | - Erik N. Bergstrom
- 0000 0001 2107 4242grid.266100.3Department of Cellular and Molecular Medicine, Department of Bioengineering, Moores Cancer Center, University of California, San Diego, CA USA
| | - S. M. Ashiqul Islam
- 0000 0001 2107 4242grid.266100.3Department of Cellular and Molecular Medicine, Department of Bioengineering, Moores Cancer Center, University of California, San Diego, CA USA
| | - Nuria Lopez-Bigas
- grid.473715.3Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain ,0000 0001 2172 2676grid.5612.0Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain ,0000 0000 9601 989Xgrid.425902.8Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Leszek J. Klimczak
- 0000 0001 2110 5790grid.280664.eIntegrative Bioinformatics Support Group, National Institute of Environmental Health Sciences (NIEHS), Durham, NC USA
| | - John R. McPherson
- 0000 0004 0385 0924grid.428397.3Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore ,0000 0004 0385 0924grid.428397.3Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Sandro Morganella
- 0000 0004 0606 5382grid.10306.34Wellcome Sanger Institute, Hinxton, UK
| | - Radhakrishnan Sabarinathan
- 0000 0001 2172 2676grid.5612.0Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain ,0000 0004 0502 9283grid.22401.35National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India ,0000 0001 1811 6966grid.7722.0Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - David A. Wheeler
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA ,0000 0001 2160 926Xgrid.39382.33Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Ville Mustonen
- 0000 0004 0410 2071grid.7737.4Department of Computer Science, University of Helsinki, Helsinki, Finland ,0000 0004 0410 2071grid.7737.4Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland ,0000 0004 0410 2071grid.7737.4Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Gad Getz
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Center for Cancer Research, Massachusetts General Hospital, Boston, MA USA ,0000 0004 0386 9924grid.32224.35Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA
| | - Steven G. Rozen
- 0000 0004 0385 0924grid.428397.3Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore ,0000 0004 0385 0924grid.428397.3Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore ,0000 0004 0620 9905grid.419385.2SingHealth, Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, Singapore
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26
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Cho RJ, Alexandrov LB, den Breems NY, Atanasova VS, Farshchian M, Purdom E, Nguyen TN, Coarfa C, Rajapakshe K, Prisco M, Sahu J, Tassone P, Greenawalt EJ, Collisson EA, Wu W, Yao H, Su X, Guttmann-Gruber C, Hofbauer JP, Hashmi R, Fuentes I, Benz SC, Golovato J, Ehli EA, Davis CM, Davies GE, Covington KR, Murrell DF, Salas-Alanis JC, Palisson F, Bruckner AL, Robinson W, Has C, Bruckner-Tuderman L, Titeux M, Jonkman MF, Rashidghamat E, Lwin SM, Mellerio JE, McGrath JA, Bauer JW, Hovnanian A, Tsai KY, South AP. APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa. Sci Transl Med 2019; 10:10/455/eaas9668. [PMID: 30135250 DOI: 10.1126/scitranslmed.aas9668] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/09/2018] [Accepted: 08/01/2018] [Indexed: 01/05/2023]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare inherited skin and mucous membrane fragility disorder complicated by early-onset, highly malignant cutaneous squamous cell carcinomas (SCCs). The molecular etiology of RDEB SCC, which arises at sites of sustained tissue damage, is unknown. We performed detailed molecular analysis using whole-exome, whole-genome, and RNA sequencing of 27 RDEB SCC tumors, including multiple tumors from the same patient and multiple regions from five individual tumors. We report that driver mutations were shared with spontaneous, ultraviolet (UV) light-induced cutaneous SCC (UV SCC) and head and neck SCC (HNSCC) and did not explain the early presentation or aggressive nature of RDEB SCC. Instead, endogenous mutation processes associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) deaminases dominated RDEB SCC. APOBEC mutation signatures were enhanced throughout RDEB SCC tumor evolution, relative to spontaneous UV SCC and HNSCC mutation profiles. Sixty-seven percent of RDEB SCC driver mutations was found to emerge as a result of APOBEC and other endogenous mutational processes previously associated with age, potentially explaining a >1000-fold increased incidence and the early onset of these SCCs. Human papillomavirus-negative basal and mesenchymal subtypes of HNSCC harbored enhanced APOBEC mutational signatures and transcriptomes similar to those of RDEB SCC, suggesting that APOBEC deaminases drive other subtypes of SCC. Collectively, these data establish specific mutagenic mechanisms associated with chronic tissue damage. Our findings reveal a cause for cancers arising at sites of persistent inflammation and identify potential therapeutic avenues to treat RDEB SCC.
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Affiliation(s)
- Raymond J Cho
- Department of Dermatology, University of California, San Francisco, CA 94115, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Velina S Atanasova
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Mehdi Farshchian
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tran N Nguyen
- Departments of Anatomic Pathology and Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Cristian Coarfa
- Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Kimal Rajapakshe
- Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Marco Prisco
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Joya Sahu
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Patrick Tassone
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Evan J Greenawalt
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Translational Medical Center, Central Hospital, Zhengzhou University, Zhengzhou, China
| | - Hui Yao
- Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoping Su
- Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christina Guttmann-Gruber
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital Salzburg, Paracelsus Medical University, A-5020 Salzburg, Austria
| | - Josefina Piñón Hofbauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital Salzburg, Paracelsus Medical University, A-5020 Salzburg, Austria
| | - Raabia Hashmi
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ignacia Fuentes
- Fundación DEBRA Chile, Santiago 7760099, Chile.,Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7710162, Chile
| | | | | | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD 57108, USA
| | | | - Gareth E Davies
- Avera Institute for Human Genetics, Sioux Falls, SD 57108, USA
| | | | - Dedee F Murrell
- St. George Hospital, University of New South Wales, Sydney, New South Wales 2217, Australia
| | - Julio C Salas-Alanis
- Escuela de Medicina y Ciencias de la Salud TecSalud del Tecnologico de Monterrey, Morones Prieto 3000, Los doctores, Monterrey, Nuevo León 64710, Mexico
| | - Francis Palisson
- Fundación DEBRA Chile, Santiago 7760099, Chile.,Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7710162, Chile
| | - Anna L Bruckner
- Departments of Dermatology and Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - William Robinson
- Cutaneous Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cristina Has
- Department of Dermatology, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | | | - Matthias Titeux
- INSERM UMR 1163, Paris, France.,Imagine Institute, 75015 Paris, France
| | - Marcel F Jonkman
- Center for Blistering Diseases, Department of Dermatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Elham Rashidghamat
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London SE1 9RT, UK
| | - Su M Lwin
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London SE1 9RT, UK
| | - Jemima E Mellerio
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London SE1 9RT, UK
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London SE1 9RT, UK
| | - Johann W Bauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital Salzburg, Paracelsus Medical University, A-5020 Salzburg, Austria
| | - Alain Hovnanian
- INSERM UMR 1163, Paris, France.,Imagine Institute, 75015 Paris, France
| | - Kenneth Y Tsai
- Departments of Anatomic Pathology and Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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27
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Durante MA, Field MG, Sanchez MI, Covington KR, Decatur CL, Dubovy SR, Harbour JW. Genomic evolution of uveal melanoma arising in ocular melanocytosis. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004051. [PMID: 31186267 PMCID: PMC6672022 DOI: 10.1101/mcs.a004051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022] Open
Abstract
Ocular melanocytosis is the most important predisposing condition for the eye cancer uveal melanoma (UM). Here, we present a patient who developed UM arising within ocular melanocytosis who was treated with enucleation (eye removal), which provided an invaluable opportunity to interrogate both the UM and adjacent uveal tissue containing the melanocytosis using whole-exome and deep-targeted sequencing. This analysis revealed a clonal PLCB4 mutation in the melanocytosis, confirming that this is indeed a neoplastic condition and explaining why it predisposes to UM. This mutation was present in 100% of analyzed UM cells, indicating that a PLCB4-mutant cell gave rise to the UM. The earliest aberrations specific to the tumor were loss of Chromosomes 1p, 3, and 9p, which were present in virtually all tumor cells. A mutation in BAP1 arose later on the other copy of Chromosome 3 in a tumor subclone, followed by a gain of Chromosome 8q. These findings provide a mechanistic explanation for the well-known clinical association between ocular melanocytosis and UM by showing that this predisposing condition introduces the first “hit” and thereby increases the stochastic likelihood of acquiring further aberrations leading to UM.
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Affiliation(s)
- Michael A Durante
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Matthew G Field
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Margaret I Sanchez
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | | | - Christina L Decatur
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Sander R Dubovy
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - J William Harbour
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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28
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Durante MA, Field MG, Sanchez MI, Covington KR, Decatur CL, Dubovy SR, Harbour JW. Abstract 2903: Genomic evolution of uveal melanoma arising in ocular melanocytosis. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Ocular melanocytosis is an congenital condition characterized by the presence of excessive hyperpigmented melanocytes in the uveal tract. Epidemiological studies have shown that this condition is the strongest predisposing risk factor for development of uveal melanoma (UM). In UM patients, the presence of ocular melanocytosis doubles the risk of metastasis. UM has well-characterized driver mutations consisting of two groups. The first group consists of mutually exclusive gain-of-function mutations in members of the Gq signaling pathway (GNAQ, GNA11, CYSLTR2 and PLCB4), and are thought to represent initiating oncogenic events that are insufficient alone to cause full malignant transformation. The second group consists of near-mutually exclusive mutations in BAP1, SF3B1, and EIF1AX, which are thought to occur later in tumor progression. The genomics of ocular melanocytosis and matched UM have not been characterized previously. The purpose of this study was to investigate the genomic evolution of matched ocular melanocytosis and UM tumors.
Methods: Exome and deep-targeted sequencing data from two matched ocular melanocytosis and primary uveal melanomas were evaluated using a previously developed bioinformatic pipeline optimized to call mutations and CNVs in UM. Data from this analysis were used in downstream mutation subclone detection algorithms to determine genomic evolutionary patterns within these matched samples.
Results: For both cases, the initiating driver mutations that are characteristic of UM occur at the same genomic site in matched ocular melanocytosis and UM samples. This finding suggests that they arose within the melanocytosis and subsequently expanded in the tumor. Monosomy of chromosome 3 was absent from the melanocytosis but present in ~100% of tumor cells, indicating that it arose early during clonal tumor expansion. In Patient 1, the BAP1 mutation was present in a tumor subclone and chromosome 8q gain was present in a smaller subclone, indicating that they arose later during tumor evolution. In Patient 2, the BAP1 mutation and other copy number variations were present in ~100% of tumor cells indicating that tumor evolution was completed in this tumor. Additionally, no Gq signaling pathway driver mutations were found in the germline DNA of these patients indicating that that the mutations in ocular melanocytosis occurred somatically during development.
Conclusions: This study provides the first genomic evidence relating ocular melanocytosis to UM. This data shows that Gq signaling pathway driver mutations are early genomic events that are necessary but not sufficient for UM tumor development.These insights help further refine our genomic model of UM tumor evolution and may help to address persistent challenges in the field such as the failure of targeted therapies aimed at inhibiting the Gq pathway.
Citation Format: Michael A. Durante, Matthew G. Field, Margaret I. Sanchez, Kyle R. Covington, Christina L. Decatur, Sander R. Dubovy, J. William Harbour. Genomic evolution of uveal melanoma arising in ocular melanocytosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2903.
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Affiliation(s)
- Michael A. Durante
- 1Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Matthew G. Field
- 1Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Margaret I. Sanchez
- 1Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | | | - Christina L. Decatur
- 1Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Sander R. Dubovy
- 1Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - J. William Harbour
- 1Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
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29
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Gastman BR, Zager JS, Messina JL, Cook RW, Covington KR, Middlebrook B, Gerami P, Wayne JD, Leachman S, Vetto JT. Performance of a 31-gene expression profile test in cutaneous melanomas of the head and neck. Head Neck 2019; 41:871-879. [PMID: 30694001 PMCID: PMC6667900 DOI: 10.1002/hed.25473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/23/2018] [Accepted: 07/05/2018] [Indexed: 12/19/2022] Open
Abstract
Background We report the performance of a gene expression profile test to classify the recurrence risk of cutaneous melanoma tumors of the head and neck as low‐risk Class 1 or high‐risk Class 2. Methods Of note, 157 primary head and neck cutaneous melanoma tumors were identified. Survival analyses were performed using Kaplan‐Meier and Cox methods. Results Gene expression profile class and node status stratified tumors into significantly different 5‐year survival groups by Kaplan‐Meier method (P < .0001 for all end points), and both were independent predictors of recurrence in multivariate analysis. Overall, 74% of distant metastases and 88% of melanoma‐specific deaths had Class 2 risk. Conclusion The gene expression profile test identifies cases at increased risk for metastasis and death independent of a clinically or pathologically negative nodal status, suggesting that incorporation of this molecular tool could improve clinical management of patients with head and neck cutaneous melanoma, especially in those with a negative sentinel lymph node biopsy.
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Affiliation(s)
- Brian R Gastman
- Department of Plastic Surgery, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Jonathan S Zager
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Jane L Messina
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Robert W Cook
- Research & Development, Castle Biosciences, Inc., Friendswood, Texas
| | - Kyle R Covington
- Research & Development, Castle Biosciences, Inc., Friendswood, Texas
| | | | - Pedram Gerami
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Skin Cancer Institute, Northwestern University, Lurie Comprehensive Cancer Center, Chicago, Illinois
| | - Jeffrey D Wayne
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Surgical Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sancy Leachman
- Department of Dermatology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - John T Vetto
- Division of Surgical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
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Schmults C, Arron ST, Wysong A, Covington KR, Cook RW, Newman J. A multi-gene risk signature for improved identification of cutaneous squamous cell carcinoma (cSCC) patients with a high risk of recurrence. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.9577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Sarah T Arron
- University of California, San Francisco, San Francisco, CA
| | - Ashley Wysong
- University of Southern California Keck School of Medicine, Los Angeles, CA
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Gastman B, Kurley S, Covington KR, Cook RW. Performance of a 31-gene expression profile melanoma test in clinically relevant clinicopathologic subgroups. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.9583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst 2018; 6:271-281.e7. [PMID: 29596782 PMCID: PMC6075717 DOI: 10.1016/j.cels.2018.03.002] [Citation(s) in RCA: 452] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/21/2018] [Accepted: 03/01/2018] [Indexed: 12/12/2022]
Abstract
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time. We present best practices for applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. The dataset created by this analysis includes 3.5 million somatic variants and forms the basis for PanCan Atlas papers. The results have been made available to the research community along with the methods used to generate them. This project is the result of collaboration from a number of institutes and demonstrates how team science drives extremely large genomics projects.
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Affiliation(s)
- Kyle Ellrott
- Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA.
| | - Matthew H Bailey
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gordon Saksena
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Kyle R Covington
- Department of Molecular and Human Genetics, Baylor College of Medicine Human Genome Sequencing Center, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Cyriac Kandoth
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Chip Stewart
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Julian Hess
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Singer Ma
- DNAnexus, 1975 W EL Camino Real, Suite 204, Mountain View, CA 94040, USA
| | - Kami E Chiotti
- Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA
| | - Michael McLellan
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Heidi J Sofia
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD 20892, USA
| | - Carolyn Hutter
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD 20892, USA
| | - Gad Getz
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - David Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine Human Genome Sequencing Center, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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Dillon LD, Gadzia JE, Davidson RS, McPhee M, Covington KR, Cook RW, Johnson C, Monzon FA, Milanese ED, Vetto J, Jarell AD, Fleming MD. Prospective, Multicenter Clinical Impact Evaluation of a 31-Gene Expression Profile Test for Management of Melanoma Patients. ACTA ACUST UNITED AC 2018. [DOI: 10.25251/skin.2.2.3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Objective: A 31-gene expression profile (GEP) test that has been clinically validated identifies melanoma patients with low (Class 1) or high (Class 2) risk of metastasis based on primary tumor biology. This study aimed to prospectively evaluate the test impact on clinical management of melanoma patients.Methods: Physicians at 16 dermatology, surgical or medical oncology centers examined patients to assess clinical features of the primary melanoma. Recommendations for clinical follow-up and surveillance were collected. Following consent of the patient and performance of the GEP test, recommendations for management were again collected, and pre- and post-test recommendations were assessed to determine changes in management resulting from the addition of GEP testing to traditional clinicopathologic risk factors. Results: Post-test management plans changed for 49% (122 of 247) of cases in the study when compared to pre-test plans. Thirty-six percent (66 of 181) of Class 1 cases had a management change, compared to 85% (56 of 66) of Class 2 cases. GEP class was a significant factor for change in care during the study (p<0.001), with Class 1 accounting for 91% (39 of 43) of cases with decreased management intensity, and Class 2 accounting for 72% (49 of 68) of cases with increases.Conclusions: The reported study show that the 31-gene GEP test improves net health outcomes in the management of cutaneous melanoma. Physicians used test results to guide risk-appropriate changes that match the biological risk of the tumor, including directing more frequent and intense surveillance to high-risk, Class 2 patients.
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Cook RW, Middlebrook B, Wilkinson J, Covington KR, Oelschlager K, Monzon FA, Stone JF. Analytic validity of DecisionDx-Melanoma, a gene expression profile test for determining metastatic risk in melanoma patients. Diagn Pathol 2018; 13:13. [PMID: 29433548 PMCID: PMC5809902 DOI: 10.1186/s13000-018-0690-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/02/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The DecisionDx-Melanoma test provides prognostic information for patients with cutaneous melanoma (CM). Using formalin-fixed paraffin-embedded primary tumor tissue, the RT-PCR-based test classifies patients into a low- (Class 1) or high-risk (Class 2) category for recurrence based on expression of 31 genes. The current study was designed to assess the analytical validity of this test. METHODS Inter-assay, inter-instrument, and inter-operator studies were performed to evaluate reliability of the 31-gene expression test results, sample stability and reagent stability. From March 2013 through June 2016, the gene expression test was performed on 8244 CM tumors. De-identified data from Pathology Reports were used to assess technical success. RESULTS Robust sample and reagent stability was observed. Inter-assay concordance on 168 specimens run on 2 consecutive days was 99% and matched probability scores were significantly correlated (R2 = 0.96). Inter-instrument concordance was 95%, and probability scores had a correlation R2 of 0.99 (p < 0.001). From 8244 CM specimens submitted since 2013, 85% (7023) fulfilled pre-specified tumor content parameters. In these samples with sufficient tumor requirements, the technical success of the test was 98%. CONCLUSION DecisionDx-Melanoma is a robust gene expression profile test that demonstrates strong reproducibility between experiments and has high technical reliability on clinical samples.
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Affiliation(s)
- Robert W Cook
- Castle Biosciences, Inc., 820 S. Friendswood Dr., Suite 201, Friendswood, TX, 77546, USA.
| | - Brooke Middlebrook
- Castle Biosciences, Inc., 820 S. Friendswood Dr., Suite 201, Friendswood, TX, 77546, USA
| | | | - Kyle R Covington
- Castle Biosciences, Inc., 820 S. Friendswood Dr., Suite 201, Friendswood, TX, 77546, USA
| | | | - Federico A Monzon
- Castle Biosciences, Inc., 820 S. Friendswood Dr., Suite 201, Friendswood, TX, 77546, USA
| | - John F Stone
- , 3737 N. 7th St. #160, Phoenix, 85014, Phoenix, USA
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Zager JS, Gastman BR, Leachman S, Gonzalez RC, Fleming MD, Ferris LK, Ho J, Miller AR, Cook RW, Covington KR, Meldi-Plasseraud K, Middlebrook B, Kaminester LH, Greisinger A, Estrada SI, Pariser DM, Cranmer LD, Messina JL, Vetto JT, Wayne JD, Delman KA, Lawson DH, Gerami P. Performance of a prognostic 31-gene expression profile in an independent cohort of 523 cutaneous melanoma patients. BMC Cancer 2018; 18:130. [PMID: 29402264 PMCID: PMC5800282 DOI: 10.1186/s12885-018-4016-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 01/22/2018] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The heterogeneous behavior of patients with melanoma makes prognostication challenging. To address this, a gene expression profile (GEP) test to predict metastatic risk was previously developed. This study evaluates the GEP's prognostic accuracy in an independent cohort of cutaneous melanoma patients. METHODS This multi-center study analyzed primary melanoma tumors from 523 patients, using the GEP to classify patients as Class 1 (low risk) and Class 2 (high risk). Molecular classification was correlated to clinical outcome and assessed along with AJCC v7 staging criteria. Primary endpoints were recurrence-free (RFS) and distant metastasis-free (DMFS) survival. RESULTS The 5-year RFS rates for Class 1 and Class 2 were 88% and 52%, respectively, and DMFS rates were 93% versus 60%, respectively (P < 0.001). The GEP was a significant predictor of RFS and DMFS in univariate analysis (hazard ratio [HR] = 5.4 and 6.6, respectively, P < 0.001 for each), along with Breslow thickness, ulceration, mitotic rate, and sentinel lymph node (SLN) status (P < 0.001 for each). GEP, tumor thickness and SLN status were significant predictors of RFS and DMFS in a multivariate model that also included ulceration and mitotic rate (RFS HR = 2.1, 1.2, and 2.5, respectively, P < 0.001 for each; and DMFS HR = 2.7, 1.3 and 3.0, respectively, P < 0.01 for each). CONCLUSIONS The GEP test is an objective predictor of metastatic risk and provides additional independent prognostic information to traditional staging to help estimate an individual's risk for recurrence. The assay identified 70% of stage I and II patients who ultimately developed distant metastasis. Its role in consideration of patients for adjuvant therapy should be examined prospectively.
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Affiliation(s)
- Jonathan S Zager
- Department of Cutaneous Oncology, Moffitt Cancer Center, 10920 N. McKinley Drive room 4123, Tampa, FL, 33612, USA
| | - Brian R Gastman
- Department of Plastic Surgery, Cleveland Clinic Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Sancy Leachman
- Department of Dermatology, Knight Cancer Institute, Oregon Health & Science University, 3303 S.W. Bond Avenue, Portland, OR, 97239, USA
| | - Rene C Gonzalez
- Department of Medical Oncology, University of Colorado School of Medicine, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Martin D Fleming
- Department of Surgical Oncology, The University of Tennessee Health Science Center, 910 Madison, Suite 303, Memphis, TN, 38163, USA
| | - Laura K Ferris
- Department of Dermatology, University of Pittsburgh Medical Center, 3601 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Jonhan Ho
- Department of Pathology, University of Pittsburgh Medical Center, 3708 Fifth Avenue, Suite 500.94, Pittsburgh, PA, 15213, USA
| | - Alexander R Miller
- START Center for Cancer Care, 4383 Medical Drive, San Antonio, TX, 78229, USA
| | - Robert W Cook
- Castle Biosciences, Inc., 820 S. Friendswood Drive, Suite 201, Friendswood, TX, 77546, USA
| | - Kyle R Covington
- Castle Biosciences, Inc., 820 S. Friendswood Drive, Suite 201, Friendswood, TX, 77546, USA
| | | | - Brooke Middlebrook
- Castle Biosciences, Inc., 820 S. Friendswood Drive, Suite 201, Friendswood, TX, 77546, USA
| | - Lewis H Kaminester
- Dermatology North Palm Beach, 840 U.S. Highway Number One, North Palm Beach, FL, 33408, USA
| | - Anthony Greisinger
- Research & Development, Kelsey Research Foundation, 5615 Kirby Drive, Suite 660, Houston, TX, 77005, USA
| | - Sarah I Estrada
- Affiliated Dermatology, 20401 North 73rd Street, Suite 230, Scottsdale, AZ, 85255, USA
| | - David M Pariser
- Pariser Dermatology Specialists, Virginia Clinical Research, Inc., 6160 Kempsville Circle, Suite 200A, Norfolk, VA, 23502, USA.,Eastern Virginia Medical School, P.O. Box 1980, Norfolk, VA, 23501-1980, USA
| | - Lee D Cranmer
- Department of Sarcoma Medical Oncology, Seattle Cancer Care Alliance, 825 Eastlake Avenue E, Seattle, WA, 98109, USA
| | - Jane L Messina
- Department of Anatomic Pathology, Moffitt Cancer Center, 10920 N. McKinley Drive, Tampa, FL, 33612, USA
| | - John T Vetto
- Division of Surgical Oncology, Knight Cancer Institute, Oregon Health & Science University, 3303 S.W. Bond Avenue, Portland, OR, 97239, USA
| | - Jeffrey D Wayne
- Department of Surgical Oncology, Northwestern University Feinberg School of Medicine, 251 East Huron Street, Chicago, IL, 60611, USA.,Department of Dermatology, Northwestern University Feinberg School of Medicine, 676 North St. Clair Street, Suite 1600, Chicago, IL, 60611, USA.,Skin Cancer Institute, Northwestern University, Lurie Comprehensive Cancer Center, 420 East Superior Street, Chicago, IL, 60611, USA
| | - Keith A Delman
- Department of Surgery, Emory University Winship Cancer Institute, 1364 Clifton Road NE, Atlanta, GA, 30322, USA
| | - David H Lawson
- Department of Hematology and Medical Oncology, Emory University Winship Cancer Institute, 550 Peachtree Street NE, Atlanta, GA, 30308, USA
| | - Pedram Gerami
- Skin Cancer Institute, Northwestern University, Lurie Comprehensive Cancer Center, 420 East Superior Street, Chicago, IL, 60611, USA. .,Departments of Dermatology and Pathology, Northwestern University Feinberg School of Medicine, 676 North St. Clair Street, Arkes 1600, Chicago, IL, 60611, USA.
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Schuitevoerder D, Heath M, Cook RW, Covington KR, Fortino J, Leachman S, Vetto JT. Impact of Gene Expression Profiling on Decision-Making in Clinically Node Negative Melanoma Patients after Surgical Staging. J Drugs Dermatol 2018; 17:196-199. [PMID: 29462228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
INTRODUCTION The surgeon's role in the follow-up of pathologic stage I and II melanoma patients has traditionally been minimal. Melanoma genetic expression profile (GEP) testing provides binary risk assessment (Class 1-low risk, Class 2-high risk), which can assist in predicting metastasis and formulating appropriate follow up. We sought to determine the impact of GEP results on the management of clinically node negative cutaneous melanoma patients staged with sentinel lymph node biopsy (SLNB). METHODS A retrospective review of prospectively gathered data consisting of patients seen from September 2015 - August 2016 was performed to determine whether GEP class influenced follow-up recommendations. Patients were stratified into four groups based on recommended follow-up plan: Dermatology alone, Surgical Oncology, Surgical Oncology with recommendation for adjuvant clinical trial, or Medical and Surgical Oncology. RESULTS Of ninety-one patients, 38 were pathologically stage I, 42 stage II, 10 stage III, and 1 stage IV. Combining all stages, GEP Class 1 patients were more likely to be followed by Dermatology alone and less like to be followed by Surgical Oncology with recommendation for adjuvant trial compared to Class 2 patients (P less than 0.001). Among stage 1 patients, Class 1 were more likely to follow up with Dermatology alone compared to Class 2 patients (82 vs. 0%; P less than 0.001). Among stage II patients, GEP Class 1 were more likely to follow up with Dermatology alone (21 vs 0%) and more Class 2 patients followed up with surgery and recommendations for adjuvant trial (36 vs 64%; P less than 0.05). There was no difference in follow up for stage III patients based on the GEP results (P=0.76). CONCLUSION GEP results were significantly associated with the management of stage I-II melanoma patients after staging with SLNB. For node negative patients, Class 2 results led to more aggressive follow up and management. J Drugs Dermatol. 2018;17(2):196-199.
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Hsueh EC, DeBloom JR, Lee J, Sussman JJ, Covington KR, Middlebrook B, Johnson C, Cook RW, Slingluff CL, McMasters KM. Erratum to: Interim analysis of survival in a prospective, multi-center registry cohort of cutaneous melanoma tested with a prognostic 31-gene expression profile test. J Hematol Oncol 2017; 10:160. [PMID: 28982385 PMCID: PMC5628449 DOI: 10.1186/s13045-017-0524-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/14/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Eddy C Hsueh
- Department of Surgery, St. Louis University, St. Louis, MO, USA
| | | | - Jonathan Lee
- Northside Melanoma and Sarcoma Specialists of Georgia, Atlanta, GA, USA
| | - Jeffrey J Sussman
- Department of Surgery, University of Cincinnati Cancer Institute, Cincinnati, OH, USA
| | - Kyle R Covington
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX, USA
| | - Brooke Middlebrook
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX, USA
| | - Clare Johnson
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX, USA
| | - Robert W Cook
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX, USA.
| | - Craig L Slingluff
- Department of Surgery and Cancer Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kelly M McMasters
- Department of Surgical Oncology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
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Hsueh EC, DeBloom JR, Lee J, Sussman JJ, Covington KR, Middlebrook B, Johnson C, Cook RW, Slingluff CL, McMasters KM. Interim analysis of survival in a prospective, multi-center registry cohort of cutaneous melanoma tested with a prognostic 31-gene expression profile test. J Hematol Oncol 2017; 10:152. [PMID: 28851416 PMCID: PMC5576286 DOI: 10.1186/s13045-017-0520-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/18/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A 31-gene expression profile (GEP) test that provides risk classification of cutaneous melanoma (CM) patients has been validated in several retrospective studies. The objective of the reported study was a prospective evaluation of the GEP performance in patients enrolled in two clinical registries. METHODS Three-hundred twenty two CM patients enrolled in the EXPAND (NCT02355587) and INTEGRATE (NCT02355574) registries met the criteria of age ≥ 16 years, successful GEP result and ≥1 follow-up visit for inclusion in this interim analysis. Primary endpoints were recurrence-free (RFS), distant metastasis-free (DMFS), and overall survival (OS). RESULTS Median follow-up was 1.5 years for event-free patients. Median age for subjects was 58 years (range 18-87) and median Breslow thickness was 1.2 mm (range 0.2-12.0). Eighty-eight percent (282/322) of cases had stage I/II disease and 74% (237/322) had a SLN biopsy. Seventy-seven percent (248/322) had class 1 molecular profiles. 1.5-year RFS, DMFS, and OS rates were 97 vs. 77%, 99 vs. 89%, and 99 vs. 92% for class 1 vs. class 2, respectively (p < 0.0001 for each). Multivariate Cox regression showed Breslow thickness, mitotic rate, and GEP class to significantly predict recurrence (p < 0.01), while tumor thickness was the only significant predictor of distant metastasis and overall survival in this interim analysis. CONCLUSIONS Interim analysis of patient outcomes from a combined prospective cohort supports the 31-gene GEP's ability to stratify early-stage CM patients into two groups with significantly different metastatic risk. RFS outcomes in this real-world cohort are consistent with previously published analyses with retrospective specimens. GEP testing complements current clinicopathologic features and increases identification of high-risk patients. TRIAL REGISTRATION ClinicalTrials.gov, NCT02355574 and NCT02355587.
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Affiliation(s)
- Eddy C. Hsueh
- Dept. of Surgery, St. Louis University, St. Louis, MO USA
| | | | - Jonathan Lee
- Northside Melanoma and Sarcoma Specialists of Georgia, Atlanta, GA USA
| | - Jeffrey J. Sussman
- Dept. of Surgery, University of Cincinnati Cancer Institute, Cincinnati, OH USA
| | - Kyle R. Covington
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX USA
| | - Brooke Middlebrook
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX USA
| | - Clare Johnson
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX USA
| | - Robert W. Cook
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX USA
| | - Craig L. Slingluff
- Dept. of Surgery and Cancer Center, University of Virginia School of Medicine, Charlottesville, VA USA
| | - Kelly M. McMasters
- Dept. of Surgical Oncology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY USA
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Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson M, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep 2017; 19:2878-2880. [PMID: 28658632 PMCID: PMC6141445 DOI: 10.1016/j.celrep.2017.06.008] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas, of a set of predominantly intrahepatic CCA cases, and propose a molecular classification scheme. We identified an IDH -mutant enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH -mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.
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Affiliation(s)
- Farshad Farshidfar
- Departments of Surgery and Oncology, Arnie Charbonneau
Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Siyuan Zheng
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
| | - Yulia Newton
- University of California Santa Cruz, Santa Cruz, CA 95064,
USA
| | - Juliann Shih
- The Eli and Edythe L. Broad Institute of Massachusetts
Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
| | - A. Gordon Robertson
- Canada’s Michael Smith Genome Sciences Centre, BC
Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Toshinori Hinoue
- Center for Epigenetics, Van Andel Research Institute, Grand
Rapids, MI 49503
| | - Katherine A. Hoadley
- Departments of Genetics and Pathology and Laboratory
Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599,
USA
- Lineberger Comprehensive Cancer Center, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ewan A. Gibb
- Canada’s Michael Smith Genome Sciences Centre, BC
Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Jason Roszik
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Kyle R. Covington
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
| | - Chia-Chin Wu
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
| | | | - Apurva Hegde
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Ju Dong Yang
- Divisions of Gastroenterology and Hepatology and
Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
55905, USA
| | - Ed Reznik
- Memorial Sloan Kettering Cancer Center, New York, NY
10005, USA
| | - Sara Sadeghi
- Canada’s Michael Smith Genome Sciences Centre, BC
Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Chandra Sekhar Pedamallu
- The Eli and Edythe L. Broad Institute of Massachusetts
Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
| | - Akinyemi I. Ojesina
- University of Alabama at Birmingham, Birmingham, AL
35294, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
35806, USA
| | - Julian M. Hess
- The Eli and Edythe L. Broad Institute of Massachusetts
Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - J. Todd Auman
- Departments of Genetics and Pathology and Laboratory
Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599,
USA
| | - Suhn K. Rhie
- University of Southern California, USC/Norris
Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Reanne Bowlby
- Canada’s Michael Smith Genome Sciences Centre, BC
Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Mitesh J. Borad
- Division of Hematology and Oncology, Mayo Clinic,
Scottsdale, AZ 85054, USA
| | | | - Andrew X Zhu
- Departments of Hematology and Oncology, Massachusetts
General Hospital, Boston, MA 02114, USA
| | - Josh M. Stuart
- University of California Santa Cruz, Santa Cruz, CA 95064,
USA
| | - Chris Sander
- Memorial Sloan Kettering Cancer Center, New York, NY
10005, USA
| | - Rehan Akbani
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Andrew D. Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts
Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
| | - Vikram Deshpande
- Departments of Pathology and Oncology, Massachusetts
General Hospital, Boston, MA 02114, USA
| | - Taofic Mounajjed
- Divisions of Gastroenterology and Hepatology and
Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
55905, USA
| | - Wai Chin Foo
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
| | - Michael Torbenson
- Divisions of Gastroenterology and Hepatology and
Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
55905, USA
| | | | - Peter W. Laird
- Center for Epigenetics, Van Andel Research Institute, Grand
Rapids, MI 49503
| | - David A. Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, TX 77030, USA
| | - Autumn J. McRee
- Lineberger Comprehensive Cancer Center, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oliver F. Bathe
- Departments of Surgery and Oncology, Arnie Charbonneau
Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jesper B. Andersen
- Biotech Research and Innovation Centre, University of
Copenhagen, DK-2200, Denmark
| | - Nabeel Bardeesy
- Departments of Pathology and Oncology, Massachusetts
General Hospital, Boston, MA 02114, USA
| | - Lewis R. Roberts
- Divisions of Gastroenterology and Hepatology and
Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
55905, USA
| | - Lawrence N. Kwong
- Departments of Genomic Medicine, Melanoma Medical Oncology,
Bioinformatics and Computational Biology, Pathology, and Translational Molecular
Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,
USA
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40
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Vetto JT, Leachman SA, Middlebrook B, Covington KR, Wayne JD, Gerami P, Zager JS. Performance of a 31-gene expression profile (GEP) test for metastatic risk prediction in cutaneous melanomas (CM) of the head and neck. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.9576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9576 Background: Accurate prognostication of distant metastatic risk using sentinel lymph node (SLN) biopsy for CM can be challenging in melanomas of the head and neck due to a higher false negative rate compared to other anatomical areas. A GEP signature that predicts metastatic risk based on primary tumor biology, providing a binary outcome of Class 1 (low risk of metastasis) or Class 2 (high risk), was previously described. The prognostic capabilities of the GEP independently and in combination with SLN status in a cohort of patients with primary head and neck CM are assessed here. Methods: All samples and clinical data were collected under an IRB-approved multicenter protocol. qPCR analysis was used to assess expression of the gene signature (Class 1 vs. Class 2). Distant metastasis-free survival (DMFS) and melanoma-specific survival (MSS) were assessed. Results: 157 subjects with primary CMs in the head and neck region were identified. 110 of 157 subjects had a SLN biopsy performed. Median age was 65 years (range 25-89) and median Breslow depth was 1.6 mm (range 0.2-15.0 mm). In 71 SLN-negative patients, 18 of 27 (67%) distant metastatic events were GEP Class 2. Overall, 73% (47 of 64) distant metastases, and 88% (22 of 25) deaths due to CM were called Class 2. By comparison, sensitivities for DMFS and MSS were 41% (26 of 64) and 52% (13 of 25), respectively, using SLN biopsy alone, and increased to 80% (51 of 64) and 88% (22 of 25), respectively, when combining the SLN status and GEP class. Kaplan-Meier 5-year DMFS and MSS rates based on SLN status alone or in combination with GEP are shown in the table. Conclusions: These data support the ability of the GEP test to accurately identify low- and high-risk cases of head and neck melanoma. The results strongly support the role of GEP testing to enhance current staging by better predicting the risk of distant metastasis and death for patients with melanoma in an anatomic region that is associated with a higher SLN biopsy false negative rate. [Table: see text]
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Affiliation(s)
- John T. Vetto
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | | | | | | | - Jeffrey D. Wayne
- Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
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41
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Fleming MD, Middlebrook B, Covington KR, Gerami P, Wayne JD, Zager JS. Performance of a prognostic 31-gene expression profile test in stage III cutaneous melanoma subjects. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.9578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9578 Background: The management of stage III cutaneous melanoma (CM) patients has changed significantly with the introduction of contemporary therapies. A 31-gene expression profile (GEP) test that provides a prediction of low or high risk of melanoma metastasis has been validated as an independent prognosticator of distant metastasis-free (DMFS) and melanoma-specific survival (MSS). We examine the prognostic accuracy of the test in a cohort of stage III, and particularly stage IIIA, subjects from a multicenter validation study. Methods: 207 primary CM tumors from 16 centers were analyzed as part of an IRB-approved study. Quantitative RT-PCR and predictive modeling were performed to classify metastasis and survival risk as Class 1 (low risk) or Class 2 (high risk). Results for Kaplan-Meier and Cox regression survival analysis are reported. Results: Of the 207 subjects with stage III melanoma, 76 were stage IIIA. The table shows 5-year DMFS and MSS rates for all stage III and stage IIIA groups. Patients with Class 2 GEP had significantly worse outcomes compared to Class 1. In univariate analyses, GEP was a significant predictor of DMFS and MSS with a hazard ratio for DMFS of 2.8 (95%-CI; 1.7-4.6) and for MSS of 4.0 (95%-CI; 1.7-9.4) for all stage III, while HR of 2.2 for DMFS (95%-CI; 1.0-4.7) and 4.3 for MSS (95%-CI; 1.2-15.2) were observed for the stage IIIA group. For all stage III cases, Breslow thickness and GEP were significant predictors of DMFS and MSS in multivariate models including ulceration and mitotic rate (p < 0.05). Conclusions: The results support the capability of the GEP to accurately predict stage III distant metastasis and survival, and that the test complements existing prognostic factors. GEP testing may be useful in identifying stage IIIA patients who are appropriate for adjuvant therapies and/or enrollment in clinical trials. [Table: see text]
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Affiliation(s)
| | | | | | | | - Jeffrey D. Wayne
- Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
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42
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Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep 2017; 18:2780-2794. [PMID: 28297679 PMCID: PMC5493145 DOI: 10.1016/j.celrep.2017.02.033] [Citation(s) in RCA: 333] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 01/04/2017] [Accepted: 02/09/2017] [Indexed: 02/07/2023] Open
Abstract
Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.
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Affiliation(s)
- Farshad Farshidfar
- Departments of Surgery and Oncology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Siyuan Zheng
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yulia Newton
- University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Juliann Shih
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Toshinori Hinoue
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Katherine A Hoadley
- Departments of Genetics and Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ewan A Gibb
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Jason Roszik
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kyle R Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chia-Chin Wu
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Apurva Hegde
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ju Dong Yang
- Divisions of Gastroenterology and Hepatology and Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Ed Reznik
- Memorial Sloan Kettering Cancer Center, New York, NY 10005, USA
| | - Sara Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Chandra Sekhar Pedamallu
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Akinyemi I Ojesina
- University of Alabama at Birmingham, Birmingham, AL 35294, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Julian M Hess
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - J Todd Auman
- Departments of Genetics and Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Suhn K Rhie
- USC/Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Mitesh J Borad
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, AZ 85054, USA
| | - Andrew X Zhu
- Departments of Hematology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Josh M Stuart
- University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chris Sander
- Memorial Sloan Kettering Cancer Center, New York, NY 10005, USA
| | - Rehan Akbani
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Vikram Deshpande
- Departments of Pathology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Taofic Mounajjed
- Divisions of Gastroenterology and Hepatology and Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Wai Chin Foo
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael S Torbenson
- Divisions of Gastroenterology and Hepatology and Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Autumn J McRee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oliver F Bathe
- Departments of Surgery and Oncology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jesper B Andersen
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
| | - Nabeel Bardeesy
- Departments of Pathology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Lewis R Roberts
- Divisions of Gastroenterology and Hepatology and Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Lawrence N Kwong
- Departments of Genomic Medicine, Melanoma Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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43
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Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun 2016; 7:12601. [PMID: 27574101 PMCID: PMC5013636 DOI: 10.1038/ncomms12601] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 07/18/2016] [Indexed: 01/21/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in USA annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). To identify potential targets for molecularly targeted chemoprevention, here we perform integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar ultraviolet radiation-driven Hairless mouse model. We identify the major transcriptional drivers of this progression sequence, showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this ultraviolet radiation-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible.
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Affiliation(s)
- Vida Chitsazzadeh
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer A Drummond
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Tri Nguyen
- Northwest Diagnostic Clinic, Houston, Texas 77090, USA
| | - Aaron Joseph
- Skin and Laser Surgery Associates, Pasadena, Texas 77505, USA
| | | | | | - Charles H Adelmann
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Grace Ching
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Tran N Nguyen
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Courtney Nicholas
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Valencia D Thomas
- Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Michael Migden
- Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Deborah MacFarlane
- Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Erika Thompson
- Sequencing and Microarray Facility, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Jianjun Shen
- Next Generation Sequencing Facility, Smithville, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Yoko Takata
- Next Generation Sequencing Facility, Smithville, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Kayla McNiece
- Department of Dermatology, University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - Maxim A Polansky
- Department of Dermatology, University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - Hussein A Abbas
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adam Gower
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02215, USA
| | - Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02215, USA
| | - Kyle R Covington
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Weimin Xiao
- Department of Biology and Biochemistry University of Houston, Houston, Texas 77204, USA
| | - Preethi Gunaratne
- Department of Biology and Biochemistry University of Houston, Houston, Texas 77204, USA
| | - Curtis Pickering
- Department of Head &Neck Surgery, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Mitchell Frederick
- Department of Head &Neck Surgery, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Jeffrey N Myers
- Department of Head &Neck Surgery, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Li Shen
- Department of Bioinformatics &Computational Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Hui Yao
- Department of Bioinformatics &Computational Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Xiaoping Su
- Department of Bioinformatics &Computational Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Ronald P Rapini
- Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - David A Wheeler
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ernest T Hawk
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Elsa R Flores
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Kenneth Y Tsai
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
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44
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Chen F, Zhang Y, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep 2016; 14:2476-89. [PMID: 26947078 DOI: 10.1016/j.celrep.2016.02.024] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/22/2015] [Accepted: 02/01/2016] [Indexed: 12/25/2022] Open
Abstract
On the basis of multidimensional and comprehensive molecular characterization (including DNA methalylation and copy number, RNA, and protein expression), we classified 894 renal cell carcinomas (RCCs) of various histologic types into nine major genomic subtypes. Site of origin within the nephron was one major determinant in the classification, reflecting differences among clear cell, chromophobe, and papillary RCC. Widespread molecular changes associated with TFE3 gene fusion or chromatin modifier genes were present within a specific subtype and spanned multiple subtypes. Differences in patient survival and in alteration of specific pathways (including hypoxia, metabolism, MAP kinase, NRF2-ARE, Hippo, immune checkpoint, and PI3K/AKT/mTOR) could further distinguish the subtypes. Immune checkpoint markers and molecular signatures of T cell infiltrates were both highest in the subtype associated with aggressive clear cell RCC. Differences between the genomic subtypes suggest that therapeutic strategies could be tailored to each RCC disease subset.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yasin Şenbabaoğlu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Lixing Yang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Ed Reznik
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Brian Shuch
- Department of Urology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Goran Micevic
- Department of Dermatology, Yale University, New Haven, CT 06510, USA; Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Guillermo De Velasco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael S Noble
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Yiling Lu
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Kyle R Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liu Xi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer A Drummond
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hyojin Kang
- Department of Convergence Technology Research, Korea Institute of Science and Technology Information (KAIST), Daejeon 305-806, Korea
| | - Junehawk Lee
- Department of Convergence Technology Research, Korea Institute of Science and Technology Information (KAIST), Daejeon 305-806, Korea; Department of Bio and Brain Engineering, KAIST, Daejeon 305-806, Korea
| | - Pheroze Tamboli
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Victor Reuter
- Department of Pathology, Memorial Sloan-Kettering Cancer, New York, NY 10065, USA
| | - Carl Simon Shelley
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Benny A Kaipparettu
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donald P Bottaro
- Urologic Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gad Getz
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Chris Sander
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elizabeth P Henske
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jane H Zhou
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
| | - David J Kwiatkowski
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ 85054, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - James J Hsieh
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - A Ari Hakimi
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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Haines K, Roy A, Wang L, Sumazin P, Covington KR, Muzny DM, Kumar V, Doddapaneni H, Chao H, Wheeler DA, Tomlinson G, Parsons DW, Plon SE, Lopez-Terrada D. Abstract A33: Discovery of chimeric transcripts involving APC and TERT in pediatric HCC by RNA sequencing. Cancer Res 2016. [DOI: 10.1158/1538-7445.pedca15-a33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Hepatocellular carcinoma (HCC) is a rare pediatric liver tumor with a poor prognosis. A characteristic DNAJB1-PRKACA gene fusion has been identified in a specific subtype, fibrolamelar HCC (FL-HCC). In the majority of pediatric cases of non-FL-HCC, a genetic cause has not been identified. We hypothesize that gene fusions could play a role in the tumorigenesis of pediatric HCC. The goal of this project is to utilize RNA sequencing to identify chimeric transcripts in pediatric HCC that could improve molecular characterization and identify potential oncogenic drivers of this disease.
Materials and Methods: We have used RNA sequencing (RNA-seq) to survey a cohort of 8 FL-HCCs, 4 pediatric HCCs, and 6 normal liver samples for chimeric transcripts. High quality RNA (RIN: 6.6-9.7) was extracted from fresh-frozen tissue and strand-specific, poly-A+ RNA-seq libraries were prepared for Illumina sequencing. Approximately 85 million paired-end reads (42.5 million fragments) of 2 x 100 bp length were generated per sample. Fusion transcripts in the tumor samples were detected using deFuse (v.0.6.1) on FASTQ files followed by subtraction of fusions also called in the normal liver dataset. The remaining calls in the HCC dataset were then filtered for the COSMIC Cancer Gene Census list to identify fusions involving known oncogenes or tumor suppressor genes. Candidate fusions were verified using BLAST and validated by RT-PCR.
Results: On average, 150 fusion transcripts were predicted per tumor sample using the deFuse algorithm. Further filtering by the normal liver dataset reduced the number of calls in the tumor datasets by ~60%. As expected, DNAJB1-PRKACA fusions were identified in the FL-HCC cohort with no additional fusions detected. Filtering by the COSMIC Cancer Gene Census list resulted in five additional fusion calls in HCC (three unique events in two tumors) two of which were confirmed by RT-PCR. The first event is an inversion within the APC and AP3B1 genes that results in the two in-frame fusion transcripts, APC-AP3B1 and APC3B1-APC, but no full-length APC transcript. The second event is a deletion encompassing the TERT promoter that results in the in-frame fusion LPCAT1-TERT. An increase in TERT expression is seen in this tumor as compared to both normal liver and other pediatric HCC tumors. Filtering for in-frame fusions involving non-COSMIC genes did not reveal any fusions in the two remaining HCCs and further analysis of these cases is ongoing.
Conclusion: The detection of chimeric transcripts by RNA-seq has allowed us to identify two unique structural events involving known cancer genes in two pediatric non-fibrolamellar HCCs. The chimeric transcripts found in these tumors provide further insight into the tumorigenic events of pediatric HCC.
Supported by research grants from Cancer Prevention and Research Institute of Texas RP101195 and RP120715 and National Institute of General Medical Sciences T32GM008307.
Citation Format: Katherine Haines, Angshumoy Roy, Linghua Wang, Pavel Sumazin, Kyle R. Covington, Donna M. Muzny, Vijetha Kumar, Harsha Doddapaneni, Hsu Chao, David A. Wheeler, Gail Tomlinson, D. Williams Parsons, Sharon E. Plon, Dolores Lopez-Terrada. Discovery of chimeric transcripts involving APC and TERT in pediatric HCC by RNA sequencing. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A33.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hsu Chao
- 1Baylor College of Medicine, Houston, TX,
| | | | - Gail Tomlinson
- 3University of Texas Health Science Center at San Antonio, San Antonio, TX
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Becnel LB, Pereira S, Drummond JA, Gingras MC, Covington KR, Kovar CL, Doddapaneni HV, Hu J, Muzny D, McGuire AL, Wheeler DA, Gibbs RA. An open access pilot freely sharing cancer genomic data from participants in Texas. Sci Data 2016; 3:160010. [PMID: 26882539 PMCID: PMC4755126 DOI: 10.1038/sdata.2016.10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/15/2016] [Indexed: 12/22/2022] Open
Abstract
Genomic data sharing in cancer has been restricted to aggregate or controlled-access initiatives to protect the privacy of research participants. By limiting access to these data, it has been argued that the autonomy of individuals who decide to participate in data sharing efforts has been superseded and the utility of the data as research and educational tools reduced. In a pilot Open Access (OA) project from the CPRIT-funded Texas Cancer Research Biobank, many Texas cancer patients were willing to openly share genomic data from tumor and normal matched pair specimens. For the first time, genetic data from 7 human cancer cases with matched normal are freely available without requirement for data use agreements nor any major restriction except that end users cannot attempt to re-identify the participants (http://txcrb.org/open.html).
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Affiliation(s)
- Lauren B Becnel
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer A Drummond
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kyle R Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
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47
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Gingras MC, Covington KR, Chang DK, Donehower LA, Gill AJ, Ittmann MM, Creighton CJ, Johns AL, Shinbrot E, Dewal N, Fisher WE, Pilarsky C, Grützmann R, Overman MJ, Jamieson NB, Van Buren G, Drummond J, Walker K, Hampton OA, Xi L, Muzny DM, Doddapaneni H, Lee SL, Bellair M, Hu J, Han Y, Dinh HH, Dahdouli M, Samra JS, Bailey P, Waddell N, Pearson JV, Harliwong I, Wang H, Aust D, Oien KA, Hruban RH, Hodges SE, McElhany A, Saengboonmee C, Duthie FR, Grimmond SM, Biankin AV, Wheeler DA, Gibbs RA. Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation. Cell Rep 2016; 14:907-919. [PMID: 26804919 PMCID: PMC4982376 DOI: 10.1016/j.celrep.2015.12.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 10/30/2015] [Accepted: 11/19/2015] [Indexed: 02/08/2023] Open
Abstract
The ampulla of Vater is a complex cellular environment from which adenocarcinomas arise to form a group of histopathologically heterogenous tumors. To evaluate the molecular features of these tumors, 98 ampullary adenocarcinomas were evaluated and compared to 44 distal bile duct and 18 duodenal adenocarcinomas. Genomic analyses revealed mutations in the WNT signaling pathway among half of the patients and in all three adenocarcinomas irrespective of their origin and histological morphology. These tumors were characterized by a high frequency of inactivating mutations of ELF3, a high rate of microsatellite instability, and common focal deletions and amplifications, suggesting common attributes in the molecular pathogenesis are at play in these tumors. The high frequency of WNT pathway activating mutation, coupled with small-molecule inhibitors of β-catenin in clinical trials, suggests future treatment decisions for these patients may be guided by genomic analysis.
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Affiliation(s)
- Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Kyle R Covington
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; The Kinghorn Cancer Centre and the Cancer Research Program Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
| | - Lawrence A Donehower
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anthony J Gill
- The Kinghorn Cancer Centre and the Cancer Research Program Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, Sydney, NSW 2065, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael M Ittmann
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Michael E. DeBakey Department of Veterans Affairs Medical Center, Houston, TX 77030, USA
| | - Chad J Creighton
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amber L Johns
- The Kinghorn Cancer Centre and the Cancer Research Program Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Eve Shinbrot
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ninad Dewal
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - William E Fisher
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; The Elkins Pancreas Center at Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; Academic Unit of Surgery, Institute of Cancer Sciences, Glasgow Royal Infirmary, Level 2, New Lister Building, University of Glasgow, Glasgow G31 2ER, UK
| | - George Van Buren
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; The Elkins Pancreas Center at Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer Drummond
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kimberly Walker
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oliver A Hampton
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liu Xi
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Lee
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michelle Bellair
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Han
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huyen H Dinh
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mike Dahdouli
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jaswinder S Samra
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; Department of Surgery, Royal North Shore Hospital, St Leonards, Sydney, NSW 2065, Australia
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
| | - Nicola Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - John V Pearson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - Ivon Harliwong
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Huamin Wang
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniela Aust
- Department of Pathology, TU Dresden, 01307 Dresden, Germany
| | - Karin A Oien
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; Department of Pathology, Southern General Hospital, Greater Glasgow and Clyde NHS, Glasgow G51 4TF, UK
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Sally E Hodges
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; The Elkins Pancreas Center at Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy McElhany
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; The Elkins Pancreas Center at Baylor College of Medicine, Houston, TX 77030, USA
| | - Charupong Saengboonmee
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Fraser R Duthie
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; Department of Pathology, Southern General Hospital, Greater Glasgow and Clyde NHS, Glasgow G51 4TF, UK
| | - Sean M Grimmond
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; The Kinghorn Cancer Centre and the Cancer Research Program Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E, Hess JM, Rheinbay E, Kim J, Maruvka YE, Braunstein LZ, Kamburov A, Hanawalt PC, Wheeler DA, Koren A, Lawrence MS, Getz G. Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair. Cell 2016; 164:538-49. [PMID: 26806129 DOI: 10.1016/j.cell.2015.12.050] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/21/2015] [Accepted: 12/24/2015] [Indexed: 12/20/2022]
Abstract
Mutational processes constantly shape the somatic genome, leading to immunity, aging, cancer, and other diseases. When cancer is the outcome, we are afforded a glimpse into these processes by the clonal expansion of the malignant cell. Here, we characterize a less explored layer of the mutational landscape of cancer: mutational asymmetries between the two DNA strands. Analyzing whole-genome sequences of 590 tumors from 14 different cancer types, we reveal widespread asymmetries across mutagenic processes, with transcriptional ("T-class") asymmetry dominating UV-, smoking-, and liver-cancer-associated mutations and replicative ("R-class") asymmetry dominating POLE-, APOBEC-, and MSI-associated mutations. We report a striking phenomenon of transcription-coupled damage (TCD) on the non-transcribed DNA strand and provide evidence that APOBEC mutagenesis occurs on the lagging-strand template during DNA replication. As more genomes are sequenced, studying and classifying their asymmetries will illuminate the underlying biological mechanisms of DNA damage and repair.
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Affiliation(s)
- Nicholas J Haradhvala
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Paz Polak
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Petar Stojanov
- Carnegie Mellon University School of Computer Science, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Kyle R Covington
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Eve Shinbrot
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Julian M Hess
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Esther Rheinbay
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jaegil Kim
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Yosef E Maruvka
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Lior Z Braunstein
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Atanas Kamburov
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Philip C Hanawalt
- Stanford University Department of Biology, 450 Serra Mall, Stanford, CA 94305, USA
| | - David A Wheeler
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Amnon Koren
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Cornell University Department of Molecular Biology and Genetics, 526 Campus Road, Ithaca, NY 14853, USA
| | - Michael S Lawrence
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
| | - Gad Getz
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
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49
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Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AAM, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho T, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J(J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni H, Drummond J, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med 2016; 374:135-45. [PMID: 26536169 PMCID: PMC4775252 DOI: 10.1056/nejmoa1505917] [Citation(s) in RCA: 895] [Impact Index Per Article: 111.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. RESULTS Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). CONCLUSIONS Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).
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Affiliation(s)
- W. Marston Linehan
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
- Corresponding Author: W. Marston Linehan, M.D., Urologic Oncology Branch, National Cancer Institute, Building 10 CRC Room 1-5940, Bethesda, MD 20892-1107 USA, Tel: 301-496-6353, Fax: 301-402-0922,
| | - Paul T. Spellman
- Oregon Health & Science University, Portland, OR
- Corresponding Author: W. Marston Linehan, M.D., Urologic Oncology Branch, National Cancer Institute, Building 10 CRC Room 1-5940, Bethesda, MD 20892-1107 USA, Tel: 301-496-6353, Fax: 301-402-0922,
| | | | | | | | | | | | - Bradley A. Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Laura Schmidt
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Cathy D. Vocke
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Myron Peto
- Oregon Health & Science University, Portland, OR
| | | | | | | | - Samira Brooks
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Angela N. Brooks
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - A. Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Denise Brooks
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Sara Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI
| | | | | | | | | | - Andrew D. Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Gordon Saksena
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Scott Haake
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Jun Li
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Han Liang
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Yiling Lu
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Rehan Akbani
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Pavana Anur
- Oregon Health & Science University, Portland, OR
| | - Donald Bottaro
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | | | | | | | | | - A. Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - James Hsieh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - William Y. Kim
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Maria J. Merino
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | | | - Ed Reznik
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - Satish Tickoo
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Daniel Crain
- The International Genomics Consortium, Phoenix, AZ
| | | | - Kevin Lau
- The International Genomics Consortium, Phoenix, AZ
| | | | - Scott Morris
- The International Genomics Consortium, Phoenix, AZ
| | | | | | | | | | - Mark Sherman
- The International Genomics Consortium, Phoenix, AZ
| | | | - Peggy Yena
- The International Genomics Consortium, Phoenix, AZ
| | - Melissa T. Avedon
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Jay Bowen
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Mark Gerken
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Kristen M. Leraas
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Nilsa C. Ramirez
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Tracie Santos
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Lisa Wise
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Erik Zmuda
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - John A. Demchok
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ina Felau
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Carolyn M. Hutter
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Margi Sheth
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Roy Tarnuzzer
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Zhining Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Liming Yang
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jean C. Zenklusen
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Brenda Ayala
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Julien Baboud
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Sudha Chudamani
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Jia Liu
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Laxmi Lolla
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Rashi Naresh
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Todd Pihl
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Qiang Sun
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Yunhu Wan
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Ye Wu
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Adrian Ally
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Miruna Balasundaram
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Saianand Balu
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Rameen Beroukhim
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Tom Bodenheimer
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Rebecca Carlsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Scott L. Carter
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Hsu Chao
- Baylor College of Medicine, Houston, TX
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Amanda Clarke
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | | | - Noreen Dhalla
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | - Stacey B. Gabriel
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - Ranabir Guin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | - D. Neil Hayes
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Robert A. Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Alan P. Hoyle
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Steven J.M. Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Corbin D. Jones
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Jie Li
- Baylor College of Medicine, Houston, TX
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Michael Mayo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Shaowu Meng
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew Meyerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - Richard A. Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Lisle E. Mose
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Joel S. Parker
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jeffrey Roach
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Steven E. Schumacher
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Yan Shi
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Janae V. Simons
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Payal Sipahimalani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Tara Skelly
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Carrie Sougnez
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Angela Tam
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Donghui Tan
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Min Wang
- Baylor College of Medicine, Houston, TX
| | | | - Tina Wong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Junyuan Wu
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liu Xi
- Baylor College of Medicine, Houston, TX
| | - Jane Zhou
- Baylor College of Medicine, Houston, TX
| | | | | | - Yao Fu
- Yale University, New Haven, CT
| | | | - David Haussler
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | - Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Phillip Lai
- University of Southern California, Los Angeles, CA
| | - Shiyun Ling
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Amie Radenbaugh
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | | | | | - Jingchun Zhu
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | - Monique Albert
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - J. Todd Auman
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - John Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sheldon Bastacky
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Julie Bergsten
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | | | - Lori Boice
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jeff Boyd
- Fox Chase Cancer Center, Philadelphia, PA
| | | | - Ying-Bei Chen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Erin Curley
- The International Genomics Consortium, Phoenix, AZ
| | - Benjamin Davies
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - April DeVolk
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Rajiv Dhir
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - John Eckman
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Jay Engel
- Kingston General Hospital, Kingston, Ontario, Canada
| | - Jodi Harr
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Ronald Hrebinko
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Mei Huang
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Mary Iacocca
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Bruce Jacobs
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Michael Lobis
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Jodi K. Maranchie
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Scott McMeekin
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jerome Myers
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Joel Nelson
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - Anil Parwani
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Nicholas Petrelli
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Brenda Rabeno
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Somak Roy
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - Joel Slaton
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | | | - Leigh Thorne
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelinda Tucker
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | | | | | | | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
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Brinkman WT, Squiers JJ, Covington KR, Wheeler DA, Arsalan M, Smith RL, Mack MJ, DiMaio JM. Mini-extracorporeal Circulation and Off-pump Techniques Associated with Less Inflammatory Gene Expression as Compared to On-Pump in the 24-hour Postoperative Window Following Coronary Artery Bypass Grafting. J Cardiothorac Surg 2015. [PMCID: PMC4693786 DOI: 10.1186/1749-8090-10-s1-a101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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