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Tosoian JJ, Zhang Y, Xiao L, Xie C, Samora NL, Niknafs YS, Chopra Z, Siddiqui J, Zheng H, Herron G, Vaishampayan N, Robinson HS, Arivoli K, Trock BJ, Ross AE, Morgan TM, Palapattu GS, Salami SS, Kunju LP, Tomlins SA, Sokoll LJ, Chan DW, Srivastava S, Feng Z, Sanda MG, Zheng Y, Wei JT, Chinnaiyan AM. Development and Validation of an 18-Gene Urine Test for High-Grade Prostate Cancer. JAMA Oncol 2024:2817657. [PMID: 38635241 DOI: 10.1001/jamaoncol.2024.0455] [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: 04/19/2024]
Abstract
Importance Benefits of prostate cancer (PCa) screening with prostate-specific antigen (PSA) alone are largely offset by excess negative biopsies and overdetection of indolent cancers resulting from the poor specificity of PSA for high-grade PCa (ie, grade group [GG] 2 or greater). Objective To develop a multiplex urinary panel for high-grade PCa and validate its external performance relative to current guideline-endorsed biomarkers. Design, Setting, and Participants RNA sequencing analysis of 58 724 genes identified 54 markers of PCa, including 17 markers uniquely overexpressed by high-grade cancers. Gene expression and clinical factors were modeled in a new urinary test for high-grade PCa (MyProstateScore 2.0 [MPS2]). Optimal models were developed in parallel without prostate volume (MPS2) and with prostate volume (MPS2+). The locked models underwent blinded external validation in a prospective National Cancer Institute trial cohort. Data were collected from January 2008 to December 2020, and data were analyzed from November 2022 to November 2023. Exposure Protocolized blood and urine collection and transrectal ultrasound-guided systematic prostate biopsy. Main Outcomes and Measures Multiple biomarker tests were assessed in the validation cohort, including serum PSA alone, the Prostate Cancer Prevention Trial risk calculator, and the Prostate Health Index (PHI) as well as derived multiplex 2-gene and 3-gene models, the original 2-gene MPS test, and the 18-gene MPS2 models. Under a testing approach with 95% sensitivity for PCa of GG 2 or greater, measures of diagnostic accuracy and clinical consequences of testing were calculated. Cancers of GG 3 or greater were assessed secondarily. Results Of 761 men included in the development cohort, the median (IQR) age was 63 (58-68) years, and the median (IQR) PSA level was 5.6 (4.6-7.2) ng/mL; of 743 men included in the validation cohort, the median (IQR) age was 62 (57-68) years, and the median (IQR) PSA level was 5.6 (4.1-8.0) ng/mL. In the validation cohort, 151 (20.3%) had high-grade PCa on biopsy. Area under the receiver operating characteristic curve values were 0.60 using PSA alone, 0.66 using the risk calculator, 0.77 using PHI, 0.76 using the derived multiplex 2-gene model, 0.72 using the derived multiplex 3-gene model, and 0.74 using the original MPS model compared with 0.81 using the MPS2 model and 0.82 using the MPS2+ model. At 95% sensitivity, the MPS2 model would have reduced unnecessary biopsies performed in the initial biopsy population (range for other tests, 15% to 30%; range for MPS2, 35% to 42%) and repeat biopsy population (range for other tests, 9% to 21%; range for MPS2, 46% to 51%). Across pertinent subgroups, the MPS2 models had negative predictive values of 95% to 99% for cancers of GG 2 or greater and of 99% for cancers of GG 3 or greater. Conclusions and Relevance In this study, a new 18-gene PCa test had higher diagnostic accuracy for high-grade PCa relative to existing biomarker tests. Clinically, use of this test would have meaningfully reduced unnecessary biopsies performed while maintaining highly sensitive detection of high-grade cancers. These data support use of this new PCa biomarker test in patients with elevated PSA levels to reduce the potential harms of PCa screening while preserving its long-term benefits.
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Affiliation(s)
- Jeffrey J Tosoian
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor
| | - Lanbo Xiao
- Department of Pathology, University of Michigan, Ann Arbor
| | - Cassie Xie
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Nathan L Samora
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Zoey Chopra
- Department of Pathology, University of Michigan, Ann Arbor
| | - Javed Siddiqui
- Department of Pathology, University of Michigan, Ann Arbor
| | - Heng Zheng
- Department of Pathology, University of Michigan, Ann Arbor
| | - Grace Herron
- Department of Pathology, University of Michigan, Ann Arbor
| | | | - Hunter S Robinson
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Bruce J Trock
- Departments of Pathology and Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ashley E Ross
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Todd M Morgan
- Department of Urology, University of Michigan, Ann Arbor
| | | | - Simpa S Salami
- Department of Urology, University of Michigan, Ann Arbor
| | | | - Scott A Tomlins
- Department of Urology, University of Michigan, Ann Arbor
- Strata Oncology, Ann Arbor, Michigan
| | - Lori J Sokoll
- Departments of Pathology and Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel W Chan
- Departments of Pathology and Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sudhir Srivastava
- Division of Cancer Prevention, National Institutes of Health, Bethesda, Maryland
| | - Ziding Feng
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Martin G Sanda
- Department of Urology, Emory University, Atlanta, Georgia
| | - Yingye Zheng
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - John T Wei
- Department of Urology, University of Michigan, Ann Arbor
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor
- Department of Urology, University of Michigan, Ann Arbor
- Howard Hughes Medical Institute, Chevy Chase, Maryland
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Bhambhani C, Kang Q, Hovelson DH, Sandford E, Olesnavich M, Dermody SM, Wolfgang J, Tuck KL, Brummel C, Bhangale AD, He K, Gutierrez MG, Lindstrom RH, Liu CJ, Tuck M, Kandarpa M, Mierzwa M, Casper K, Prince ME, Krauss JC, Talpaz M, Henry NL, Giraldez MD, Ramnath N, Tomlins SA, Swiecicki PL, Brenner JC, Tewari M. ctDNA transiting into urine is ultrashort and facilitates noninvasive liquid biopsy of HPV+ oropharyngeal cancer. JCI Insight 2024; 9:e177759. [PMID: 38516891 PMCID: PMC11018327 DOI: 10.1172/jci.insight.177759] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUNDTransrenal cell-free tumor DNA (TR-ctDNA), which transits from the bloodstream into urine, has the potential to enable noninvasive cancer detection for a wide variety of nonurologic cancer types.MethodsUsing whole-genome sequencing, we discovered that urine TR-ctDNA fragments across multiple cancer types are predominantly ultrashort (<50 bp) and, therefore, likely to be missed by conventional ctDNA assays. We developed an ultrashort droplet digital PCR assay to detect TR-ctDNA originating from HPV-associated oropharyngeal squamous cell carcinoma (HPV+ OPSCC) and confirmed that assaying ultrashort DNA is critical for sensitive cancer detection from urine samples.ResultsTR-ctDNA was concordant with plasma ctDNA for cancer detection in patients with HPV+ OPSCC. As proof of concept for using urine TR-ctDNA for posttreatment surveillance, in a small longitudinal case series, TR-ctDNA showed promise for noninvasive detection of recurrence of HPV+ OPSCC.ConclusionOur data indicate that focusing on ultrashort fragments of TR-ctDNA will be important for realizing the full potential of urine-based cancer diagnostics. This has implications for urine-based detection of a wide variety of cancer types and for facilitating access to care through at-home specimen collections.FundingNIH grants R33 CA229023, R21 CA225493; NIH/National Cancer Institute grants U01 CA183848, R01 CA184153, and P30CA046592; American Cancer Society RSG-18-062-01-TBG; American Cancer Society Mission Boost grant MBGI-22-056-01-MBG; and the A. Alfred Taubman Medical Research Institute.
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Affiliation(s)
| | - Qing Kang
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Daniel H. Hovelson
- Michigan Center for Translational Pathology
- Department of Computational Medicine & Bioinformatics
| | - Erin Sandford
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Mary Olesnavich
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | - Jenny Wolfgang
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Kirsten L. Tuck
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | | | - Kuang He
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | | | - Chia-Jen Liu
- Michigan Center for Translational Pathology
- Department of Pathology
| | - Melissa Tuck
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Malathi Kandarpa
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Michelle Mierzwa
- Department of Radiation Oncology, and
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Keith Casper
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark E. Prince
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - John C. Krauss
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Moshe Talpaz
- Department of Internal Medicine, Division of Hematology/Oncology
| | - N. Lynn Henry
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Maria D. Giraldez
- Department of Internal Medicine, Division of Hematology/Oncology
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, Seville, Spain
| | - Nithya Ramnath
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Scott A. Tomlins
- Michigan Center for Translational Pathology
- Department of Pathology
- Department of Urology
| | - Paul L. Swiecicki
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Chad Brenner
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Pharmacology
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, and
- Center for Computational Biology and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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Bulen BJ, Khazanov NA, Hovelson DH, Lamb LE, Matrana M, Burkard ME, Yang ESH, Edenfield WJ, Claire Dees E, Onitilo AA, Buchschacher GL, Miller AM, Parsons BM, Wassenaar TR, Suga JM, Siegel RD, Irvin W, Nair S, Slim JN, Misleh J, Khatri J, Masters GA, Thomas S, Safa MM, Anderson DM, Mowers J, Dusenbery AC, Drewery S, Plouffe K, Reeder T, Vakil H, Patrias L, Falzetta A, Hamilton R, Kwiatkowski K, Johnson DB, Rhodes DR, Tomlins SA. Validation of Immunotherapy Response Score as Predictive of Pan-solid Tumor Anti-PD-1/PD-L1 Benefit. Cancer Res Commun 2023; 3:1335-1349. [PMID: 37497337 PMCID: PMC10367935 DOI: 10.1158/2767-9764.crc-23-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/16/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023]
Abstract
Immunotherapy response score (IRS) integrates tumor mutation burden (TMB) and quantitative expression biomarkers to predict anti-PD-1/PD-L1 [PD-(L)1] monotherapy benefit. Here, we evaluated IRS in additional cohorts. Patients from an observational trial (NCT03061305) treated with anti-PD-(L)1 monotherapy were included and assigned to IRS-High (-H) versus -Low (-L) groups. Associations with real-world progression-free survival (rwPFS) and overall survival (OS) were determined by Cox proportional hazards (CPH) modeling. Those with available PD-L1 IHC treated with anti-PD-(L)1 with or without chemotherapy were separately assessed. Patients treated with PD-(L)1 and/or chemotherapy (five relevant tumor types) were assigned to three IRS groups [IRS-L divided into IRS-Ultra-Low (-UL) and Intermediate-Low (-IL), and similarly assessed]. In the 352 patient anti-PD-(L)1 monotherapy validation cohort (31 tumor types), IRS-H versus IRS-L patients had significantly longer rwPFS and OS. IRS significantly improved CPH associations with rwPFS and OS beyond microsatellite instability (MSI)/TMB alone. In a 189 patient (10 tumor types) PD-L1 IHC comparison cohort, IRS, but not PD-L1 IHC nor TMB, was significantly associated with anti-PD-L1 rwPFS. In a 1,103-patient cohort (from five relevant tumor types), rwPFS did not significantly differ in IRS-UL patients treated with chemotherapy versus chemotherapy plus anti-PD-(L)1, nor in IRS-H patients treated with anti-PD-(L)1 versus anti-PD-(L)1 + chemotherapy. IRS associations were consistent across subgroups, including both Europeans and non-Europeans. These results confirm the utility of IRS utility for predicting pan-solid tumor PD-(L)1 monotherapy benefit beyond available biomarkers and demonstrate utility for informing on anti-PD-(L)1 and/or chemotherapy treatment. Significance This study confirms the utility of the integrative IRS biomarker for predicting anti-PD-L1/PD-1 benefit. IRS significantly improved upon currently available biomarkers, including PD-L1 IHC, TMB, and MSI status. Additional utility for informing on chemotherapy, anti-PD-L1/PD-1, and anti-PD-L1/PD-1 plus chemotherapy treatments decisions is shown.
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Affiliation(s)
| | | | | | | | - Marc Matrana
- Ochsner Cancer Institute, New Orleans, Louisiana
| | - Mark E. Burkard
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| | - Eddy Shih-Hsin Yang
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | | | | | - Adedayo A. Onitilo
- Cancer Care and Research Center, Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | | | | | | | | | | | | | | | - Suresh Nair
- Lehigh Valley Topper Cancer Institute, Allentown, Pennsylvania
| | | | | | - Jamil Khatri
- ChristianaCare Oncology Hematology, Newark, Delaware
| | - Gregory A. Masters
- Medical Oncology Hematology Consultants, Helen F Graham Cancer Center and Research Institute, Newark, Delaware
| | - Sachdev Thomas
- Kaiser Permanente Northern California, Oakland, California
| | | | - Daniel M. Anderson
- Metro-Minnesota Community Oncology Research Consortium, St. Louis Park, Minnesota
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4
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Mehra R, Shah T, Liu CJ, Plouffe KR, Wang X, Mannan R, Cao X, Chinnaiyan AM, Tomlins SA, Udager AM. Highly Recurrent IDH1 Mutations in Prostate Cancer With Psammomatous Calcification. Mod Pathol 2023; 36:100146. [PMID: 36828361 DOI: 10.1016/j.modpat.2023.100146] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Prostate cancer is a heterogeneous disease with several well-recognized morphologic subtypes and histologic variants-subsets of which are enriched for or associated with specific genomic alterations. Herein, we report a cohort of 4 unique prostate cancers characterized by intratumoral psammomatous calcification-which we have termed prostate cancer with psammomatous calcification (PCWPC). Clinicopathologic review demonstrates that PCWPCs are high-grade (grade group ≥3) tumors that involve the anterior prostate, and integrative targeted next-generation sequencing reveals recurrent hotspot IDH1 mutations. This morphology-molecular correlation is independently confirmed in The Cancer Genome Atlas prostatic adenocarcinoma cohort, with 3 of the 5 IDH1-mutant prostate cancers showing psammomatous calcification (rφ = 0.67; Fisher exact test, P < .0001). Overall, these findings suggest that PCWPC represents a novel subtype of prostate cancer enriched for an anterior location and the presence of hotspot IDH1 mutations. Recognition of these unique morphologic features could help identify IDH1-mutant prostate cancer cases retrospectively and prospectively-facilitating future large research studies and enabling clinical trial enrollment and precision medicine approaches for patients with advanced and/or aggressive disease.
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Affiliation(s)
- Rohit Mehra
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; University of Michigan Rogel Cancer Center, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan
| | - Tanmay Shah
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Komal R Plouffe
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xiaoming Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan
| | - Rahul Mannan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan
| | - Xuhong Cao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; University of Michigan Rogel Cancer Center, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan; Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan; Howard Hughes Medical Institute, Ann Arbor, Michigan
| | - Scott A Tomlins
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Aaron M Udager
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; University of Michigan Rogel Cancer Center, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan.
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5
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Albrecht EA, Carter JD, Garbar V, Choudhary A, Tomlins SA. Intracellular Zinc Trafficking during Crotalus atrox Venom Wound Development. Int J Mol Sci 2023; 24:ijms24076763. [PMID: 37047742 PMCID: PMC10094922 DOI: 10.3390/ijms24076763] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
In this study, we examined zinc trafficking in human umbilical vein endothelial cells (HUVEC) stimulated with Crotalus atrox (CA venom) snake venom. We utilized MTS cytotoxicity assays to monitor the cytotoxic range of CA venom. HUVEC monolayers stimulated with 10 µg/mL CA venom for 3 h displayed cellular retraction, which coincided with 53.0 ± 6.5 percent viability. In contrast, venom concentrations of 100 µg/mL produced a complete disruption of cellular adherence and viability decreased to 36.6 ± 1.0. The zinc probe Fluozin-3AM was used to detect intracellular zinc in non-stimulated controls, HUVEC stimulated with 10 µg/mL CA venom or HUVEC preincubated with TPEN for 2 h then stimulated with 10 µg/mL CA venom. Fluorescent intensity analysis returned values of 1434.3 ± 197.4 for CA venom demonstrating an increase of about two orders of magnitude in labile zinc compared to non-stimulated controls. Endothelial response to CA venom induced a 96.1 ± 3.0- and 4.4 ± 0.41-fold increase in metallothionein 1X (MT1X) and metallothionein 2A (MT2A) gene expression. Zinc chelation during CA venom stimulation significantly increased cell viability, suggesting that the maintenance of zinc homeostasis during envenomation injury improves cell survival.
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Affiliation(s)
- Eric A Albrecht
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Jasmine D Carter
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Veronica Garbar
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Abeeha Choudhary
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Scott A Tomlins
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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Khazanov NA, Lamb LE, Hovelson DH, Kwiatkowski K, Johnson DB, Rhodes DR, Tomlins SA. Abstract 2171: A multivariate biomarker predicts sacituzumab govitecan response in solid tumors. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2171] [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: 04/07/2023]
Abstract
Abstract
Despite the recent clinical success of antibody drug conjugates (ADC) in oncology, predictive biomarkers are lacking, potentially limiting their impact. Herein, we evaluated the ability of candidate biomarkers alone and in combination to predict objective response rates observed in solid tumor patients treated with the TROP2-targeted ADC, sacituzumab govitecan (SG), as determined in the IMMU-12-01 basket trial. We leveraged available next generation sequencing (NGS)-based molecular profiling data from an independent advanced solid tumor cohort (n = 23,968) and developed a multivariate biomarker algorithm that produced biomarker positive rates correlating with the objective response rates (ORR) observed in IMMU-12-01. Candidate biomarkers evaluated included TROP2 gene expression, proliferation (by gene expression) and tumor cellularity. Notably, while TROP2 gene expression was highly correlated with protein expression across 45 tumor types (r = 0.93), TROP2 gene expression alone did not significantly predict ORR across 9 tumor types (r = 0.40, p = 0.29). In contrast, a biomarker algorithm combining TROP2 and proliferation by gene expression with tumor cellularity strongly predicted response both when using tumor type-specific biomarker rates in a discovery cohort (r = 0.83, p = 0.006) and in an independent validation cohort (r = 0.82, p = 0.007). These results indicate that the multivariate biomarker accounts for 67% of the variability observed in response rates and may thus identify patients likely to benefit from SG. Among tumor types with objective responses in IMMU-12-01, biomarker positive rates ranged from 9.9% in colorectal cancer to 57.4% in bladder cancer. Additional tumor types with biomarker positive rates >30% included cancers of the head and neck, cervix, salivary gland, skin (non-melanoma) and ovary, all with positive biomarker rates >30%. Interestingly, most tumor types had biomarker positive rates >5%, suggesting the potential for a tumor type-agnostic approach to patient selection. Considering SG and other ADC’s mechanism of action, a plausible model for response is that (1) higher target expression increases ADC drug delivery, (2) higher tumor cellularity increases ADC bystander effect and (3) higher tumor cell proliferation increases tumor cell death. In summary, we uncovered a novel biomarker algorithm capable of predicting SG response across solid tumors that may be generalizable to ADCs as a class, with the potential to further optimize use and maximize benefit.
Citation Format: Nickolay A. Khazanov, Laura E. Lamb, Daniel H. Hovelson, Kat Kwiatkowski, D. Bryan Johnson, Daniel R. Rhodes, Scott A. Tomlins. A multivariate biomarker predicts sacituzumab govitecan response in solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2171.
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Lamb LE, Khazanov NA, Hovelson DH, Kwiatkowski K, Johnson DB, Rhodes DR, Tomlins SA. Abstract 968: Evaluation of Her2 RNA expression as a potential predictive biomarker for anti-Her2 therapy. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-968] [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: 04/07/2023]
Abstract
Abstract
Trastuzumab deruxtecan (Enhertu) is effective in "HER2 Low" breast cancer, defined by 1+ or 2+ expression by immunohistochemistry (IHC). Interest has now turned toward defining a sub-population of IHC 0+ tumors that may have HER2 expression below the limit of IHC detection/quantification and may thus also be responsive. We previously validated a high dynamic range HER2 RNA expression assay run as part of our comprehensive genomic profiling test, StrataNGS.
Herein, we evaluated the HER2 RNA expression data together with copy number and clinical outcome data from the Strata Clinical Molecular Database (SCMD) in advanced breast cancer (n = 3,063) and other advanced solid tumors (n = 26,715). As expected, HER2 gene expression was significantly higher in tumors with DNA amplification (>=6 copies; median: 13.9 vs. 10.0 in log2 units; p < 1e-100). Despite similar copy number levels in amplified breast vs. other cancers (median: 21.8 vs. 19.8 copies), HER2 expression levels were ~2-fold higher (median: 14.5 vs. 13.5; p = 1.3e-10). Similarly, HER2 expression levels were higher in non-amplified breast vs. other cancers (median: 10.7 vs. 9.9; p<1e-100), suggesting that DNA amplification and cell lineage affect HER2 expression. Using our previously validated HER2 threshold, among 75 eligible SCMD breast cancer patients treated with 1st or 2nd line systemic trastuzumab or pertuzumab containing therapy, HER2 RNA High patients (n=46, 59%) had significantly longer time to next therapy (TTNT) compared to HER2 RNA Not High patients (median TTNT 26.9 vs. 5.6 months, adjusted hazard ratio 0.31, p=0.005 when adjusted for 1st vs. 2nd line, pertuzumab inclusion, and inclusion of chemotherapy or hormonal therapy).
In patients with available IHC data (n = 388), HER2 RNA expression trended with IHC across the 0-3+ range, however, while 3+ tumors had distinctly high RNA expression (median: 14.4), 0-2+ tumors had lower expression with overlapping distributions (median: 10.5, 10.9, 11.5, respectively), suggesting that 0-2+ tumors do not represent distinct biological groups, but rather a continuum of low expression. We defined a HER2 RNA Low threshold (>10.6), corresponding to the top 75% of IHC 1-2+ breast cancers. Importantly, at this threshold, nearly half (44.1%) of 0+ breast cancers were also classified as HER2 RNA Low. Additionally, 25.8% of all non-breast solid tumors were classified as HER2 RNA Low. Given that HER2 RNA High predicted benefit from 1st generation anti-HER2 therapies, future studies should consider HER2 RNA Low as an alternative biomarker to Her2 IHC Low, with the opportunity to further expand trastuzumab deruxtecan use into the IHC 0+ breast cancer population and potentially to additional solid tumors.
Citation Format: Laura E. Lamb, Nickolay A. Khazanov, Daniel H. Hovelson, Kat Kwiatkowski, D. Bryan Johnson, Daniel R. Rhodes, Scott A. Tomlins. Evaluation of Her2 RNA expression as a potential predictive biomarker for anti-Her2 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 968.
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Affiliation(s)
- Neal D Shore
- Carolina Urologic Research Center, Myrtle Beach, South Carolina
| | | | - Scott A Tomlins
- Departments of Pathology and Urology, Rogel Cancer Center, University of Michigan Medical School, Ann Arbor
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Shore ND, Renzulli J, Fleshner NE, Hollowell CMP, Vourganti S, Silberstein J, Siddiqui R, Hairston J, Elsouda D, Russell D, Cooperberg MR, Tomlins SA. Enzalutamide Monotherapy vs Active Surveillance in Patients With Low-risk or Intermediate-risk Localized Prostate Cancer: The ENACT Randomized Clinical Trial. JAMA Oncol 2022; 8:1128-1136. [PMID: 35708696 PMCID: PMC9204619 DOI: 10.1001/jamaoncol.2022.1641] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Importance There are few published studies prospectively assessing pharmacological interventions that may delay prostate cancer progression in patients undergoing active surveillance (AS). Objective To compare the efficacy and safety of enzalutamide monotherapy plus AS vs AS alone in patients with low-risk or intermediate-risk prostate cancer. Design, Setting, and Participants The ENACT study was a phase 2, open-label, randomized clinical trial conducted from June 2016 to August 2020 at 66 US and Canadian sites. Eligible patients were 18 years or older, had received a diagnosis of histologically proven low-risk or intermediate-risk localized prostate cancer within 6 months of screening, and were undergoing AS. Patients were monitored during 1 year of treatment and up to 2 years of follow-up. Data analysis was conducted in February 2021. Interventions Randomized 1:1 to enzalutamide, 160 mg, monotherapy for 1 year or continued AS, as stratified by cancer risk and follow-up biopsy type. Main Outcomes and Measures The primary end point was time to pathological or therapeutic prostate cancer progression (pathological, ≥1 increase in primary or secondary Gleason pattern or ≥15% increased cancer-positive cores; therapeutic, earliest occurrence of primary therapy for prostate cancer). Secondary end points included incidence of a negative biopsy result, percentage of cancer-positive cores, and incidence of a secondary rise in serum prostate-specific antigen (PSA) levels at 1 and 2 years, as well as time to PSA progression. Adverse events were monitored to assess safety. Results A total of 114 patients were randomized to treatment with enzalutamide plus AS and 113 to AS alone; baseline characteristics were similar between treatment arms (mean [SD] age, 66.1 [7.8] years; 1 Asian individual [0.4%], 21 Black or African American individuals [9.3%], 1 Hispanic individual [0.4%], and 204 White individuals [89.9%]). Enzalutamide significantly reduced the risk of prostate cancer progression by 46% vs AS (hazard ratio, 0.54; 95% CI, 0.33-0.89; P = .02). Compared with AS, odds of a negative biopsy result were 3.5 times higher; there was a significant reduction in the percentage of cancer-positive cores and the odds of a secondary rise in serum PSA levels at 1 year with treatment with enzalutamide; no significant difference was observed at 2 years. Treatment with enzalutamide also significantly delayed PSA progression by 6 months vs AS (hazard ratio, 0.71; 95% CI, 0.53-0.97; P = .03). The most commonly reported adverse events during enzalutamide treatment were fatigue (62 [55.4%]) and gynecomastia (41 [36.6%]). Three patients in the enzalutamide arm died; none were receiving the study drug at the time of death. No deaths were considered treatment-related. Conclusions and Relevance The results of this randomized clinical trial suggest that enzalutamide monotherapy was well-tolerated and demonstrated a significant treatment response in patients with low-risk or intermediate-risk localized prostate cancer. Enzalutamide may provide an alternative treatment option for patients undergoing AS. Trial Registration ClinicalTrials.gov Identifier: NCT02799745.
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Affiliation(s)
- Neal D. Shore
- Carolina Urologic Research Center, Myrtle Beach, South Carolina
| | | | | | | | | | | | | | | | | | | | | | - Scott A. Tomlins
- Departments of Pathology and Urology, Rogel Cancer Center, University of Michigan Medical School, Ann Arbor
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10
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Cani AK, Hu K, Liu CJ, Siddiqui J, Zheng Y, Han S, Nallandhighal S, Hovelson DH, Xiao L, Pham T, Eyrich NW, Zheng H, Vince R, Tosoian JJ, Palapattu GS, Morgan TM, Wei JT, Udager AM, Chinnaiyan AM, Tomlins SA, Salami SS. Development of a Whole-urine, Multiplexed, Next-generation RNA-sequencing Assay for Early Detection of Aggressive Prostate Cancer. Eur Urol Oncol 2022; 5:430-439. [PMID: 33812851 DOI: 10.1016/j.euo.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 11/27/2020] [Revised: 02/22/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Despite biomarker development advances, early detection of aggressive prostate cancer (PCa) remains challenging. We previously developed a clinical-grade urine test (Michigan Prostate Score [MiPS]) for individualized aggressive PCa risk prediction. MiPS combines serum prostate-specific antigen (PSA), the TMPRSS2:ERG (T2:ERG) gene fusion, and PCA3 lncRNA in whole urine after digital rectal examination (DRE). OBJECTIVE To improve on MiPS with a novel next-generation sequencing (NGS) multibiomarker urine assay for early detection of aggressive PCa. DESIGN, SETTING, AND PARTICIPANTS Preclinical development and validation of a post-DRE urine RNA NGS assay (Urine Prostate Seq [UPSeq]) assessing 84 PCa transcriptomic biomarkers, including T2:ERG, PCA3, additional PCa fusions/isoforms, mRNAs, lncRNAs, and expressed mutations. Our UPSeq model was trained on 73 patients and validated on a held-out set of 36 patients representing the spectrum of disease (benign to grade group [GG] 5 PCa). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The area under the receiver operating characteristic curve (AUC) of UPSeq was compared with PSA, MiPS, and other existing models/biomarkers for predicting GG ≥3 PCa. RESULTS AND LIMITATIONS UPSeq demonstrated high analytical accuracy and concordance with MiPS, and was able to detect expressed germline HOXB13 and somatic SPOP mutations. In an extreme design cohort (n = 109; benign/GG 1 vs GG ≥3 PCa, stratified to exclude GG 2 cancer in order to capture signal difference between extreme ends of disease), UPSeq showed differential expression for T2:ERG.T1E4 (1.2 vs 78.8 median normalized reads, p < 0.00001) and PCA3 (1024 vs 2521, p = 0.02), additional T2:ERG splice isoforms, and other candidate biomarkers. Using machine learning, we developed a 15-transcript model on the training set (n = 73) that outperformed serum PSA and sequencing-derived MiPS in predicting GG ≥3 PCa in the held-out validation set (n = 36; AUC 0.82 vs 0.69 and 0.69, respectively). CONCLUSIONS These results support the potential utility of our novel urine-based RNA NGS assay to supplement PSA for improved early detection of aggressive PCa. PATIENT SUMMARY We have developed a new urine-based test for the detection of aggressive prostate cancer, which promises improvement upon current biomarker tests.
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Affiliation(s)
- Andi K Cani
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Kevin Hu
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yingye Zheng
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sumin Han
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Daniel H Hovelson
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Trinh Pham
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicholas W Eyrich
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Heng Zheng
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Randy Vince
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jeffrey J Tosoian
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ganesh S Palapattu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John T Wei
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aaron M Udager
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Simpa S Salami
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA.
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11
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Cani AK, Dolce EM, Liu CJ, Rupp B, Darga EP, Paoletti C, Thomas DG, Wu YM, Robinson DR, Nagrath S, Chinnaiyan AM, Tomlins SA, Udager AM, Carethers JM, Cobain EF, Hayes DF. Abstract 611: Assessment of tumor mutation burden and microsatellite instability by single-cell circulating tumor cell genomic profiling. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-611] [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
The success of immune checkpoint inhibitors rests on biomarkers such as tumor mutation burden (TMB) and microsatellite instability (MSI), both FDA-approved predictors of anti PD-1/L1 therapy benefit. Tissue biopsies often collected once in the metastatic setting through an invasive procedure, or archived primary tumor tissue often collected much prior to treatment consideration, are the specimen types of choice for biomarker identification. The tissue sample originates from a limited region of one disease site, which may limit its usefulness given intra-patient tumor heterogeneity. TMB and MSI measurement by liquid biopsy, including proteins, circulating tumor cells (CTC), and cell-free circulating tumor DNA (ctDNA), is an attractive, minimally-invasive way to obtain a real-time picture of the entire disease. While TMB and MSI assessment from ctDNA have been reported, their measurement can be limited by low ctDNA tumor fraction. Single-cell next generation sequencing of CTC, on the other hand, is a particularly well-suited, but largely unexplored method of measuring TMB and MSI to complement tissue and ctDNA for better overall specificity of detection. In this proof-of-concept study, we show the ability to detect single-cell TMB and MSI. We analyzed 14 CTC and 4 ctDNA samples from 6 metastatic breast cancer patients, as well as 3 single cells and 1 cell pellet sample each from HCT-116 (MSI-High) and WiDr (MSI-Low) cell lines. CTC and cell line cells were enriched with the CellSearch® system and/or isolated with the DEPArray™ system. Whole genome amplified single-cell DNA was sequenced with the Oncomine Comprehensive Assay covering ~500 genes and 1.1Mb of genomic space. TMB and MSI scores obtained in CTC and ctDNA were compared to those measured in matched clinical tissue biopsies. Single-cell TMB scores and MSI status were assessable in all CTC tested. CTC TMB scores were highly concordant with the matched tissue samples (r=1.00), as were ctDNA TMB scores (r=0.98) in patients with assessable TMB scores in both biospecimen types compared. Importantly, TMB was detectable in CTC from one patient whose tissue sample was inadequate for clinical sequencing, and from another patient with inadequate, low tumor fraction ctDNA. Intriguingly, one patient harbored 3 TMB-high and 2 TMB-low CTC, potentially indicating intra-patient TMB heterogeneity. The known MSI-low status from clinical tumor tissue sequencing was correctly detected in CTC and ctDNA from all patients. MSI status and scores from single cells of HCT-116 and WiDr cell lines purified with the DEPArray™ system (mimicking CTC isolation), perfectly matched that of the corresponding cell pellet samples (r=1.00). Taken together, these data suggest the potential validity and continued interrogation of potential utility of CTC TMB and MSI detection to complement tissue and ctDNA in guiding checkpoint inhibitor immunotherapy.
Citation Format: Andi K. Cani, Emily M. Dolce, Chia-Jen Liu, Brittany Rupp, Elizabeth P. Darga, Costanza Paoletti, Dafydd G. Thomas, Yi-Mi Wu, Dan R. Robinson, Sunitha Nagrath, Arul M. Chinnaiyan, Scott A. Tomlins, Aaron M. Udager, John M. Carethers, Erin F. Cobain, Daniel F. Hayes. Assessment of tumor mutation burden and microsatellite instability by single-cell circulating tumor cell genomic profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 611.
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Affiliation(s)
| | | | | | | | | | | | | | - Yi-Mi Wu
- 1University of Michigan, Ann Arbor, MI
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12
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Cani AK, Dolce EM, Darga EP, Hu K, Liu CJ, Rae JM, Thomas DG, Tomlins SA, Chinnaiyan AM, Udager AM, Paoletti C, Cobain EF, Hayes DF. Abstract 1700: Serial monitoring of single-cell circulating tumor cell genomics in metastatic lobular breast cancer to identify precision and immuno-oncology biomarkers with therapeutic implications. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1700] [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
Clinical decisions for precision and immuno-oncology therapies are based on predictive biomarkers commonly obtained from a single metastatic biopsy, or from archived primary tumor material. Circulating genomic biomarkers present a minimally invasive way to monitor the intra-patient tumor heterogeneity and its fluctuations in order to provide a real-time evaluation of the changing clonal architecture with potential therapeutic implications. Single-cell DNA next generation sequencing (scNGS) of circulating tumor cells (CTC) is a particularly well-suited method of unraveling and monitoring that heterogeneity to complement biomarker information obtained from tissue and cell-free circulating tumor DNA (ctDNA). In this proof-of-concept study we analyzed 123 CTC, 15 white blood cells (WBC), and ctDNA from 15 CTC-positive lobular breast cancer patients, five of whom had CTC available at both metastatic baseline and after progression on a variety of therapies chosen at their physician’s discretion. CTC were enriched with the CellSearch® system and isolated as single cells with the DEPArray™ system. Whole genome amplified CTC DNA underwent scNGS with the Oncomine Comprehensive Assay covering ~500 genes and 1.1Mb of genomic space to detect mutations, copy number alterations, tumor mutation burden (TMB) and microsatellite instability (MSI). 99.1% of cells were informative, with a mean sequencing depth of 664x. Using our previously developed, CTC-based precision medicine reporting platform, MI-CTCSeq, multiple CTC in seven of 15 patients (47%) had mutations that were actionable by FDA-approved targeted therapies including in the oncogenes PIK3CA (alpelisib) and FGFR2 (erdafitinib). 13 patients (87%) displayed intra-patient, inter-CTC genomic heterogeneity of putative driver mutations. Two of five (40%) patients with CTC at both baseline and progression displayed fluctuations in their CTC subclonal makeup between timepoints. One of the two harbored a baseline ESR1 (estrogen receptor α) p.D538G activating mutation that largely disappeared at progression and was replaced by a CTC subclone with a different ESR1 activating mutation, p.Y537S. Intriguingly, this patient’s CTC also harbored an FGFR2 p.K659M mutation in an actionable “hotspot” at progression, which was absent at baseline, suggesting potential utility of serial monitoring by CTC scNGS. TMB scores and MSI status in CTC were highly concordant with those measured in clinical tissue biopsies. Taken together, these data suggest the non-invasive interrogation of the CTC genomic landscape and its serial monitoring to inform precision and immuno-oncology treatments in real time.
Citation Format: Andi K. Cani, Emily M. Dolce, Elizabeth P. Darga, Kevin Hu, Chia-Jen Liu, James M. Rae, Daffyd G. Thomas, Scott A. Tomlins, Arul M. Chinnaiyan, Aaron M. Udager, Costanza Paoletti, Erin F. Cobain, Daniel F. Hayes. Serial monitoring of single-cell circulating tumor cell genomics in metastatic lobular breast cancer to identify precision and immuno-oncology biomarkers with therapeutic implications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1700.
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Affiliation(s)
| | | | | | - Kevin Hu
- 1University of Michigan, Ann Arbor, MI
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13
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Tosoian JJ, Singhal U, Davenport MS, Wei JT, Montgomery JS, George AK, Salami SS, Mukundi SG, Siddiqui J, Kunju LP, Tooke BP, Ryder CY, Dugan SP, Chopra Z, Botbyl R, Feng Y, Sessine MS, Eyrich NW, Ross AE, Trock BJ, Tomlins SA, Palapattu GS, Chinnaiyan AM, Niknafs YS, Morgan TM. Urinary MyProstateScore (MPS) to Rule out Clinically-Significant Cancer in Men with Equivocal (PI-RADS 3) Multiparametric MRI: Addressing an Unmet Clinical Need. Urology 2022; 164:184-190. [PMID: 34906585 PMCID: PMC10171463 DOI: 10.1016/j.urology.2021.11.033] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To evaluate the complementary value of urinary MyProstateScore (MPS) testing and multiparametric MRI (mpMRI) and assess outcomes in patients with equivocal mpMRI. MATERIALS AND METHODS Included patients underwent mpMRI followed by urine collection and prostate biopsy at the University of Michigan between 2015 -2019. MPS values were calculated from urine specimens using the validated model based on serum PSA, urinary PCA3, and urinary TMPRSS2:ERG. In the PI-RADS 3 population, the discriminative accuracy of PSA, PSAD, and MPS for GG≥2 cancer was quantified by the AUC curve. Decision curve analysis was used to assess net benefit of MPS relative to PSAD. RESULTS There were 540 patients that underwent mpMRI and biopsy with MPS available. The prevalence of GG≥2 cancer was 13% for PI-RADS 3, 56% for PI-RADS 4, and 87% for PI-RADS 5. MPS was significantly higher in men with GG≥2 cancer [median 44.9, IQR (29.4 -57.5)] than those with negative or GG1 biopsy [median 29.2, IQR (14.8 -44.2); P <.001] in the overall population and when stratified by PI-RADS score. In the PI-RADS 3 population (n = 121), the AUC for predicting GG≥2 cancer was 0.55 for PSA, 0.62 for PSAD, and 0.73 for MPS. MPS provided the highest net clinical benefit across all pertinent threshold probabilities. CONCLUSION In patients that underwent mpMRI and biopsy, MPS was significantly associated with GG≥2 cancer across all PI-RADS scores. In the PI-RADS 3 population, MPS significantly outperformed PSAD in ruling out GG≥2 cancer. These findings suggest a complementary role of MPS testing in patients that have undergone mpMRI.
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Affiliation(s)
- Jeffrey J Tosoian
- Department of Urology, Vanderbilt University, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN; Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI.
| | - Udit Singhal
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Department of Urology, Mayo Clinic, Rochester, MN
| | - Matthew S Davenport
- Department of Urology, University of Michigan, Ann Arbor, MI; Department of Radiology, University of Michigan, Ann Arbor, MI
| | - John T Wei
- Department of Urology, University of Michigan, Ann Arbor, MI
| | - Jeffrey S Montgomery
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | - Arvin K George
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | - Simpa S Salami
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | | | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Lakshmi P Kunju
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | | | | | - Sarah P Dugan
- University of Michigan Medical School, Ann Arbor, MI
| | - Zoey Chopra
- University of Michigan Medical School, Ann Arbor, MI
| | - Rachel Botbyl
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Yilin Feng
- University of Michigan Medical School, Ann Arbor, MI
| | | | | | - Ashley E Ross
- Department of Urology, Northwestern Feinberg School of Medicine, Chicago, IL
| | - Bruce J Trock
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ganesh S Palapattu
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Arul M Chinnaiyan
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
| | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Todd M Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
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14
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Rodriguez-Calero A, Gallon J, Akhoundova D, Maletti S, Ferguson A, Cyrta J, Amstutz U, Garofoli A, Paradiso V, Tomlins SA, Hewer E, Genitsch V, Fleischmann A, Vassella E, Rushing EJ, Grobholz R, Fischer I, Jochum W, Cathomas G, Osunkoya AO, Bubendorf L, Moch H, Thalmann G, Ng CKY, Gillessen S, Piscuoglio S, Rubin MA. Alterations in homologous recombination repair genes in prostate cancer brain metastases. Nat Commun 2022; 13:2400. [PMID: 35504881 PMCID: PMC9065149 DOI: 10.1038/s41467-022-30003-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 05/06/2020] [Accepted: 04/12/2022] [Indexed: 12/31/2022] Open
Abstract
Improved survival rates for prostate cancer through more effective therapies have also led to an increase in the diagnosis of metastases to infrequent locations such as the brain. Here we investigate the repertoire of somatic genetic alterations present in brain metastases from 51 patients with prostate cancer brain metastases (PCBM). We highlight the clonal evolution occurring in PCBM and demonstrate an increased mutational burden, concomitant with an enrichment of the homologous recombination deficiency mutational signature in PCBM compared to non-brain metastases. Focusing on known pathogenic alterations within homologous recombination repair genes, we find 10 patients (19.6%) fulfilling the inclusion criteria used in the PROfound clinical trial, which assessed the efficacy of PARP inhibitors (PARPi) in homologous recombination deficient prostate cancer. Eight (15.7%) patients show biallelic loss of one of the 15 genes included in the trial, while 5 patients (9.8%) harbor pathogenic alterations in BRCA1/2 specifically. Uncovering these molecular features of PCBM may have therapeutic implications, suggesting the need of clinical trial enrollment of PCBM patients when evaluating potential benefit from PARPi.
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Affiliation(s)
- Antonio Rodriguez-Calero
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Dilara Akhoundova
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Sina Maletti
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Alison Ferguson
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Oncology, Ludwig Cancer Centre, University of Lausanne, Lausanne, Switzerland
| | - Joanna Cyrta
- Department of Pathology, Institut Curie, University Paris Sciences et Lettres, Paris, France
| | - Ursula Amstutz
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrea Garofoli
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Viola Paradiso
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Scott A Tomlins
- Departments of Pathology and Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ekkehard Hewer
- Institute of Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Vera Genitsch
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Achim Fleischmann
- Institute of Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology, Cantonal Hospital Thurgau, Münsterlingen, Switzerland
| | - Erik Vassella
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Elisabeth J Rushing
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Rainer Grobholz
- Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Ingeborg Fischer
- Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Wolfram Jochum
- Institute of Pathology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Gieri Cathomas
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Adeboye O Osunkoya
- Departments of Pathology and Laboratory Medicine, and Urology, Emory University School of Medicine, Atlanta, USA
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - George Thalmann
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Silke Gillessen
- Faculty of Biomedical Sciences, USI, Lugano, Switzerland
- Department of Oncology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- Bern Center for Precision Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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15
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Cani AK, Dolce EM, Darga EP, Hu K, Liu C, Pierce J, Bradbury K, Kilgour E, Aung K, Schiavon G, Carroll D, Carr TH, Klinowska T, Lindemann J, Marshall G, Rowlands V, Harrington EA, Barrett JC, Sathiyayogan N, Morrow C, Sero V, Armstrong AC, Baird R, Hamilton E, Im S, Jhaveri K, Patel MR, Dive C, Tomlins SA, Udager AM, Hayes DF, Paoletti C. Serial monitoring of genomic alterations in circulating tumor cells of ER-positive/HER2-negative advanced breast cancer: feasibility of precision oncology biomarker detection. Mol Oncol 2022; 16:1969-1985. [PMID: 34866317 PMCID: PMC9120891 DOI: 10.1002/1878-0261.13150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 08/09/2021] [Revised: 10/02/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Nearly all estrogen receptor (ER)-positive (POS) metastatic breast cancers become refractory to endocrine (ET) and other therapies, leading to lethal disease presumably due to evolving genomic alterations. Timely monitoring of the molecular events associated with response/progression by serial tissue biopsies is logistically difficult. Use of liquid biopsies, including circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), might provide highly informative, yet easily obtainable, evidence for better precision oncology care. Although ctDNA profiling has been well investigated, the CTC precision oncology genomic landscape and the advantages it may offer over ctDNA in ER-POS breast cancer remain largely unexplored. Whole-blood (WB) specimens were collected at serial time points from patients with advanced ER-POS/HER2-negative (NEG) advanced breast cancer in a phase I trial of AZD9496, an oral selective ER degrader (SERD) ET. Individual CTC were isolated from WB using tandem CellSearch® /DEPArray™ technologies and genomically profiled by targeted single-cell DNA next-generation sequencing (scNGS). High-quality CTC (n = 123) from 12 patients profiled by scNGS showed 100% concordance with ctDNA detection of driver estrogen receptor α (ESR1) mutations. We developed a novel CTC-based framework for precision medicine actionability reporting (MI-CTCseq) that incorporates novel features, such as clonal predominance and zygosity of targetable alterations, both unambiguously identifiable in CTC compared to ctDNA. Thus, we nominated opportunities for targeted therapies in 73% of patients, directed at alterations in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), fibroblast growth factor receptor 2 (FGFR2), and KIT proto-oncogene, receptor tyrosine kinase (KIT). Intrapatient, inter-CTC genomic heterogeneity was observed, at times between time points, in subclonal alterations. Our analysis suggests that serial monitoring of the CTC genome is feasible and should enable real-time tracking of tumor evolution during progression, permitting more combination precision medicine interventions.
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16
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Cyrta J, Prandi D, Arora A, Hovelson DH, Sboner A, Rodriguez A, Fedrizzi T, Beltran H, Robinson DR, Gopalan A, True L, Nelson PS, Robinson BD, Mosquera JM, Tomlins SA, Shen R, Demichelis F, Rubin MA. Comparative genomics of primary prostate cancer and paired metastases: insights from 12 molecular case studies. J Pathol 2022; 257:274-284. [PMID: 35220606 PMCID: PMC9311708 DOI: 10.1002/path.5887] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 08/23/2021] [Revised: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022]
Abstract
Primary prostate cancer (PCa) can show marked molecular heterogeneity. However, systematic analyses comparing primary PCa and matched metastases in individual patients are lacking. We aimed to address the molecular aspects of metastatic progression while accounting for the heterogeneity of primary PCa. In this pilot study, we collected 12 radical prostatectomy (RP) specimens from men who subsequently developed metastatic castration‐resistant prostate cancer (mCRPC). We used histomorphology (Gleason grade, focus size, stage) and immunohistochemistry (IHC) (ERG and p53) to identify independent tumors and/or distinct subclones of primary PCa. We then compared molecular profiles of these primary PCa areas to matched metastatic samples using whole‐exome sequencing (WES) and amplicon‐based DNA and RNA sequencing. Based on combined pathology and molecular analysis, seven (58%) RP specimens harbored monoclonal and topographically continuous disease, albeit with some degree of intratumor heterogeneity; four (33%) specimens showed true multifocal disease; and one displayed monoclonal disease with discontinuous topography. Early (truncal) events in primary PCa included SPOP p.F133V (one patient), BRAF p.K601E (one patient), and TMPRSS2:ETS rearrangements (eight patients). Activating AR alterations were seen in nine (75%) mCRPC patients, but not in matched primary PCa. Hotspot TP53 mutations, found in metastases from three patients, were readily present in matched primary disease. Alterations in genes encoding epigenetic modifiers were observed in several patients (either shared between primary foci and metastases or in metastatic samples only). WES‐based phylogenetic reconstruction and/or clonality scores were consistent with the index focus designated by pathology review in six out of nine (67%) cases. The three instances of discordance pertained to monoclonal, topographically continuous tumors, which would have been considered as unique disease in routine practice. Overall, our results emphasize pathologic and molecular heterogeneity of primary PCa, and suggest that comprehensive IHC‐assisted pathology review and genomic analysis are highly concordant in nominating the ‘index’ primary PCa area. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Joanna Cyrta
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
- Department for BioMedical Research University of Bern Bern Switzerland
| | - Davide Prandi
- Department of Cellular Computational and Integrative Biology, University of Trento Trento Italy
| | - Arshi Arora
- Department of Epidemiology and Biostatistics Memorial Sloan‐Kettering Cancer Center New York NY USA
| | - Daniel H. Hovelson
- Center for Computational Medicine and Bioinformatics Univ. Michigan Ann Arbor MA USA
| | - Andrea Sboner
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA
| | - Antonio Rodriguez
- Department for BioMedical Research University of Bern Bern Switzerland
- Institute of Pathology University of Bern Bern Switzerland
| | - Tarcisio Fedrizzi
- Department of Epidemiology and Biostatistics Memorial Sloan‐Kettering Cancer Center New York NY USA
| | - Himisha Beltran
- Department of Medicine Division of Medical Oncology, Weill Cornell Medicine New York NY USA
- Department of Medical Oncology Dana Farber Cancer Institute Boston MA USA
| | - Dan R. Robinson
- Department of Pathology University of Michigan Ann Arbor MI USA
| | - Anurandha Gopalan
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Lawrence True
- Department of Pathology Univ. of Washington Seattle WA USA
| | | | - Brian D. Robinson
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
| | | | - Ronglai Shen
- Department of Epidemiology and Biostatistics Memorial Sloan‐Kettering Cancer Center New York NY USA
| | - Francesca Demichelis
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
- Department of Cellular Computational and Integrative Biology, University of Trento Trento Italy
| | - Mark A. Rubin
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
- Department for BioMedical Research University of Bern Bern Switzerland
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17
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Cotta B, Nallandhighal S, Stangl-Kremser J, Pham T, Tosoian JJ, Marchetti K, Berends J, Maruf M, Tomlins SA, Morgan TM, Palapattu GS, Adbulfatah E, Udager AM, Salami S. Validation of a 22-gene epithelial-mesenchymal transition (EMT) prognostic signature in clear cell renal cell carcinoma. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.6_suppl.377] [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
377 Background: Current predictors of metastatic progression after radical nephrectomy for localized clear cell renal cell carcinoma (ccRCC) include clinicopathologic features such as tumor stage and grade. The addition of molecular tumor characteristics in a prognostic score may improve risk stratification and patient selection for enhanced follow up strategies or adjuvant therapies. Methods: We retrospectively identified consecutive patients with ccRCC who underwent radical nephrectomy (RNx) for localized disease. Those who developed metastasis were identified. Whole-transcriptome mRNA sequencing of primary tumors was performed followed by gene set enrichment analysis (GSEA) for the most significant cancer hallmark pathways enriched in patients who did or did not develop metastasis. For each patient, the 22-gene epithelial mesenchymal transition (EMT) score was calculated (high vs. low), using cut-offs from a prior study using TCGA data. The prognostic impact of the EMT score was evaluated by performing multivariable cox-proportional hazard testing and Kaplan-Meier (KM) survival analysis. Results: We analyzed 82 patients with median age 62 years and median tumor size 6 ±2.9 cm. The median time to metastasis after radical nephrectomy for patients who developed metastasis (n = 12) was 18.2 months and 31.1 months for patients who did not develop metastasis (n = 70). We observed a significant enrichment of EMT, myogenesis, inflammatory response and hypoxia hallmark pathways in patients with metastasis vs. those without metastasis. Multivariable analysis controlling for relevant clinicopathologic features such as age, sex, tumor size, tumor stage etc. revealed high EMT score to be significantly associated with development of metastasis [hazard ratio (HR) 7.2; 95% CI 1.15-44.8; ]. Conclusions: Here we validate a prognostic 22-gene epithelial mesenchymal transition (EMT) score in patients treated with radical nephrectomy for localized ccRCC. Pending further studies, the EMT score may improve risk stratification and select patients for adjuvant therapy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Aaron M. Udager
- University of Michigan Department of Pathology, Ann Arbor, MI
| | - Simpa Salami
- University of Michigan Department of Urology, Ann Arbor, MI
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18
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Singhal U, Nallandhighal S, Tosoian JJ, Pham T, Liu CJ, Kareem R, Kunder KR, Morgan TM, Lucianò R, Shariat SF, Dambrosio L, Doglioni C, Tomlins SA, Briganti A, Palapattu GS, Udager AM, Salami S. Molecular characterization to delineate the clonal evolution of primary prostate cancer with synchronous lymph node metastasis. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.6_suppl.266] [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
266 Background: Primary prostate cancers (PCa) harbor multiple spatially distinct tumors with significant inter-lesion molecular heterogeneity. This diversity can result in many subclones that compete for biological and clinical dominance. The defining features of primary PCa that give rise to lymph node (LN) metastases is unknown. We performed multiregional targeted DNA/RNA next generation sequencing (NGS) of primary PCa with synchronous LN metastases to identify primary PCa foci capable of metastasis. Methods: Patients who underwent radical prostatectomy and LN dissection with pathologic node positive disease were identified. Punch biopsies were performed from pre-identified regions of cancer on formalin fixed paraffin embedded (FFPE) prostate and LN specimens and DNA/RNA samples were co-isolated. Targeted NGS was performed to characterize the genomic profile of each tumor region and to evaluate gene fusion status of each sample. We compared somatic DNA mutations, copy number alterations (CNA), and gene fusion status between primary and LN disease. Phylogenetic analysis was performed using the Phylip’s dollo and parsimony, neighbor-joining method to determine the likely clonal source of LN metastasis. Results: We analyzed 88 primary tumor (1°) and 23 LN-metastases samples from 14 patients. After quality control, 11 patients (69 and 18 primary and LN tumor samples, respectively) had sufficient quality data for analyses. Seven had evidence of extraprostatic extension (EPE), with phylogenetic analysis supporting this as the source of LN-metastasis in 4 cases. One patient had concordant TP53 and TPR non-synonymous mutations and broad CNAs between all 1°and two LN-metastasis foci, with two of the 1° regions showing high-level CNAs with both LN-metastasis foci. In two patients with pT2N1 disease, sub-clonal seeding and clonal evolution was observed with metastases arising from a GG5 area. Seven had cribriform pattern in both LN and 1° foci. One patient showed CDK12 mutation within the 1° and LN foci. FOXA1 was mutated in two patients within 1° and LN foci. Conclusions: Using targeted DNA/RNA NGS to assess primary PCa and synchronous LN metastases, we demonstrate that LN metastases is related to a combination of histopathologic and genomic factors. This highlights the need to develop robust prognostic biomarkers for identification of novel therapeutic targets for LN metastasis.
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Affiliation(s)
- Udit Singhal
- Department of Urology, University of Michigan, Ann Arbor, MI
| | | | | | | | | | | | | | | | - Roberta Lucianò
- IRCCS Ospedale San Raffaele, Department of Pathology, Milan, Italy
| | | | | | - Claudio Doglioni
- Department of Pathology, Istituto Scientifico Ospedale San Raffaele, Milan, Italy
| | | | | | | | - Aaron M. Udager
- University of Michigan Department of Pathology, Ann Arbor, MI
| | - Simpa Salami
- University of Michigan Department of Urology, Ann Arbor, MI
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19
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Mandigo AC, Tomlins SA, Kelly WK, Knudsen KE. Relevance of pRB Loss in Human Malignancies. Clin Cancer Res 2022; 28:255-264. [PMID: 34407969 PMCID: PMC9306333 DOI: 10.1158/1078-0432.ccr-21-1565] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 04/27/2021] [Revised: 06/24/2021] [Accepted: 08/10/2021] [Indexed: 01/07/2023]
Abstract
The retinoblastoma tumor suppressor protein (pRB) is a known regulator of cell-cycle control; however, recent studies identified critical functions for pRB in regulating cancer-associated gene networks that influence the DNA damage response, apoptosis, and cell metabolism. Understanding the impact of these pRB functions on cancer development and progression in the clinical setting will be essential, given the prevalence of pRB loss of function across disease types. Moreover, the current state of evidence supports the concept that pRB loss results in pleiotropic effects distinct from tumor proliferation. Here, the implications of pRB loss (and resultant pathway deregulation) on disease progression and therapeutic response will be reviewed, based on clinical observation. Developing a better understanding of the pRB-regulated pathways that underpin the aggressive features of pRB-deficient tumors will be essential for further developing pRB as a biomarker of disease progression and for stratifying pRB-deficient tumors into more effective treatment regimens.
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Affiliation(s)
- Amy C. Mandigo
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Scott A. Tomlins
- Departments of Pathology and Urology, Michigan Center for Translational Pathology, Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - William K. Kelly
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E. Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Corresponding Author: Karen E. Knudsen, Thomas Jefferson University, 233 South 10th Street, BLSB 1050, Philadelphia, PA 19107. Phone: 215-503-5692; E-mail:
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20
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Eyrich NW, Wei JT, Niknafs YS, Siddiqui J, Ellimoottil C, Salami SS, Palapattu GS, Mehra R, Kunju LP, Tomlins SA, Chinnaiyan AM, Morgan TM, Tosoian JJ. Association of MyProstateScore (MPS) with prostate cancer grade in the radical prostatectomy specimen. Urol Oncol 2021; 40:4.e1-4.e7. [PMID: 34753659 DOI: 10.1016/j.urolonc.2021.09.007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 09/02/2021] [Accepted: 09/19/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND To evaluate the association between urinary MyProstateScore (MPS) and pathologic grade group (GG) at surgery in men diagnosed with GG1 prostate cancer (PCa) on biopsy. METHODS Using an institutional biospecimen protocol, we identified men with GG1 PCa on biopsy and PSA ≤10 ng/ml who underwent radical prostatectomy (RP) at the University of Michigan. MPS was retrospectively calculated using prospectively collected, post-DRE urine samples. The primary outcome was upgrading on RP pathology, defined as GG ≥ 2. The associations of MPS, PSA, and PSA density (PSAD) with upgrading were assessed on univariable logistic regression, and the predictive accuracy of each marker was estimated by the area under the receiver operating characteristic curve (AUC). RESULTS There were 52 men with urinary specimens available that met study criteria, based on biopsy Gleason Grade and specimen collection. At RP, 17 men (33%) had GG1 cancer and 35 (67%) had GG ≥ 2 cancer. Preoperative MPS was significantly higher in patients with GG ≥ 2 cancer at surgery (median 37.8 [IQR, 22.2-52.4]) as compared to GG1 (19.3 [IQR, 9.2-29.4]; P = 0.001). On univariable logistic regression, increasing MPS values were significantly associated with upgrading (odds ratio 1.07 per one-unit MPS increase, 95% confidence interval 1.02-1.12, P = 0.004), while PSA and PSAD were not significantly associated with upgrading. Similarly, the discriminative ability of the MPS model (AUC 0.78) for upgrading at RP was higher compared to models based on PSA (AUC 0.52) and PSAD (AUC 0.62). CONCLUSIONS In men diagnosed with GG1 PCa who underwent surgery, MPS was significantly associated with RP cancer grade. In this limited cohort of men, these findings suggest that MPS could help identify patients with undetected high-grade cancer. Additional studies are needed to better characterize this association.
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Affiliation(s)
- Nicholas W Eyrich
- Department of Urology, University of Michigan, Ann Arbor, MI; Department of Urology, Emory University School of Medicine, Atlanta, GA
| | - John T Wei
- Department of Urology, University of Michigan, Ann Arbor, MI; Dow Division of Health Services Research, University of Michigan, Ann Arbor, MI
| | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Javed Siddiqui
- Department of Urology, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Chad Ellimoottil
- Department of Urology, University of Michigan, Ann Arbor, MI; Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI
| | - Simpa S Salami
- Department of Urology, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | - Ganesh S Palapattu
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Scott A Tomlins
- Department of Urology, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | - Arul M Chinnaiyan
- Department of Urology, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
| | - Todd M Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | - Jeffrey J Tosoian
- Department of Urology, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Department of Urology, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN.
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21
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Balikov DA, Hu K, Liu CJ, Betz BL, Chinnaiyan AM, Devisetty LV, Venneti S, Tomlins SA, Cani AK, Rao RC. Comparative Molecular Analysis of Primary Central Nervous System Lymphomas and Matched Vitreoretinal Lymphomas by Vitreous Liquid Biopsy. Int J Mol Sci 2021; 22:9992. [PMID: 34576156 PMCID: PMC8471952 DOI: 10.3390/ijms22189992] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 07/31/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Primary Central Nervous System Lymphoma (PCNSL) is a lymphoid malignancy of the brain that occurs in ~1500 patients per year in the US. PCNSL can spread to the vitreous and retina, where it is known as vitreoretinal lymphoma (VRL). While confirmatory testing for diagnosis is dependent on invasive brain tissue or cerebrospinal fluid sampling, the ability to access the vitreous as a proximal biofluid for liquid biopsy to diagnose PCNSL is an attractive prospect given ease of access and minimization of risks and complications from other biopsy strategies. However, the extent to which VRL, previously considered genetically identical to PCNSL, resembles PCNSL in the same individual with respect to genetic alterations, diagnostic strategies, and precision-medicine based approaches has hitherto not been explored. Furthermore, the degree of intra-patient tumor genomic heterogeneity between the brain and vitreous sites has not been studied. In this work, we report on targeted DNA next-generation sequencing (NGS) of matched brain and vitreous samples in two patients who each harbored VRL and PCSNL. Our strategy showed enhanced sensitivity for molecular diagnosis confirmation over current clinically used vitreous liquid biopsy methods. We observed a clonal relationship between the eye and brain samples in both patients, which carried clonal CDKN2A deep deletions, a highly recurrent alteration in VRL patients, as well as MYD88 p.L265P activating mutation in one patient. Several subclonal alterations, however, in the genes SETD2, BRCA2, TERT, and broad chromosomal regions showed heterogeneity between the brain and the eyes, between the two eyes, and among different regions of the PCNSL brain lesion. Taken together, our data show that NGS of vitreous liquid biopsies in PCNSL patients with VRL highlights shared and distinct genetic alterations that suggest a common origin for these lymphomas, but with additional site-specific alterations. Liquid biopsy of VRL accurately replicates the findings for PCNSL truncal (tumor-initiating) genomic alterations; it can also nominate precision medicine interventions and shows intra-patient heterogeneity in subclonal alterations. To the best of our knowledge, this study represents the first interrogation of genetic underpinnings of PCNSL with matched VRL samples. Our findings support continued investigation into the utility of vitreous liquid biopsy in precision diagnosis and treatment of PCNSL/VRL.
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Affiliation(s)
- Daniel A. Balikov
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48109, USA; (D.A.B.); (L.V.D.)
| | - Kevin Hu
- Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bryan L. Betz
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laxmi V. Devisetty
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48109, USA; (D.A.B.); (L.V.D.)
| | - Sriram Venneti
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott A. Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andi K. Cani
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Hematology/Oncology Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rajesh C. Rao
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48109, USA; (D.A.B.); (L.V.D.)
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Division of Ophthalmology, Surgical Service, Veterans Administration Ann Arbor Healthcare System, Ann Arbor, MI 48109, USA
- A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Tomlins SA, Hovelson DH, Harms P, Drewery S, Falkner J, Fischer A, Hipp J, Kwiatkowski K, Lazo de la Vega L, Mitchell K, Reeder T, Siddiqui J, Vakil H, Johnson DB, Rhodes DR. Development and Validation of StrataNGS, a Multiplex PCR, Semiconductor Sequencing-Based Comprehensive Genomic Profiling Test. J Mol Diagn 2021; 23:1515-1533. [PMID: 34454112 DOI: 10.1016/j.jmoldx.2021.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 07/09/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Despite widespread use in targeted tumor testing, multiplex PCR/semiconductor (Ion Torrent) sequencing-based assessment of all comprehensive genomic profiling (CGP) variant classes has been limited. Herein, we describe the development and validation of StrataNGS, a 429-gene, multiplex PCR/semiconductor sequencing-based CGP laboratory-developed test performed on co-isolated DNA and RNA from formalin-fixed, paraffin-embedded tumor specimens with ≥2 mm2 tumor surface area. Validation was performed in accordance with MolDX CGP validation guidelines using 1986 clinical formalin-fixed, paraffin-embedded samples and an in-house developed optimized bioinformatics pipeline. Across CGP variant classes, accuracy ranged from 0.945 for tumor mutational burden (TMB) status to >0.999 for mutations and gene fusions, positive predictive value ranged from 0.915 for TMB status to 1.00 for gene fusions, and reproducibility ranged from 0.998 for copy number alterations to 1.00 for splice variants and insertions/deletions. StrataNGS TMB estimates were highly correlated to those from whole exome- or FoundationOne CDx-determined TMB (Pearson r = 0.998 and 0.960, respectively); TMB reproducibility was 0.996 (concordance correlation coefficient). Limit of detection for all variant classes was <20% tumor content. Together, we demonstrate that multiplex PCR/semiconductor sequencing-based tumor tissue CGP is feasible using optimized bioinformatic approaches described herein.
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Affiliation(s)
| | | | - Paul Harms
- Departments of Pathology and Dermatology, University of Michigan, Ann Arbor, Michigan
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Tomlins SA, Hovelson DH, Suga JM, Anderson DM, Koh HA, Dees EC, McNulty B, Burkard ME, Guarino M, Khatri J, Safa MM, Matrana MR, Yang ES, Menter AR, Parsons BM, Slim JN, Thompson MA, Hwang L, Edenfield WJ, Nair S, Onitilo A, Siegel R, Miller A, Wassenaar T, Irvin WJ, Schulz W, Padmanabhan A, Harish V, Gonzalez A, Mansoor AH, Kellum A, Harms P, Drewery S, Falkner J, Fischer A, Hipp J, Kwiatkowski K, Lazo de la Vega L, Mitchell K, Reeder T, Siddiqui J, Vakil H, Johnson DB, Rhodes DR. Real-World Performance of a Comprehensive Genomic Profiling Test Optimized for Small Tumor Samples. JCO Precis Oncol 2021; 5:PO.20.00472. [PMID: 34476329 PMCID: PMC8384401 DOI: 10.1200/po.20.00472] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/18/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Tissue-based comprehensive genomic profiling (CGP) is increasingly used for treatment selection in patients with advanced cancer; however, tissue availability may limit widespread implementation. Here, we established real-world CGP tissue availability and assessed CGP performance on consecutively received samples. MATERIALS AND METHODS We conducted a post hoc, nonprespecified analysis of 32,048 consecutive tumor tissue samples received for StrataNGS, a multiplex polymerase chain reaction (PCR)-based comprehensive genomic profiling (PCR-CGP) test, as part of an ongoing observational trial (NCT03061305). Sample characteristics and PCR-CGP performance were assessed across all tested samples, including exception samples not meeting minimum input quality control (QC) requirements (< 20% tumor content [TC], < 2 mm2 tumor surface area [TSA], DNA or RNA yield < 1 ng/µL, or specimen age > 5 years). Tests reporting ≥ 1 prioritized alteration or meeting TC and sequencing QC were considered successful. For prostate carcinoma and lung adenocarcinoma, tests reporting ≥ 1 actionable or informative alteration or meeting TC and sequencing QC were considered actionable. RESULTS Among 31,165 (97.2%) samples where PCR-CGP was attempted, 10.7% had < 20% TC and 59.2% were small (< 25 mm2 tumor surface area). Of 31,101 samples evaluable for input requirements, 8,089 (26.0%) were exceptions not meeting requirements. However, 94.2% of the 31,101 tested samples were successfully reported, including 80.5% of exception samples. Positive predictive value of PCR-CGP for ERBB2 amplification in exceptions and/or sequencing QC-failure breast cancer samples was 96.7%. Importantly, 84.0% of tested prostate carcinomas and 87.9% of lung adenocarcinomas yielded results informing treatment selection. CONCLUSION Most real-world tissue samples from patients with advanced cancer desiring CGP are limited, requiring optimized CGP approaches to produce meaningful results. An optimized PCR-CGP test, coupled with an inclusive exception testing policy, delivered reportable results for > 94% of samples, potentially expanding the proportion of CGP-testable patients and impact of biomarker-guided therapies.
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Affiliation(s)
| | | | | | - Daniel M. Anderson
- Metro-Minnesota Community Oncology Research Consortium (MMCORC), St Louis Park, MN
| | | | - Elizabeth C. Dees
- The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC
| | | | | | - Michael Guarino
- ChristianaCare's Helen F. Graham Cancer Center & Research Institute, Newark, DE
| | - Jamil Khatri
- ChristianaCare's Helen F. Graham Cancer Center & Research Institute, Newark, DE
| | | | | | - Eddy S. Yang
- University of Alabama at Birmingham, Birmingham, AL
| | | | | | | | | | - Leon Hwang
- Kaiser Permanente Mid Atlantic, Rockville, MD
| | | | | | | | - Robert Siegel
- Bon Secours St Francis Cancer Center, Greenville, SC
| | | | | | - William J. Irvin
- Bon Secours St Francis Medical Center Midlothian, Midlothian, VA
| | | | | | | | | | | | | | - Paul Harms
- University of Michigan Health Systems, Ann Arbor, MI
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24
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Cani AK, Dolce EM, Darga EP, Hu K, Brown M, Liu CJ, Pierce J, Bradbury K, Aung K, Schiavon G, Carroll D, Carr TH, Klinowska T, Lindemann J, Marshall G, Rowlands V, Harrington EA, Barrett J, Armstrong A, Baird R, Hamilton E, Im SA, Jhaveri K, Patel MR, Dive C, Tomlins SA, Udager AM, Hayes DF, Paoletti C. Abstract 3143: Monitoring circulating tumor cell (CTC) and circulating tumor DNA (ctDNA) genomic alterations in ER positive (POS)/HER2 negative (NEG) advanced breast cancer during endocrine therapy: correlative study of AZD9496 oral SERD phase I trial. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-3143] [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
Purpose: The vast majority of advanced ER POS breast cancers eventually cease responding to endocrine (ET) and other therapies leading to evolution of lethal disease. However, timely monitoring of the molecular events associated with response/progression in tissue biopsies is logistically difficult. The use of liquid biopsies, such as CTC and ctDNA, in this context has been of recent interest.
Patients and Methods: Individual CTC and ctDNA were obtained at different time points from patients with advanced ER POS/HER2 NEG breast cancer enrolled in a Phase I trial of AZD9496, an oral selective estrogen receptor degrader (SERD) ET. The CTC, purified using tandem CellSearch®/DepArray™ technologies, were genomically profiled by DNA single cell next generation sequencing (scNGS). Plasma ctDNA was isolated from blood collected in Streck BCT tubes. Genomic profiling was performed by targeted gene panel scNGS for CTC and ddPCR for ERα gene (ESR1) mutations in ctDNA.
Results: 123 high-quality CTCs from 12 patients profiled by scNGS showed 100% concordance with ctDNA in detection of driver ESR1 somatic mutations. CTC scNGS additionally revealed extensive intra-patient heterogeneity of driver alterations, that would have been unresolvable by bulk ctDNA profiling, including separate subclonal CTC populations emerging within the same patient. ScNGS revealed potential opportunities for targeted therapies in 73% of patients, directed at alterations in PIK3CA, FGFR2, KIT and BRAF, at times present as 2 or more targets in the same or different cell populations. In one patient, an emergent, distinct, BRAF p.V600E targetable alteration was detected in a subpopulation of CTCs collected at the progression time point but not at baseline.
Conclusion: Serial monitoring of CTC and ctDNA genomic alterations is feasible and should enable real-time tracking of response/progression, tumor evolution and opportunities for precision medicine interventions.
Citation Format: Andi K. Cani, Emily M. Dolce, Elizabeth P. Darga, Kevin Hu, Martha Brown, Chia-Jen Liu, Jackie Pierce, Kieran Bradbury, Kimberly Aung, Gaia Schiavon, Danielle Carroll, T. H. Carr, Teresa Klinowska, Justin Lindemann, Gayle Marshall, Vicky Rowlands, Elizabeth A. Harrington, J. Barrett, Anne Armstrong, Richard Baird, Erika Hamilton, Seock-Ah Im, Komal Jhaveri, Manish R. Patel, Caroline Dive, Scott A. Tomlins, Aaron M. Udager, Daniel F. Hayes, Costanza Paoletti. Monitoring circulating tumor cell (CTC) and circulating tumor DNA (ctDNA) genomic alterations in ER positive (POS)/HER2 negative (NEG) advanced breast cancer during endocrine therapy: correlative study of AZD9496 oral SERD phase I trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3143.
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Affiliation(s)
| | | | | | - Kevin Hu
- 1University of Michigan, Ann Arbor, MI
| | | | | | - Jackie Pierce
- 2CRUK Manchester Institute, Manchester, United Kingdom
| | | | | | | | | | - T. H. Carr
- 3AstraZeneca plc, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | - Richard Baird
- 6Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
| | - Erika Hamilton
- 7Sarah Cannon Research Institute/Tennessee Oncology, PLLC, Nashville, TN
| | - Seock-Ah Im
- 8Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Komal Jhaveri
- 9Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manish R. Patel
- 10Sarah Cannon Research Institute/Florida Cancer Specialists, Sarasota, FL
| | - Caroline Dive
- 2CRUK Manchester Institute, Manchester, United Kingdom
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25
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Cani AK, Toral MA, Balikov DA, Betz BL, Hu K, Liu CJ, Prifti MV, Chinnaiyan AM, Tomlins SA, Mahajan VB, Rao RC. Molecular Characterization of a Rare Case of Bilateral Vitreoretinal T Cell Lymphoma through Vitreous Liquid Biopsy. Int J Mol Sci 2021; 22:ijms22116099. [PMID: 34198843 PMCID: PMC8201094 DOI: 10.3390/ijms22116099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/30/2021] [Indexed: 02/04/2023] Open
Abstract
Vitreoretinal lymphoma (VRL) is an uncommon eye malignancy, and VRLs of T cell origin are rare. They are difficult to treat, and their molecular underpinnings, including actionable genomic alterations, remain to be elucidated. At present, vitreous fluid liquid biopsies represent a valuable VRL sample for molecular analysis to study VRLs. In this study, we report the molecular diagnostic workup of a rare case of bilateral T cell VRL and characterize its genomic landscape, including identification of potentially targetable alterations. Using next-generation sequencing of vitreous-derived DNA with a pan-cancer 126-gene panel, we found a copy number gain of BRAF and copy number loss of tumor suppressor DNMT3A. To the best of our knowledge, this represents the first exploration of the T cell VRL cancer genome and supports vitreous liquid biopsy as a suitable approach for precision oncology treatments.
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Affiliation(s)
- Andi K. Cani
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48105, USA;
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Marcus A. Toral
- Medical Scientist Training Program, University of Iowa, Iowa City, IA 52242, USA;
- Graduate Program in Molecular Medicine, University of Iowa, Iowa City, IA 52242, USA
- Molecular Surgery Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA 94303, USA
| | - Daniel A. Balikov
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48105, USA;
| | - Bryan L. Betz
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
| | - Kevin Hu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew V. Prifti
- A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI 48105, USA;
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Arul M. Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott A. Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vinit B. Mahajan
- Molecular Surgery Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA 94303, USA
- Palo Alto Veterans Health Care System, Palo Alto, CA 94304, USA
- Correspondence: (V.B.M.); (R.C.R.); Tel.: +1-650-723-6995 (V.B.M.); +1-734-647-1226 (R.C.R.); Fax: +1-650-498-1528 (V.B.M.); +1-734-232-8030 (R.C.R.)
| | - Rajesh C. Rao
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA;
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48105, USA;
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI 48105, USA;
- Division of Ophthalmology, Surgical Service, Veterans Administration Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
- Correspondence: (V.B.M.); (R.C.R.); Tel.: +1-650-723-6995 (V.B.M.); +1-734-647-1226 (R.C.R.); Fax: +1-650-498-1528 (V.B.M.); +1-734-232-8030 (R.C.R.)
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26
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Tosoian JJ, Dunn RL, Niknafs YS, Saha A, Vince RA, St Sauver JL, Jacobson DJ, McGree ME, Siddiqui J, Groskopf J, Jacobsen SJ, Tomlins SA, Kunju LP, Morgan TM, Salami SS, Wei JT, Chinnaiyan AM, Sarma AV. Association of Urinary MyProstateScore, Age, and Prostate Volume in a Longitudinal Cohort of Healthy Men: Long-term Findings from the Olmsted County Study. EUR UROL SUPPL 2021; 29:30-35. [PMID: 34337531 PMCID: PMC8317796 DOI: 10.1016/j.euros.2021.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 11/02/2022] Open
Abstract
Background Serum prostate-specific antigen (PSA), used in prostate cancer screening, is nonspecific for cancer and is affected by age and prostate volume. More specific biomarkers could be more accurate for early detection of prostate cancer and reduce unnecessary prostate biopsies. Objective To evaluate the association of age and prostate volume with urinary MyProstateScore (MPS) in a screened, longitudinal cohort without evidence of prostate cancer. Design setting and participants The Olmsted County Study included men aged 40-79 yr who underwent biennial prostate cancer screening. PSA ≥4.0 ng/ml or abnormal rectal examination triggered prostate biopsy, and patients with cancer were excluded. The remaining men submitted urinary specimens for PCA3 and TMPRSS2:ERG testing. Outcome measurements and statistical analysis MPS was calculated using the validated, locked model for grade group ≥2 cancer that includes serum PSA, urinary PCA3, and urinary TMPRSS2:ERG. The associations of age and volume with biomarkers were assessed in multivariable regression models. The t statistic was used to quantify the strength of associations independent of the unit of measurement, and R 2 values were used to estimate the proportion of biomarker variance explained by each factor. Results and limitations The study included 314 screened men without evidence of cancer. In multivariable models including age and volume, PCA3 score was significantly associated with age (t = 7.51; p < 0.001), while T2:ERG score was not associated with age or volume. MPS was significantly associated with both age (t = 7.45; p < 0.001) and volume (t = 3.56; p < 0.001), but accounting for age alone explained the variability observed (R 2 = 0.29) in a similar way to the model including age and volume (R 2 = 0.31). The variability of PCA3, T2:ERG, and MPS was less dependent on age and volume than the variability for PSA (R 2 = 0.45). Conclusions In a cohort of longitudinally screened men without evidence of cancer, we found that MPS demonstrated less variability with noncancer factors (age, prostate volume) than PSA did. These findings support the biology of these markers as more cancer-specific than PSA and highlight their promise in reducing the morbidity associated with PSA-based screening. Patient summary In a group of men with no evidence of prostate cancer, we found that each of three urine-based markers of cancer-PCA3, T2:ERG, and the commercially available MyProstateScore test-showed less variability with noncancer factors (age and prostate volume) than serum PSA (prostate-specific antigen) did. These findings support their proposed use as noninvasive markers of prostate cancer that could improve the accuracy of early detection.
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Affiliation(s)
- Jeffrey J Tosoian
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rodney L Dunn
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Anjan Saha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Randy A Vince
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Debra J Jacobson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Michaela E McGree
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Javed Siddiqui
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Steven J Jacobsen
- Department of Research and Evaluation, Kaiser Permanente of Southern California, Pasadena, CA, USA
| | - Scott A Tomlins
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lakshmi P Kunju
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Todd M Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Simpa S Salami
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - John T Wei
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Aruna V Sarma
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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Rhodes D, Hovelson DH, Safa MM, Burkard ME, Yang ESH, Edenfield WJ, Reeder T, Vakil H, Kwiatkowski K, Mitchell K, Johnson B, Tomlins SA. Comprehensive genomic and transcriptomic profiling (CGTP) to predict pembrolizumab (P) benefit in patients (pts) with advanced solid tumors (STs). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.2609] [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
2609 Background: P is approved in many ST types, however predictive biomarkers and the proportion of pts who benefit vary widely. Biomarkers beyond PD-L1 immunohistochemistry and comprehensive genomic profiling (CGP) based tumor mutation burden (TMB) may improve benefit prediction. We determined if treatment data and CGTP collected in an ongoing observational trial (NCT03061305) could predict pan-ST P benefit. Methods: Eligible advanced ST pts had QC-passing TMB and expression data from multiplex PCR based tissue CGTP on FFPE tissue (StrataNGS and an investigational test) and documented P treatment > 1 month. Real-world time to next treatment (TTNT) was defined as time in months from therapy start to new therapy start (after stopping initial therapy) or death. TMB and gene expression biomarker association with P TTNT was evaluated. Backward stepwise regression was performed to fit a multivariate Cox proportional hazards model; pts were assigned to four score groups (IRS 1-4) based on overlapping TTNT curves from 8 equal bins. P TTNT were compared between IRS groups by log-rank test. A chemotherapy (C) comparator cohort was established from C TTNT for pts in this cohort. Results were stratified by ST type, P mono vs. C combo, and TMB status. Results: 610 pts (254 [41.6%] NSCLC; 356 [58.4%] from 23 other ST types) with CGTP and P treatment were identified; P TTNT was highly correlated to overall survival (n=146; Pearsons r2=0.75). By univariate analysis of TMB and 9 expression biomarkers, TMB, two independent PD-L1 expression amplicons, and PD-L2 expression were significantly associated with P TTNT (all p ≤ 0.002). The most significant multivariate model included 5 variables, with 1) increasing TMB, PD-L1, and PD-L2, and 2) decreasing TOP2A (proliferation) and GZMA as P TTNT predictors. Median P TTNT, but not C TTNT (345 courses from 254 pts), differed significantly by IRS group (Table). Median P TTNT by IRS group did not significantly differ by non-small cell lung vs. other ST type or P mono vs. C combo (both p > 0.05); excluding TMB-high patients, median P TTNT was still significantly longer in IRS groups 3/4 vs. 1/2 (p = 5.0e-4). Across 19,623 total evaluable pts in NCT03061305, 12.2% were in IRS groups 3/4 and outside of P approved ST types/TMB-low. Conclusions: CGTP in an observational trial cohort demonstrated that TMB, PD-L1 and PD-L2 independently predicted pan-ST P benefit as assessed by OS-validated TTNT. A multivariate CGTP signature predicted P benefit relative to C across ST types. If further validated, such a signature may enable improved P benefit prediction. P versus C TTNT by IRS group. Clinical trial information: NCT03061305. [Table: see text]
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Palmbos PL, Daignault-Newton S, Tomlins SA, Agarwal N, Twardowski P, Morgans AK, Kelly WK, Arora VK, Antonarakis ES, Siddiqui J, Jacobson JA, Davenport MS, Robinson DR, Chinnaiyan AM, Knudsen KE, Hussain M. A Randomized Phase II Study of Androgen Deprivation Therapy with or without Palbociclib in RB-positive Metastatic Hormone-Sensitive Prostate Cancer. Clin Cancer Res 2021; 27:3017-3027. [PMID: 33727260 DOI: 10.1158/1078-0432.ccr-21-0024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/16/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022]
Abstract
PURPOSE Palbociclib, a cyclin-dependent kinase (CDK) 4/6 inhibitor, blocks proliferation in a RB and cyclin D-dependent manner in preclinical prostate cancer models. We hypothesized that cotargeting androgen receptor and cell cycle with palbociclib would improve outcomes in patients with metastatic hormone-sensitive prostate cancer (mHSPC). PATIENTS AND METHODS A total of 60 patients with RB-intact mHSPC were randomized (1:2) to Arm 1: androgen deprivation (AD) or Arm 2: AD + palbociclib. Primary endpoint was PSA response rate (RR) after 28 weeks of therapy. Secondary endpoints included safety, PSA, and clinical progression-free survival (PFS), as well as PSA and radiographic RR. Tumors underwent exome sequencing when available. Circulating tumor cells (CTC) were enumerated at various timepoints. RESULTS A total of 72 patients with mHSPC underwent metastatic disease biopsy and 64 had adequate tissue for RB assessment. A total of 62 of 64 (97%) retained RB expression. A total of 60 patients initiated therapy (Arm 1: 20; Arm 2: 40). Neutropenia was the most common grade 3/4 adverse event in Arm 2. Eighty percent of patients (Arm 1: 16/20, Arm 2: 32/40; P = 0.87) met primary PSA endpoint ≤4 ng/mL at 28 weeks. PSA undetectable rate at 28 weeks was 50% and 43% in Arms 1 and 2, respectively (P = 0.5). Radiographic RR was 89% in both arms. Twelve-month biochemical PFS was 69% and 74% in Arms 1 and 2, respectively (P = 0.72). TP53 and PIK3 pathway mutations, 8q gains, and pretreatment CTCs were associated with reduced PSA PFS. CONCLUSIONS Palbociclib did not impact outcome in RB-intact mHSPC. Pretreatment CTC, TP53 and PIK3 pathway mutations, and 8q gain were associated with poor outcome.
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Affiliation(s)
| | | | | | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Alicia K Morgans
- Northwestern University/Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois
| | - Wm Kevin Kelly
- Sidney Kimmel Cancer Center at Jefferson Health and Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Vivek K Arora
- Washington University in St. Louis, St. Louis, Missouri
| | | | - Javed Siddiqui
- Michigan Medicine Rogel Cancer Center, Ann Arbor, Michigan
| | - Jon A Jacobson
- Michigan Medicine Rogel Cancer Center, Ann Arbor, Michigan
| | | | - Dan R Robinson
- Michigan Medicine Rogel Cancer Center, Ann Arbor, Michigan
| | | | - Karen E Knudsen
- Sidney Kimmel Cancer Center at Jefferson Health and Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Maha Hussain
- Northwestern University/Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois.
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29
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Harms KL, Zhao L, Johnson B, Wang X, Carskadon S, Palanisamy N, Rhodes DR, Mannan R, Vo JN, Choi JE, Chan MP, Fullen DR, Patel RM, Siddiqui J, Ma VT, Hrycaj S, McLean SA, Hughes TM, Bichakjian CK, Tomlins SA, Harms PW. Virus-positive Merkel Cell Carcinoma Is an Independent Prognostic Group with Distinct Predictive Biomarkers. Clin Cancer Res 2021; 27:2494-2504. [PMID: 33547200 DOI: 10.1158/1078-0432.ccr-20-0864] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 12/31/2020] [Accepted: 02/02/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma that can be divided into two classes: virus-positive (VP) MCC, associated with oncogenic Merkel cell polyomavirus (MCPyV); and virus-negative (VN) MCC, associated with photodamage. EXPERIMENTAL DESIGN We classified 346 MCC tumors from 300 patients for MCPyV using a combination of IHC, ISH, and qPCR assays. In a subset of tumors, we profiled mutation status and expression of cancer-relevant genes. MCPyV and molecular profiling results were correlated with disease-specific outcomes. Potential prognostic biomarkers were further validated by IHC. RESULTS A total of 177 tumors were classified as VP-MCC, 151 tumors were VN-MCC, and 17 tumors were indeterminate. MCPyV positivity in primary tumors was associated with longer disease-specific and recurrence-free survival in univariate analysis, and in multivariate analysis incorporating age, sex, immune status, and stage at presentation. Prioritized oncogene or tumor suppressor mutations were frequent in VN-MCC but rare in VP-MCC. TP53 mutation developed with recurrence in one VP-MCC case. Importantly, for the first time we find that VP-MCC and VN-MCC display distinct sets of prognostic molecular biomarkers. For VP-MCC, shorter survival was associated with decreased expression of immune markers including granzyme and IDO1. For VN-MCC, shorter survival correlated with high expression of several genes including UBE2C. CONCLUSIONS MCPyV status is an independent prognostic factor for MCC. Features of the tumor genome, transcriptome, and microenvironment may modify prognosis in a manner specific to viral status. MCPyV status has clinicopathologic significance and allows for identification of additional prognostic subgroups.
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Affiliation(s)
- Kelly L Harms
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Lili Zhao
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | | | - Xiaoming Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Shannon Carskadon
- Department of Urology, Vattikuti Urology Institute, Henry Ford Health System, Detroit, Michigan
| | - Nallasivam Palanisamy
- Department of Urology, Vattikuti Urology Institute, Henry Ford Health System, Detroit, Michigan
| | | | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Josh N Vo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - May P Chan
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Douglas R Fullen
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Rajiv M Patel
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Vincent T Ma
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Steven Hrycaj
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Scott A McLean
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Tasha M Hughes
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Christopher K Bichakjian
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Scott A Tomlins
- Strata Oncology, Ann Arbor, Michigan.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Paul W Harms
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan. .,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
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30
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Freeman ZT, Nirschl TR, Hovelson DH, Johnston RJ, Engelhardt JJ, Selby MJ, Kochel CM, Lan RY, Zhai J, Ghasemzadeh A, Gupta A, Skaist AM, Wheelan SJ, Jiang H, Pearson AT, Snyder LA, Korman AJ, Tomlins SA, Yegnasubramanian S, Drake CG. A conserved intratumoral regulatory T cell signature identifies 4-1BB as a pan-cancer target. J Clin Invest 2020; 130:1405-1416. [PMID: 32015231 DOI: 10.1172/jci128672] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [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: 03/11/2019] [Accepted: 11/13/2019] [Indexed: 12/19/2022] Open
Abstract
Despite advancements in targeting the immune checkpoints program cell death protein 1 (PD-1), programmed death ligand 1 (PD-L1), and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) for cancer immunotherapy, a large number of patients and cancer types remain unresponsive. Current immunotherapies focus on modulating an antitumor immune response by directly or indirectly expanding antitumor CD8 T cells. A complementary strategy might involve inhibition of Tregs that otherwise suppress antitumor immune responses. Here, we sought to identify functional immune molecules preferentially expressed on tumor-infiltrating Tregs. Using genome-wide RNA-Seq analysis of purified Tregs sorted from multiple human cancer types, we identified a conserved Treg immune checkpoint signature. Using immunocompetent murine tumor models, we found that antibody-mediated depletion of 4-1BB-expressing cells (4-1BB is also known as TNFRSF9 or CD137) decreased tumor growth without negatively affecting CD8 T cell function. Furthermore, we found that the immune checkpoint 4-1BB had a high selectivity for human tumor Tregs and was associated with worse survival outcomes in patients with multiple tumor types. Thus, antibody-mediated depletion of 4-1BB-expressing Tregs represents a strategy with potential activity across cancer types.
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Affiliation(s)
- Zachary T Freeman
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Unit for Laboratory Animal Medicine, Medical School.,Rogel Cancer Center, and
| | - Thomas R Nirschl
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daniel H Hovelson
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Mark J Selby
- Bristol-Myers Squibb, Redwood City, California, USA
| | - Christina M Kochel
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ruth Y Lan
- Bristol-Myers Squibb, Redwood City, California, USA
| | - Jingyi Zhai
- Department of Biostatistics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Ali Ghasemzadeh
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Anuj Gupta
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Alyza M Skaist
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah J Wheelan
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hui Jiang
- Rogel Cancer Center, and.,Department of Biostatistics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexander T Pearson
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Linda A Snyder
- Oncology Discovery, Janssen R&D, Spring House, Pennsylvania, USA
| | | | - Scott A Tomlins
- Rogel Cancer Center, and.,Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Translational Pathology, Department of Pathology, and.,Department of Urology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Srinivasan Yegnasubramanian
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Charles G Drake
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Division of Hematology and Oncology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
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31
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Jo J, Siddiqui J, Zhu Y, Ni L, Kothapalli SR, Tomlins SA, Wei JT, Keller ET, Udager AM, Wang X, Xu G. Photoacoustic spectral analysis at ultraviolet wavelengths for characterizing the Gleason grades of prostate cancer. Opt Lett 2020; 45:6042-6045. [PMID: 33137064 PMCID: PMC7687867 DOI: 10.1364/ol.409249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
The diagnosis of aggressive prostate cancer (PCa) has relied on microscopic architectures, namely Gleason patterns, of tissues extracted through core biopsies. Technology capable of assessing the tissue architecture without tissue extraction will reduce the invasiveness of PCa diagnosis and improve diagnostic accuracy by allowing for more sampling locations. Our recently developed photoacoustic spectral analysis (PASA) has achieved quantification of tissue architectural heterogeneity interstitially. Taking advantage of the unique optical absorption of cell nuclei at ultraviolet (UV) wavelengths, this study investigated PASA at 266 nm for quantifying the tissue architecture heterogeneity in prostates. The results have shown significant differences among the normal, early cancer, and late cancer stages in mouse prostates ex vivo and in vivo (n=20, p<0.05). The study with human samples ex vivo has shown a correlation of 0.80 (n=11, p<0.05) between PASA quantification and pathologic diagnosis.
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Affiliation(s)
- Janggun Jo
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Javed Siddiqui
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yunhao Zhu
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Linyu Ni
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | | | - Scott A. Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - John T Wei
- Department of Urology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Evan T. Keller
- Department of Urology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Aaron M. Udager
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xueding Wang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Guan Xu
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA
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Nanba K, Yamazaki Y, Bick N, Onodera K, Tezuka Y, Omata K, Ono Y, Blinder AR, Tomlins SA, Rainey WE, Satoh F, Sasano H. Prevalence of Somatic Mutations in Aldosterone-Producing Adenomas in Japanese Patients. J Clin Endocrinol Metab 2020; 105:5897223. [PMID: 32844168 PMCID: PMC7947976 DOI: 10.1210/clinem/dgaa595] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/24/2020] [Indexed: 11/19/2022]
Abstract
CONTEXT Results of previous studies demonstrated clear racial differences in the prevalence of somatic mutations among patients with aldosterone-producing adenoma (APA). For instance, those in East Asian countries have a high prevalence of somatic mutations in KCNJ5, whereas somatic mutations in other aldosterone-driving genes are rare. OBJECTIVES To determine somatic mutation prevalence in Japanese APA patients using an aldosterone synthase (CYP11B2) immunohistochemistry (IHC)-guided sequencing approach. METHOD Patients with a unilateral form of primary aldosteronism who underwent adrenalectomy at the Tohoku University Hospital were studied. Based on CYP11B2 immunolocalization of resected adrenals, genomic DNA was isolated from the relevant positive area of 10% formalin-fixed, paraffin-embedded tissue of the APAs. Somatic mutations in aldosterone-driving genes were studied in APAs by direct Sanger sequencing and targeted next-generation sequencing. RESULTS CYP11B2 IHC-guided sequencing determined APA-related somatic mutations in 102 out of 106 APAs (96%). Somatic KCNJ5 mutation was the most frequent genetic alteration (73%) in this cohort of Japanese patients. Somatic mutations in other aldosterone-driving genes were also identified: CACNA1D (14%), ATP1A1 (5%), ATP2B3 (4%), and CACNA1H (1%), including 2 previously unreported mutations. KCNJ5 mutations were more often detected in APAs from female patients compared with those from male patients [95% (36/38) vs 60% (41/68); P < 0.0001]. CONCLUSION IHC-guided sequencing defined somatic mutations in over 95% of Japanese APAs. While the dominance of KCNJ5 mutations in this particular cohort was confirmed, a significantly higher KCNJ5 prevalence was detected in female patients. This study provides a better understanding of genetic spectrum of Japanese APA patients.
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Affiliation(s)
- Kazutaka Nanba
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
- Department of Endocrinology and Metabolism, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Yuto Yamazaki
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Nolan Bick
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Kei Onodera
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuta Tezuka
- Division of Nephrology, Endocrinology and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
- Division of Clinical Hypertension, Endocrinology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kei Omata
- Division of Nephrology, Endocrinology and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Division of Clinical Hypertension, Endocrinology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshikiyo Ono
- Division of Nephrology, Endocrinology and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Division of Clinical Hypertension, Endocrinology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Amy R Blinder
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Scott A Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
- Department of Urology, University of Michigan, Ann Arbor, Michigan
| | - William E Rainey
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Fumitoshi Satoh
- Division of Nephrology, Endocrinology and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Division of Clinical Hypertension, Endocrinology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hironobu Sasano
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Correspondence and Reprint Requests: Hironobu Sasano, MD, PhD, Department of Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan. E-mail:
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Lebastchi AH, Russell CM, Niknafs YS, Eyrich NW, Chopra Z, Botbyl R, Kabeer R, Osawa T, Siddiqui J, Siddiqui R, Davenport MS, Mehra R, Tomlins SA, Kunju LP, Chinnaiyan AM, Wei JT, Tosoian JJ, Morgan TM. Impact of the MyProstateScore (MPS) Test on the Clinical Decision to Undergo Prostate Biopsy: Results From a Contemporary Academic Practice. Urology 2020; 145:204-210. [PMID: 32777370 DOI: 10.1016/j.urology.2020.07.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To evaluate the association of the MyProstateScore (MPS) urine test on the decision to undergo biopsy in men referred for prostate biopsy in urology practice. METHODS MPS testing was offered as an alternative to immediate biopsy in men referred to the University of Michigan for prostate biopsy from October 2013 through October 2016. The primary endpoint was the decision to perform biopsy. The proportion of patients undergoing biopsy was compared to predicted risk scores from the Prostate Cancer Prevention Trial risk calculator (PCPTrc). Analyses were stratified by the use of multiparametric magnetic resonance imaging (mpMRI). The associations of PCPTrc, MPS, and mpMRI with the decision to undergo biopsy were explored in a multivariable logistic regression model. RESULTS Of 248 patients, 134 (54%) proceeded to prostate biopsy. MPS was significantly higher in biopsied patients (median 29 vs14, P < .001). The use of biopsy was strongly associated with MPS, with biopsy rates of 26%, 38%, 58%, 90%, and 85% in the first through fifth quintiles, respectively (P < .001). MPS association with biopsy persisted upon stratification by mpMRI. On multivariable analysis, MPS was strongly associated with the decision to undergo biopsy when modeled as both a continuous (odds ratio [OR] 1.05, 95%; confidence interval [CI] 1.04-1.08; <.001) and binary (OR 7.76, 95%; CI 4.14-14.5; P < .001) variable. CONCLUSION Many patients (46%) undergoing clinical MPS testing as an alternative to immediate prostate biopsy were able to avoid biopsy. Increasing MPS was strongly associated with biopsy rates. These findings were robust to use of mpMRI.
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Affiliation(s)
| | | | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | | | - Zoey Chopra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Rachel Botbyl
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Rana Kabeer
- Department of Urology, University of Michigan, Ann Arbor, MI
| | - Takahiro Osawa
- Department of Urology, University of Michigan, Ann Arbor, MI
| | - Javed Siddiqui
- Department of Urology, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Rabia Siddiqui
- Department of Urology, University of Michigan, Ann Arbor, MI
| | | | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Lakshimi P Kunju
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Arul M Chinnaiyan
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI; Department of Pathology, University of Michigan, Ann Arbor, MI; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
| | - John T Wei
- Department of Urology, University of Michigan, Ann Arbor, MI; Dow Division of Health Services Research, University of Michigan, Ann Arbor, MI
| | - Jeffrey J Tosoian
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI.
| | - Todd M Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI; Rogel Cancer Center, University of Michigan, Ann Arbor, MI; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
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Plaska SW, Liu CJ, Lim JS, Rege J, Bick NR, Lerario AM, Hammer GD, Giordano TJ, Else T, Tomlins SA, Rainey WE, Udager AM. Targeted RNAseq of Formalin-Fixed Paraffin-Embedded Tissue to Differentiate Among Benign and Malignant Adrenal Cortical Tumors. Horm Metab Res 2020; 52:607-613. [PMID: 32791542 PMCID: PMC7880170 DOI: 10.1055/a-1212-8803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lack of routine fresh or frozen tissue is a barrier to widespread transcriptomic analysis of adrenal cortical tumors and an impediment to translational research in endocrinology and endocrine oncology. Our group has previously pioneered the use of targeted amplicon-based next-generation sequencing for archival formalin-fixed paraffin-embedded (FFPE) adrenal tissue specimens to characterize the spectrum of somatic mutations in various forms of primary aldosteronism. Herein, we developed and validated a novel 194-amplicon targeted next-generation RNA sequencing (RNAseq) assay for transcriptomic analysis of adrenal tumors using clinical-grade FFPE specimens. Targeted RNAseq-derived expression values for 27 adrenal cortical tumors, including aldosterone-producing adenomas (APA; n=8), cortisol-producing adenomas (CPA; n=11), and adrenal cortical carcinomas (ACC; n=8), highlighted known differentially-expressed genes (DEGs; i. e., CYP11B2, IGF2, etc.) and tumor type-specific transcriptional modules (i. e., high cell cycle/proliferation transcript expression in ACC, etc.), and a subset of DEGs was validated orthogonally using quantitative reverse transcription PCR (qRT-PCR). Finally, unsupervised hierarchical clustering using a subset of high-confidence DEGs revealed three discrete clusters representing APA, CPA, and ACC tumors with corresponding unique gene expression signatures, suggesting potential clinical utility for a transcriptomic-based approach to tumor classification. Overall, these data support the use of targeted amplicon-based RNAseq for comprehensive transcriptomic profiling of archival FFPE adrenal tumor material and indicate that this approach may facilitate important translational research opportunities for the study of these tumors.
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Affiliation(s)
- Samuel W. Plaska
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, Ann Arbor, Michigan, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jung Soo Lim
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, South Korea
| | - Juilee Rege
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Nolan R. Bick
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Antonio M. Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrine, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Gary D. Hammer
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Metabolism, Endocrine, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas J. Giordano
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Metabolism, Endocrine, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Tobias Else
- Department of Internal Medicine, Division of Metabolism, Endocrine, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Scott A. Tomlins
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - William E. Rainey
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Metabolism, Endocrine, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Co-corresponding authors: Aaron M. Udager, MD, PhD, Department of Pathology, University of Michigan Medical School, 3308 Rogel Cancer Center, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, UDA, , Phone: (734) 232-6399, Fax: (734) 763-4095, William E. Rainey, PhD, Department of Molecular and Integrative Physiology, University of Michigan Medical School, 2558 Medical Science Research Building II, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, USA, , Phone: (734) 764-7514, Fax: (734) 936-8813
| | - Aaron M. Udager
- Michigan Center for Translational Pathology, Ann Arbor, Michigan, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Co-corresponding authors: Aaron M. Udager, MD, PhD, Department of Pathology, University of Michigan Medical School, 3308 Rogel Cancer Center, 1500 E. Medical Center Dr., Ann Arbor, MI, 48109, UDA, , Phone: (734) 232-6399, Fax: (734) 763-4095, William E. Rainey, PhD, Department of Molecular and Integrative Physiology, University of Michigan Medical School, 2558 Medical Science Research Building II, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, USA, , Phone: (734) 764-7514, Fax: (734) 936-8813
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Fenstermaker M, Tomlins SA, Singh K, Wiens J, Morgan TM. Development and Validation of a Deep-learning Model to Assist With Renal Cell Carcinoma Histopathologic Interpretation. Urology 2020; 144:152-157. [PMID: 32711010 DOI: 10.1016/j.urology.2020.05.094] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/22/2020] [Accepted: 05/17/2020] [Indexed: 01/19/2023]
Abstract
OBJECTIVE To develop and test the ability of a convolutional neural network (CNN) to accurately identify the presence of renal cell carcinoma (RCC) on histopathology specimens, as well as differentiate RCC histologic subtype and grade. MATERIALS AND METHODS Digital hematoxylin and eosin stained biopsy images were downloaded from The Cancer Genome Atlas. A CNN model was trained on 100 um2 samples of either normal (3000 samples) or RCC (12,168 samples) tissue samples from 42 patients. RCC specimens included clear cell, chromophobe, and papillary histiotypes, as well as tissue of Fuhrman grades 1 through 4. Model testing was performed on an additional held-out cohort of benign and RCC specimens. Model performance was assessed on the basis of diagnostic accuracy, sensitivity, specificity, positive predictive value, and negative predictive value. RESULTS The CNN model achieved an overall accuracy of 99.1% in the testing cohort for distinguishing normal parenchyma from RCC (sensitivity 100%, specificity 97.1%). Accuracy for distinguishing between clear cell, papillary, and chromophobehistiotypes was 97.5%. Accuracy for predicting Fuhrman grade was 98.4%. CONCLUSION CNNs are able to rapidly and accurately identify the presence of RCC, distinguish RCC histologic subtypes, and identify tumor grade by analyzing histopathology specimens.
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Affiliation(s)
| | - Scott A Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, MI; University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Karandeep Singh
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Jenna Wiens
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI
| | - Todd M Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI; University of Michigan Rogel Cancer Center, Ann Arbor, MI
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36
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Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nat Genet 2020; 52:778-789. [PMID: 32661416 PMCID: PMC7454228 DOI: 10.1038/s41588-020-0648-8] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [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: 01/11/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023]
Abstract
Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes only detectable with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hyper-methylation and somatic mutations in TET2, DNMT3B, IDH1, and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer and provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Denise Playdle
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Travis J Barnard
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adina M Bailey
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA
| | - Marc D Perry
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Ruhollah Moussavi-Baygi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - S Laura Chang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Division of Hematology/Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew B Rettig
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA.,Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Yvonne Kim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hui Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tanushree Shenoy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Nupam P Mahajan
- Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Surgery, Washington University, St. Louis, MO, USA
| | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.,Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA.,Department of Urologic Surgery, University of California Davis, Sacramento, CA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Housheng H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Arul M Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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37
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Salami SS, Tosoian JJ, Nallandhighal S, Jones TA, Brockman S, Elkhoury FF, Bazzi S, Plouffe KR, Siddiqui J, Liu CJ, Kunju LP, Morgan TM, Natarajan S, Boonstra PS, Sumida L, Tomlins SA, Udager AM, Sisk AE, Marks LS, Palapattu GS. Serial Molecular Profiling of Low-grade Prostate Cancer to Assess Tumor Upgrading: A Longitudinal Cohort Study. Eur Urol 2020; 79:456-465. [PMID: 32631746 DOI: 10.1016/j.eururo.2020.06.041] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/17/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND The potential for low-grade (grade group 1 [GG1]) prostate cancer (PCa) to progress to high-grade disease remains unclear. OBJECTIVE To interrogate the molecular and biological features of low-grade PCa serially over time. DESIGN, SETTING, AND PARTICIPANTS Nested longitudinal cohort study in an academic active surveillance (AS) program. Men were on AS for GG1 PCa from 2012 to 2017. INTERVENTION Electronic tracking and resampling of PCa using magnetic resonance imaging/ultrasound fusion biopsy. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS ERG immunohistochemistry (IHC) and targeted DNA/RNA next-generation sequencing were performed on initial and repeat biopsies. Tumor clonality was assessed. Molecular data were compared between men who upgraded and those who did not upgrade to GG ≥ 2 cancer. RESULTS AND LIMITATIONS Sixty-six men with median age 64 yr (interquartile range [IQR], 59-69) and prostate-specific antigen 4.9 ng/mL (IQR, 3.3-6.4) underwent repeat sampling of a tracked tumor focus (median interval, 11 mo; IQR, 6-13). IHC-based ERG fusion status was concordant at initial and repeat biopsies in 63 men (95% vs expected 50%, p < 0.001), and RNAseq-based fusion and isoform expression were concordant in nine of 13 (69%) ERG+ patients, supporting focal resampling. Among 15 men who upgraded with complete data at both time points, integrated DNA/RNAseq analysis provided evidence of shared clonality in at least five cases. Such cases could reflect initial undersampling, but also support the possibility of clonal temporal progression of low-grade cancer. Our assessment was limited by sample size and use of targeted sequencing. CONCLUSIONS Repeat molecular assessment of low-grade tumors suggests that clonal progression could be one mechanism of upgrading. These data underscore the importance of serial tumor assessment in men pursuing AS of low-grade PCa. PATIENT SUMMARY We performed targeted rebiopsy and molecular testing of low-grade tumors on active surveillance. Our findings highlight the importance of periodic biopsy as a component of monitoring for cancer upgrading during surveillance.
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Affiliation(s)
- Simpa S Salami
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA.
| | - Jeffrey J Tosoian
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | | | - Tonye A Jones
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Scott Brockman
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
| | - Fuad F Elkhoury
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Selena Bazzi
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
| | - Komal R Plouffe
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Lakshmi P Kunju
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Todd M Morgan
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Shyam Natarajan
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Philip S Boonstra
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Lauren Sumida
- Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Scott A Tomlins
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Aaron M Udager
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Anthony E Sisk
- Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Leonard S Marks
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ganesh S Palapattu
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Urology, Medical University of Vienna, Vienna, Austria
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Palanisamy N, Yang J, Shepherd PDA, Li-Ning-Tapia EM, Labanca E, Manyam GC, Ravoori MK, Kundra V, Araujo JC, Efstathiou E, Pisters LL, Wan X, Wang X, Vazquez ES, Aparicio AM, Carskadon SL, Tomlins SA, Kunju LP, Chinnaiyan AM, Broom BM, Logothetis CJ, Troncoso P, Navone NM. The MD Anderson Prostate Cancer Patient-derived Xenograft Series (MDA PCa PDX) Captures the Molecular Landscape of Prostate Cancer and Facilitates Marker-driven Therapy Development. Clin Cancer Res 2020; 26:4933-4946. [PMID: 32576626 DOI: 10.1158/1078-0432.ccr-20-0479] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/08/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE Advances in prostate cancer lag behind other tumor types partly due to the paucity of models reflecting key milestones in prostate cancer progression. Therefore, we develop clinically relevant prostate cancer models. EXPERIMENTAL DESIGN Since 1996, we have generated clinically annotated patient-derived xenografts (PDXs; the MDA PCa PDX series) linked to specific phenotypes reflecting all aspects of clinical prostate cancer. RESULTS We studied two cell line-derived xenografts and the first 80 PDXs derived from 47 human prostate cancer donors. Of these, 47 PDXs derived from 22 donors are working models and can be expanded either as cell lines (MDA PCa 2a and 2b) or PDXs. The histopathologic, genomic, and molecular characteristics (androgen receptor, ERG, and PTEN loss) maintain fidelity with the human tumor and correlate with published findings. PDX growth response to mouse castration and targeted therapy illustrate their clinical utility. Comparative genomic hybridization and sequencing show significant differences in oncogenic pathways in pairs of PDXs derived from different areas of the same tumor. We also identified a recurrent focal deletion in an area that includes the speckle-type POZ protein-like (SPOPL) gene in PDXs derived from seven human donors of 28 studied (25%). SPOPL is a SPOP paralog, and SPOP mutations define a molecular subclass of prostate cancer. SPOPL deletions are found in 7% of The Cancer Genome Atlas prostate cancers, which suggests that our cohort is a reliable platform for targeted drug development. CONCLUSIONS The MDA PCa PDX series is a dynamic resource that captures the molecular landscape of prostate cancers progressing under novel treatments and enables optimization of prostate cancer-specific, marker-driven therapy.
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Affiliation(s)
- Nallasivam Palanisamy
- Department of Urology, Vattikuti Urology Institute, Henry Ford Health System, Detroit, Michigan.,Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Jun Yang
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter D A Shepherd
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elsa M Li-Ning-Tapia
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Estefania Labanca
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ganiraju C Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Murali K Ravoori
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vikas Kundra
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John C Araujo
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eleni Efstathiou
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Louis L Pisters
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xinhai Wan
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xuemei Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elba S Vazquez
- CONICET-Universidad de Buenos Aires. Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Ana M Aparicio
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shannon L Carskadon
- Department of Urology, Vattikuti Urology Institute, Henry Ford Health System, Detroit, Michigan.,Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Scott A Tomlins
- Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Lakshmi P Kunju
- Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Arul M Chinnaiyan
- Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Bradley M Broom
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher J Logothetis
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patricia Troncoso
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nora M Navone
- Department of Genitourinary Medical Oncology and the David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Rhodes D, Hovelson DH, Suga JM, Anderson DM, Dees EC, Koh HA, Burkard ME, Khatri J, Safa MM, Matrana MR, Yang ESH, Menter AR, Parsons BM, Slim JN, Falkner J, Reeder T, Vakil H, Kwiatkowski K, Johnson B, Tomlins SA. PCR-based comprehensive genomic profiling (PCR-CGP): Feasibility from >20,000 tumor tissue specimens (TTS) and predicted impact on actionable biomarker identification versus hybrid capture (H)-CGP and plasma (P)-CGP. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3574] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3574 Background: Tissue-based h-CGP is increasingly utilized for treatment selection in patients with advanced solid tumors but has high tumor surface area [TSA] requirements (≥25mm2 for leading commercial tests). P-CGP is recommended when tissue is insufficient for H-CGP. Here we assessed the feasibility and clinical impact on actionable biomarker identification of PCR-CGP. Methods: We performed a post-hoc, non-prespecified analysis on 21,743 consecutive subjects with advanced solid tumors who sent TTS for PCR-CGP from 5/17-12/19 as part of an ongoing observational trial at > 20 U.S. health systems (NCT03061305). PCR-CGP was performed using StrataNGS, a single-site laboratory developed test assessing all CGP biomarker classes (including microsatellite instability (MSI) status and tumor mutation burden [TMB]). We predicted actionable biomarker identification rates for PCR-CGP, H-CGP and P-CGP if applied to all U.S. patients with advanced solid tumors through incorporating population incidence, biomarker frequencies, test TSA and tumor content requirements (or cfDNA detection rates), and performance characteristics. Actionable biomarkers were the 30 in 11 tumor types from the MolDX p-CGP local coverage determination (L38043), pan-tumor NTRK fusions and MSI, and TMB in lung cancer. Results: Among TTS from 21,734 patients with advanced cancer, 20,493 (94.3%) met TSA requirements for PCR-CGP (≥2mm2) vs. 9,281 (42.7%) for H-CGP. PCR-CGP reported results for 98.0% and 95.0% of patients with large (≥25mm2 TSA) and small (2-24mm2) TS, respectively, in a median of 7 business days. Compared to 1,882 orthogonal actionable biomarker results, PCR-CGP accuracy was 96.6% and 96.5% in large and small TTS, respectively. Actionable biomarker frequency was highly correlated in PCR-CGP tested large vs. small TTS (r2= 0.99), as well as in this PCR-CGP cohort vs. a MSKCC institutional pan-cancer H-CGP cohort (r2= 0.92). If applied to all U.S. patients with advanced solid tumors, PCR-CGP has significantly greater predicted actionable biomarker identification rate (88.5%) compared to P-CGP (77.0%, N-1 chi-squared test, p < 0.0001) or H-CGP (54.3%, p < 0.0001). Conclusions: Half of TTS submitted for PCR-CGP did not meet H-CGP tissue requirements. PCR-CGP is feasible for the vast majority of patients and is predicted to expand the actionable biomarker evaluable proportion of patients with advanced solid tumors compared to H-CGP or P-CGP. Clinical trial information: NCT03061305 .
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Affiliation(s)
| | | | | | | | - Elizabeth Claire Dees
- The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC
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40
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Zarzour A, Morgans AK, Palmbos P, Jovanovic B, Tomlins SA, VanderWeele DJ, Yang XJ, Schaeffer EM, Sharifi R, Meeks JJ, Abdulkadir S, Hussain MHA. Evaluating the clinical, environmental, genetic, and genomic profile of men with early-onset aggressive prostate cancer (PCa). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e17517] [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
e17517 Background: Although PCa incidence has stabilized/decreased in most age groups, the incidence of metastatic disease has increased among men 50-69 years-old. The incidence of fatal PCa has decreased for most age groups, it has remained unchanged in men under 55 years-old. Studies have described genetic abnormalities in aggressive localized or end-stage PCa, but early-onset cases are not included or are under-represented. The primary objective of this study is to characterize the clinical, environmental, genetic and genomic features of high-risk advanced PCa. Methods: Study cohort includes men with PCa ≤ 60 years old with N1 or M1 stage at diagnosis or who develop metastases in 5-years after local therapy. Clinical (race, family history (Hx), environmental exposure), laboratory,/pathology, cell-free DNA germline analysis were collected. Primary/metastatic tumor tissue tested via the Tempus-Xe platform (DNA sequencing, whole transcriptome expression profiling, copy number analysis, comprehensive fusion gene analysis and calculation of tumor mutational burden). We report interim analysis. Results: Study completed accrual with 30 pts. Median age 55 years (41-60), 87% are white, 13% are black, 77% had a family Hx of malignancy in 1-6 family members, including 40% with family hx of PCa. Only 33% had Hx of smoking. Median Gleason score 9. Only 27% had nodal disease, and 73% had metastatic disease at diagnosis. Molecular data are available in 25 pts. Most common germline mutations: BRCA2 (12%), ATM (12%), RB1 (8%), MSH3 (8%) and MYBPC3 (8%). Most common somatic mutations:TP53 (40%), TMPRSS2-ERG fusion (32%), MUC4 (16%), PTEN (12%), C2CD4D (12%), SPOP (12%), OBSCN (12%), MXRA5 (12%), and MYO15A (12%). Microsatellite stability status was available in 15 pts and all were stable. Tumor mutational burden was low in all pts, ranging between 0.7 to 2.7 mutations/megabase. Conclusions: Our preliminary data suggest high rates of germline mutations in early onset lethal PCa. This aggressive subset of disease requires further studying to better characterize the underlying clinical/genomic factors driving this disease.
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Affiliation(s)
- Ahmad Zarzour
- Northwestern University, Feinberg School of Medicine, Chicago, IL
| | | | | | - Borko Jovanovic
- Northwestern University Department of Preventive Medicine, Chicago, IL
| | | | | | | | | | | | | | - Sarki Abdulkadir
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Maha H. A. Hussain
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
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41
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Palmbos PL, Tomlins SA, Daignault S, Agarwal N, Twardowski P, Morgans AK, Kelly WK, Arora V, Antonarakis ES, Siddiqui J, Robinson D, Knudsen KE, Chinnaiyan A, Hussain MHA. Clinical outcomes and markers of treatment response in a randomized phase II study of androgen deprivation therapy with or without palbociclib in RB-intact metastatic hormone-sensitive prostate cancer (mHSPC). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.5573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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
5573 Background: Targeted therapies based on tumor molecular markers are not currently used in mHSPC. Palbociclib, a CDK4/6 inhibitor, blocked proliferation and promoted G1 arrest in a Rb-and Cyclin D-dependent manner in preclinical models of HSPC. We hypothesized that co-targeting AR (ADT) and cell cycle (palbociclib) would improve outcomes in mHSPC pts. Methods: mHSPC pts with Rb intact tumors based on IHC of metastatic tumor biopsy were stratified and randomized (1:2) to Arm A: ADT or Arm B: ADT+ palbociclib (125mg 3 weeks on, 1 week off). Primary endpoint was confirmed PSA RR (≤ 4 ng/mL) after 28 weeks of therapy. Secondary endpoints included safety/tolerability, PFS, PSA and radiographic RR. Metastatic biopsy and primary tumors were subjected to whole exome and transcriptomic sequencing where available. CTC’s were enumerated at various time points. Results: 72 eligible pts (median age 67 years, PSA 73ng/mL) with newly diagnosed mHSPC were registered and underwent biopsy. 97% retained RB expression (IHC). 62 pts were stratified by disease extent and early initiation of ADT, and randomized. 60 pts initiated therapy (Arm A: 20; Arm B: 40). Adverse events were reported previously. 80% of pts (Arm A: 16/20, Arm B: 32/40; p = 0.87) on both arms met primary PSA endpoint (≤4ng/mL at 28 weeks). PSA undetectable rate at 28 weeks was Arm A: 50% (10/20) and Arm B: 43% (17/40; p = 0.5). Measurable disease RR: Arm A: 89% and Arm B: 89%. 12-month biochemical PFS was Arm A 69% (95%CI: 44-85%), Arm B 74% (95%CI: 57-85%). 41 patients on trial underwent sequencing of metastatic biopsy and 10 patients had matched primary prostate tumor sequencing results. CCND1 amp, 8q gain, PTEN and KMT2C mutations were each observed in metastatic, but not paired prostate primary tumors. TP53, PIK3 pathway (PIK3CA, AKT1, PTEN) mutations and 8q gains were associated with reduced PSA PFS [HR (95%CI): 3.0 (1.2-7.2), p = 0.018; 3.2(1.03-10),p = 0.044; 4.96 (1.8-12), p = 0.001, respectively]. Pretreatment CTCs were associated with lower PSA CR (p = 0.04) and shorter PFS (12-month PFS: 58% vs. 86%, p = 0.031). Conclusions: A tissue based biomarker preselected trial is feasible in mHSPC. ADT + palbociclib did not impact outcomes. Pretreatment CTC counts, TP53 and PIK3 pathway mutations, and 8q gain may offer prognostic value in mHSPC. Support: Movember-PCF Challenge Award, Pfizer. Clinical trial information: NCT02059213 .
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Affiliation(s)
| | | | | | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | | | | | - William Kevin Kelly
- Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA
| | - Vivek Arora
- Washington University in St. Louis, St. Louis, MO
| | | | - Javed Siddiqui
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
| | - Dan Robinson
- Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Karen E. Knudsen
- Sidney Kimmel Cancer Center at Jefferson Health, Philadelphia, PA
| | | | - Maha H. A. Hussain
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
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Nallandhighal S, Tosoian JJ, Singhal U, Karim R, Mathieu R, Plouffe K, Rioux-Leclercq N, Siddiqui J, Liu CJ, Hovelson DH, Doglioni C, Morgan TM, Susani M, Luciano Luciano R, Shariat SF, Tomlins SA, Briganti A, Palapattu GS, Udager AM, Salami SS. Dissection of primary prostate cancer to determine the clonal origin of synchronous lymph node metastasis. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e17614] [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
e17614 Background: Primary prostate cancer often consists of multiple, genomically-distinct clones. The clonal source of lymph node metastasis in multifocal disease is unknown. We sought to analyze and determine the histopathologic and molecular characteristics of the tumor sub-clones capable of metastasis in primary prostate cancers with synchronous lymph node metastasis. Methods: We identified patients with primary prostate cancer found to have lymph node (LN) metastasis at the time of radical prostatectomy, including those with multifocal disease. Punch biopsies were obtained from multiple regions of primary tumors and LN metastases. Targeted next generation sequencing to assess somatic DNA mutations, copy number alterations (CNA), and TMPRSS2:ERG fusion status. Bioinformatic analyses were performed using in-house developed pipelines. Phylogenetic evolutionary analyses were performed to delineate the primary cancer clone responsible for LN metastasis. Results: We identified 2 patients with LN cancer regions. In one patient, while all four Grade Group (GG) 5 primary tumor (PT) regions showed concordant TP53 and TPR non-synonymous mutations and broad copy number alterations (CNAs) with two LN foci, only two regions shared high level CNAs with both lymph node foci. In this case, a GG1 tumor focus showed no TP53 somatic mutation or CNA overlap with the high-grade tumor or lymph node samples. Critically, phylogenetic analysis revealed that the GG5 PT with extra-prostatic extension (EPE) showed higher concordance with the LN metastases than regions confined to the prostate. In another patient with four PT, phylogenetic analysis revealed that the PT with EPE closely resembled the LN metastasis; both were TMPRSS2:ERG fusion positive share PTEN copy number loss. Two PT (GG1 and 2) appeared to be independent clones and were TMPRSS2:ERG fusion negative. One of the six circulating tumor cells (isolated pre-prostatectomy) from this patient demonstrated a significant PTEN copy loss consistent with the findings in the region of EPE and the LN metastasis. Conclusions: Our findings confirm molecular heterogeneity of primary prostate cancers and homogeneity of LN metastases supporting the use of shared molecular alterations to infer clonal lineage. Our results highlight the critical role of adverse pathologic features, such as grade and EPE, in prostate cancer with synchronous lymph node metastasis.
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Affiliation(s)
| | | | - Udit Singhal
- Department of Urology, University of Michigan, Ann Arbor, MI
| | | | | | | | | | - Javed Siddiqui
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
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43
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Baker JE, Nanba K, Blinder AR, Bick N, Wachtel H, Cohen DL, Williams TA, Reincke M, Else T, Tomlins SA, Giordano TJ, Rainey WE. SAT-554 Genetic Profile of Early-Onset Aldosterone-Producing Adenomas. J Endocr Soc 2020. [PMCID: PMC7208325 DOI: 10.1210/jendso/bvaa046.910] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background: Aldosterone-producing adenoma (APA) is a major subtype of primary aldosteronism (PA) which is the most common cause of endocrine-related hypertension. The Endocrine Society clinical practice guideline suggests that young patients (< 35 years old) with a CT-detected adrenocortical adenoma and typical phenotype of PA may not need adrenal venous sampling prior to adrenalectomy. In recent years, aldosterone-driver somatic mutations have been identified in APA, and prevalence studies suggest potential effects of patient age and sex. However, the rare nature of early-onset PA has prevented a detailed study of the histologic characteristics and aldosterone-driver somatic mutations in adrenal tumors from these patients. Objective: To determine histologic and somatic mutation profile in early-onset APA. Methods: Fifty-five formalin-fixed paraffin-embedded (FFPE) adrenals from patients at the age of 35 years old or younger who underwent adrenalectomy at the participating centers were studied (45 women, 9 men, and 1 unknown sex). CYP11B2 immunohistochemistry (IHC)-guided tumor capturing was used to selectively obtain DNA from APA. Mutation status was determined either by Sanger sequencing or targeted next-generation sequencing. Results: CYP11B2 IHC identified APAs in all adrenal specimens. Solitary APAs were found in 53 adrenals. One adrenal had multiple APAs and one had a dominant CYP11B2-negative tumor and a smaller APA. In total, DNA from 57 APAs were sequenced. Two APAs were excluded from the analysis due to low sample quality. In 52 of the 55 APAs, somatic mutations were identified in one of the aldosterone-driver genes or CTNNB1 gene, encoding β-catenin. The most common genetic alteration was seen in KCNJ5 (37/55, 67%), followed by CACNA1D (7/55, 13%), ATP1A1 (3/55, 5%), CTNNB1 (3/55, 5%), and ATP2B3 (2/55, 4%). No sex difference in the prevalence of KCNJ5 mutation was observed in this age group. Conclusion: The majority of adrenals from early-onset PA patients had a solitary APA. Regardless of sex, the most common genetic cause of early-onset APA was somatic mutations in KCNJ5.
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Affiliation(s)
- Jessica E Baker
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Kazutaka Nanba
- Department of Endocrinology and Metabolism, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Amy R Blinder
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Nolan Bick
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Heather Wachtel
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Debbie L Cohen
- Department of Surgery, Division of Endocrine and Oncologic Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Tracy Ann Williams
- Department of Medicine, Division of Renal, Electrolyte and Hypertension, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Martin Reincke
- Department of Medicine, Division of Renal, Electrolyte and Hypertension, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Tobias Else
- Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Scott A Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Thomas J Giordano
- Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - William E Rainey
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
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44
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Saha AK, Contreras-Galindo R, Niknafs YS, Iyer M, Qin T, Padmanabhan K, Siddiqui J, Palande M, Wang C, Qian B, Ward E, Tang T, Tomlins SA, Gitlin SD, Sartor MA, Omenn GS, Chinnaiyan AM, Markovitz DM. The role of the histone H3 variant CENPA in prostate cancer. J Biol Chem 2020; 295:8537-8549. [PMID: 32371391 PMCID: PMC7307189 DOI: 10.1074/jbc.ra119.010080] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 07/05/2019] [Revised: 04/14/2020] [Indexed: 01/26/2023] Open
Abstract
Overexpression of centromeric proteins has been identified in a number of human malignancies, but the functional and mechanistic contributions of these proteins to disease progression have not been characterized. The centromeric histone H3 variant centromere protein A (CENPA) is an epigenetic mark that determines centromere identity. Here, using an array of approaches, including RNA-sequencing and ChIP-sequencing analyses, immunohistochemistry-based tissue microarrays, and various cell biology assays, we demonstrate that CENPA is highly overexpressed in prostate cancer in both tissue and cell lines and that the level of CENPA expression correlates with the disease stage in a large cohort of patients. Gain-of-function and loss-of-function experiments confirmed that CENPA promotes prostate cancer cell line growth. The results from the integrated sequencing experiments suggested a previously unidentified function of CENPA as a transcriptional regulator that modulates expression of critical proliferation, cell-cycle, and centromere/kinetochore genes. Taken together, our findings show that CENPA overexpression is crucial to prostate cancer growth.
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Affiliation(s)
- Anjan K Saha
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Yashar S Niknafs
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Iyer
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Karthik Padmanabhan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Monica Palande
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Claire Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Brian Qian
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth Ward
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Tara Tang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott D Gitlin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Gilbert S Omenn
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Arul M Chinnaiyan
- Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - David M Markovitz
- Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA .,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA
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45
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Ono Y, Yamazaki Y, Omata K, Else T, Tomlins SA, Rhayem Y, Williams TA, Reincke M, Carling T, Monticone S, Mulatero P, Beuschlein F, Ito S, Satoh F, Rainey WE, Sasano H. Histological Characterization of Aldosterone-producing Adrenocortical Adenomas with Different Somatic Mutations. J Clin Endocrinol Metab 2020; 105:5649299. [PMID: 31789380 PMCID: PMC7048684 DOI: 10.1210/clinem/dgz235] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023]
Abstract
CONTEXT Aldosterone-producing adrenocortical adenomas (APAs) are mainly composed of clear (lipid rich) and compact (eosinophilic) tumor cells. The detailed association between these histological features and somatic mutations (KCNJ5, ATP1A1, ATP2B3, and CACNA1D) in APAs is unknown. OBJECTIVE To examine the association between histological features and individual genotypes in APAs. METHODS Examination of 39 APAs subjected to targeted next-generation sequencing (11 KCNJ5, 10 ATP1A1, 10 ATP2B3, and 8 CACNA1D) and quantitative morphological and immunohistochemical (CYP11B2 and CYP17A1) analyses using digital imaging software. RESULTS KCNJ5- and ATP2B3-mutated APAs had clear cell dominant features (KCNJ5: clear 59.8% [54.4-64.6%] vs compact 40.2% (35.4-45.6%), P = .0022; ATP2B3: clear 54.3% [48.2-62.4 %] vs compact 45.7% (37.6-51.8 %), P = .0696). ATP1A1- and CACNA1D-mutated APAs presented with marked intratumoral heterogeneity. A significantly positive correlation of immunoreactivity was detected between CYP11B2 and CYP17A1 in tumor cells of KCNJ5-mutated APAs (P = .0112; ρ = 0.7237), in contrast, significantly inverse correlation was detected in ATP1A1-mutated APAs (P = .0025; ρ = -0.8667). CONCLUSION KCNJ5-mutated APAs, coexpressing CYP11B2 and CYP17A1, were more deviated in terms of zonation-specific differentiation of adrenocortical cells than ATP1A1- and ATP2B3-mutated APAs.
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Affiliation(s)
- Yoshikiyo Ono
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Hospital, Sendai, Japan
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Departments of Molecular and Integrative Physiology & Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Yuto Yamazaki
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kei Omata
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Hospital, Sendai, Japan
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Tobias Else
- Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Scott A Tomlins
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan
- Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Yara Rhayem
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tracy Ann Williams
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tobias Carling
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, Connecticut
| | - Silvia Monticone
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Paolo Mulatero
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Felix Beuschlein
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, Universitätsspital Zürich, Zurich, Switzerland
| | - Sadayoshi Ito
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Hospital, Sendai, Japan
| | - Fumitoshi Satoh
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Hospital, Sendai, Japan
- Division of Clinical Hypertension, Endocrinology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - William E Rainey
- Departments of Molecular and Integrative Physiology & Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Hironobu Sasano
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Correspondence and Reprint Requests: Hironobu Sasano, MD, PhD, Department of Pathology, Tohoku University School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980- 8575 JAPAN. E-mail:
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Nanba K, Blinder AR, Rege J, Hattangady NG, Else T, Liu CJ, Tomlins SA, Vats P, Kumar-Sinha C, Giordano TJ, Rainey WE. Somatic CACNA1H Mutation As a Cause of Aldosterone-Producing Adenoma. Hypertension 2020; 75:645-649. [PMID: 31983310 DOI: 10.1161/hypertensionaha.119.14349] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [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: 11/16/2022]
Abstract
Driver somatic mutations for aldosterone excess have been found in ≈90% of aldosterone-producing adenomas (APAs) using an aldosterone synthase (CYP11B2)-guided sequencing approach. In the present study, we identified a novel somatic CACNA1H mutation (c.T4289C, p.I1430T) in an APA without any currently known aldosterone-driver mutations using CYP11B2 immunohistochemistry-guided whole exome sequencing. The CACNA1H gene encodes a voltage-dependent T-type calcium channel alpha-1H subunit. Germline variants in this gene are known as a cause of familial hyperaldosteronism IV. Targeted next-generation sequencing detected identical CACNA1H variants in 2 additional APAs in a cohort of the University of Michigan, resulting in a prevalence of 4% (3/75) in APAs. We tested the functional effect of the variant on adrenal cell aldosterone production and CYP11B2 mRNA expression using the human adrenocortical HAC15 cell line with a doxycycline-inducible CACNA1HI1430T mutation. Doxycycline treatment increased CYP11B2 mRNA levels as well as aldosterone production, supporting a pathological role of the CACNA1H p.I1430T mutation on the development of primary aldosteronism. In conclusion, somatic CACNA1H mutation is a genetic cause of APAs. Although the prevalence of this mutation is low, this study will provide better understanding of molecular mechanism of inappropriate aldosterone production in APAs.
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Affiliation(s)
- Kazutaka Nanba
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor (K.N., A.R.B., J.R., W.E.R.).,Department of Endocrinology and Metabolism, National Hospital Organization Kyoto Medical Center, Kyoto, Japan (K.N.)
| | - Amy R Blinder
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor (K.N., A.R.B., J.R., W.E.R.)
| | - Juilee Rege
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor (K.N., A.R.B., J.R., W.E.R.)
| | - Namita G Hattangady
- Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor (N.G.H., T.E., T.J.G., W.E.R.)
| | - Tobias Else
- Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor (N.G.H., T.E., T.J.G., W.E.R.)
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S., T.J.G.).,Rogel Cancer Center, University of Michigan, Ann Arbor (C.J.-L., S.A.T., T.J.G.).,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S.)
| | - Scott A Tomlins
- Department of Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S., T.J.G.).,Rogel Cancer Center, University of Michigan, Ann Arbor (C.J.-L., S.A.T., T.J.G.).,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S.)
| | - Pankaj Vats
- Department of Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S., T.J.G.).,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S.)
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S., T.J.G.).,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S.)
| | - Thomas J Giordano
- Department of Pathology, University of Michigan, Ann Arbor (C.-J.L., S.A.T., P.V., C.K.-S., T.J.G.).,Rogel Cancer Center, University of Michigan, Ann Arbor (C.J.-L., S.A.T., T.J.G.)
| | - William E Rainey
- From the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor (K.N., A.R.B., J.R., W.E.R.).,Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor (N.G.H., T.E., T.J.G., W.E.R.)
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47
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Faisal FA, Murali S, Kaur H, Vidotto T, Guedes LB, Salles DC, Kothari V, Tosoian JJ, Han S, Hovelson DH, Hu K, Spratt DE, Baras AS, Tomlins SA, Schaeffer EM, Lotan TL. CDKN1B Deletions are Associated with Metastasis in African American Men with Clinically Localized, Surgically Treated Prostate Cancer. Clin Cancer Res 2020; 26:2595-2602. [PMID: 31969336 DOI: 10.1158/1078-0432.ccr-19-1669] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/25/2019] [Accepted: 01/17/2020] [Indexed: 01/30/2023]
Abstract
PURPOSE The potential biological determinants of aggressive prostate cancer in African American (AA) men are unknown. Here we characterize prostate cancer genomic alterations in the largest cohort to date of AA men with clinical follow-up for metastasis, with the aim to elucidate the key molecular drivers associated with poor prognosis in this population. EXPERIMENTAL DESIGN Targeted sequencing was retrospectively performed on 205 prostate tumors from AA men treated with radical prostatectomy (RP) to examine somatic genomic alterations and percent of the genome with copy-number alterations (PGA). Cox proportional hazards analyses assessed the association of genomic alterations with risk of metastasis. RESULTS At RP, 71% (145/205) of patients had grade group ≥3 disease, and 49% (99/202) were non-organ confined. The median PGA was 3.7% (IQR = 0.9%-9.4%) and differed by pathologic grade (P < 0.001) and stage (P = 0.02). Median follow-up was 5 years. AA men with the highest quartile of PGA had increased risks of metastasis (multivariable: HR = 13.45; 95% CI, 2.55-70.86; P = 0.002). The most common somatic mutations were SPOP (11.2%), FOXA1 (8.3%), and TP53 (3.9%). The most common loci altered at the copy number level were CDKN1B (6.3%), CHD1 (4.4%), and PTEN (3.4%). TP53 mutations and deep deletions in CDKN1B were associated with increased risks of metastasis on multivariable analyses (TP53: HR = 9.5; 95% CI, 2.2-40.6; P = 0.002; CDKN1B: HR = 6.7; 95% CI, 1.3-35.2; P = 0.026). CONCLUSIONS Overall, PGA, somatic TP53 mutations, and a novel finding of deep deletions in CDKN1B were associated with poor prognosis in AA men. These findings require confirmation in additional AA cohorts.
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Affiliation(s)
- Farzana A Faisal
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sanjana Murali
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harsimar Kaur
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Thiago Vidotto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Liana B Guedes
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniela Correia Salles
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vishal Kothari
- Polsky Urologic Cancer Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jeffrey J Tosoian
- Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Sumin Han
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Daniel H Hovelson
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kevin Hu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Daniel E Spratt
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alexander S Baras
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Scott A Tomlins
- Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan. .,Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Edward M Schaeffer
- Polsky Urologic Cancer Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Tamara L Lotan
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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48
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McCool KW, Freeman ZT, Zhai Y, Wu R, Hu K, Liu CJ, Tomlins SA, Fearon ER, Magnuson B, Kuick R, Cho KR. Murine Oviductal High-Grade Serous Carcinomas Mirror the Genomic Alterations, Gene Expression Profiles, and Immune Microenvironment of Their Human Counterparts. Cancer Res 2019; 80:877-889. [PMID: 31806642 DOI: 10.1158/0008-5472.can-19-2558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/30/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022]
Abstract
Robust preclinical models of ovarian high-grade serous carcinoma (HGSC) are needed to advance our understanding of HGSC pathogenesis and to test novel strategies aimed at improving clinical outcomes for women with the disease. Genetically engineered mouse models of HGSC recapitulating the likely cell of origin (fallopian tube), underlying genetic defects, histology, and biologic behavior of human HGSCs have been developed. However, the degree to which the mouse tumors acquire the somatic genomic changes, gene expression profiles, and immune microenvironment that characterize human HGSCs remains unclear. We used integrated molecular characterization of oviductal HGSCs arising in the context of Brca1, Trp53, Rb1, and Nf1 (BPRN) inactivation to determine whether the mouse tumors recapitulate human HGSCs across multiple domains of molecular features. Targeted DNA sequencing showed the mouse BPRN tumors, but not endometrioid carcinoma-like tumors based on different genetic defects (e.g., Apc and Pten), acquire somatic mutations and widespread copy number alterations similar to those observed in human HGSCs. RNA sequencing showed the mouse HGSCs most closely resemble the so-called immunoreactive and mesenchymal subsets of human HGSCs. A combined immuno-genomic analysis demonstrated the immune microenvironment of BPRN tumors models key aspects of tumor-immune dynamics in the immunoreactive and mesenchymal subtypes of human HGSC, with enrichment of immunosuppressive cell subsets such as myeloid-derived suppressor cells and regulatory T cells. The findings further validate the BPRN model as a robust preclinical experimental platform to address current barriers to improved prevention, diagnosis, and treatment of this often lethal cancer. SIGNIFICANCE: The acquired gene mutations, broad genomic alterations, and gene expression and immune cell-tumor axis changes in a mouse model of oviductal serous carcinoma closely mirror those of human tubo-ovarian high-grade serous carcinoma.
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Affiliation(s)
- Kevin W McCool
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Zachary T Freeman
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, Michigan.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Yali Zhai
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Rong Wu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kevin Hu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Scott A Tomlins
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Eric R Fearon
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Brian Magnuson
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Rork Kuick
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.,Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Kathleen R Cho
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan .,Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
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49
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Gupta S, Hovelson DH, Kemeny G, Halabi S, Foo WC, Anand M, Somarelli JA, Tomlins SA, Antonarakis ES, Luo J, Dittamore RV, George DJ, Rothwell C, Nanus DM, Armstrong AJ, Gregory SG. Discordant and heterogeneous clinically relevant genomic alterations in circulating tumor cells vs plasma DNA from men with metastatic castration resistant prostate cancer. Genes Chromosomes Cancer 2019; 59:225-239. [PMID: 31705765 DOI: 10.1002/gcc.22824] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor cell (CTC) and cell-free (cf) DNA-based genomic alterations are increasingly being used for clinical decision-making in oncology. However, the concordance and discordance between paired CTC and cfDNA genomic profiles remain largely unknown. We performed comparative genomic hybridization (CGH) on CTCs and cfDNA, and low-pass whole genome sequencing (lpWGS) on cfDNA to characterize genomic alterations (CNA) and tumor content in two independent prospective studies of 93 men with mCRPC treated with enzalutamide/abiraterone, or radium-223. Comprehensive analysis of 69 patient CTCs and 72 cfDNA samples from 93 men with mCRPC, including 64 paired samples, identified common concordant gains in FOXA1, AR, and MYC, and losses in BRCA1, PTEN, and RB1 between CTCs and cfDNA. Concordant PTEN loss and discordant BRCA2 gain were associated with significantly worse outcomes in Epic AR-V7 negative men with mCRPC treated with abiraterone/enzalutamide. We identified and externally validated CTC-specific genomic alternations that were discordant in paired cfDNA, even in samples with high tumor content. These CTC/cfDNA-discordant regions included key genomic regulators of lineage plasticity, osteomimicry, and cellular differentiation, including MYCN gain in CTCs (31%) that was rarely detected in cfDNA. CTC MYCN gain was associated with poor clinical outcomes in AR-V7 negative men and small cell transformation. In conclusion, we demonstrated concordance of multiple genomic alterations across CTC and cfDNA platforms; however, some genomic alterations displayed substantial discordance between CTC DNA and cfDNA despite the use of identical copy number analysis methods, suggesting tumor heterogeneity and divergent evolution associated with poor clinical outcomes.
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Affiliation(s)
- Santosh Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Daniel H Hovelson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Gabor Kemeny
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Susan Halabi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Wen-Chi Foo
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Monika Anand
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Jason A Somarelli
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Department of Medicine, Surgery, Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Emmanuel S Antonarakis
- Prostate Cancer Research Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jun Luo
- James Buchanan Brady Urological Institute and the Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Daniel J George
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Colin Rothwell
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - David M Nanus
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Department of Medicine, Surgery, Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Simon G Gregory
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
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50
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Nanba K, Omata K, Gomez-Sanchez CE, Stratakis CA, Demidowich AP, Suzuki M, Thompson LDR, Cohen DL, Luther JM, Gellert L, Vaidya A, Barletta JA, Else T, Giordano TJ, Tomlins SA, Rainey WE. Genetic Characteristics of Aldosterone-Producing Adenomas in Blacks. Hypertension 2019; 73:885-892. [PMID: 30739536 DOI: 10.1161/hypertensionaha.118.12070] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [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: 12/23/2022]
Abstract
Somatic mutations have been identified in aldosterone-producing adenomas (APAs) in genes that include KCNJ5, ATP1A1, ATP2B3, and CACNA1D. Based on independent studies, there appears to be racial differences in the prevalence of somatic KCNJ5 mutations, particularly between East Asians and Europeans. Despite the high cardiovascular disease mortality of blacks, there have been no studies focusing on somatic mutations in APAs in this population. In the present study, we investigated genetic characteristics of APAs in blacks using a CYP11B2 (aldosterone synthase) immunohistochemistry-guided next-generation sequencing approach. The adrenal glands with adrenocortical adenomas from 79 black patients with primary aldosteronism were studied. Seventy-three tumors from 69 adrenal glands were confirmed to be APAs by CYP11B2 immunohistochemistry. Sixty-five of 73 APAs (89%) had somatic mutations in aldosterone-driver genes. Somatic CACNA1D mutations were the most prevalent genetic alteration (42%), followed by KCNJ5 (34%), ATP1A1 (8%), and ATP2B3 mutations (4%). CACNA1D mutations were more often observed in APAs from males than those from females (55% versus 29%, P=0.033), whereas KCNJ5 mutations were more prevalent in APAs from females compared with those from males (57% versus 13%, P<0.001). No somatic mutations in aldosterone-driver genes were identified in tumors without CYP11B2 expression. In conclusion, 89% of APAs in blacks harbor aldosterone-driving mutations, and unlike Europeans and East Asians, the most frequently mutated aldosterone-driver gene was CACNA1D. Determination of racial differences in the prevalence of aldosterone-driver gene mutations may facilitate the development of personalized medicines for patients with primary aldosteronism.
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Affiliation(s)
- Kazutaka Nanba
- From the Department of Molecular and Integrative Physiology (K.N., W.E.R.), University of Michigan, Ann Arbor
| | - Kei Omata
- Department of Pathology (K.O., T.J.G., S.A.T.), University of Michigan, Ann Arbor
| | - Celso E Gomez-Sanchez
- Endocrine and Research Service, G.V. (Sonny) Montgomery VA Medical Center, Jackson, MS (C.E.G.-S.).,Division of Endocrinology, University of Mississippi Medical Center, Jackson (C.E.G.-S.)
| | - Constantine A Stratakis
- Section of Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (C.A.S., A.P.D., M.S.)
| | - Andrew P Demidowich
- Section of Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (C.A.S., A.P.D., M.S.)
| | - Mari Suzuki
- Section of Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (C.A.S., A.P.D., M.S.)
| | - Lester D R Thompson
- Department of Pathology, Woodland Hills Medical Center, Southern California Permanente Medical Group (L.D.R.T.)
| | - Debbie L Cohen
- Renal, Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia (D.L.C.)
| | - James M Luther
- Division of Clinical Pharmacology (J.M.L.), Vanderbilt University Medical Center, Nashville, TN
| | - Lan Gellert
- Department of Pathology, Microbiology and Immunology (L.G.), Vanderbilt University Medical Center, Nashville, TN
| | - Anand Vaidya
- Center for Adrenal Disorders, Division of Endocrinology, Diabetes, and Hypertension (A.V.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Justine A Barletta
- Department of Pathology (J.A.B.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Tobias Else
- Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine (T.E., T.J.G., W.E.R.), University of Michigan, Ann Arbor
| | - Thomas J Giordano
- Department of Pathology (K.O., T.J.G., S.A.T.), University of Michigan, Ann Arbor.,Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine (T.E., T.J.G., W.E.R.), University of Michigan, Ann Arbor.,Rogel Cancer Center (T.J.G., S.A.T.), University of Michigan, Ann Arbor
| | - Scott A Tomlins
- Department of Pathology (K.O., T.J.G., S.A.T.), University of Michigan, Ann Arbor.,Rogel Cancer Center (T.J.G., S.A.T.), University of Michigan, Ann Arbor.,Department of Urology (S.A.T.), University of Michigan, Ann Arbor.,Michigan Center for Translational Pathology (S.A.T.), University of Michigan, Ann Arbor
| | - William E Rainey
- From the Department of Molecular and Integrative Physiology (K.N., W.E.R.), University of Michigan, Ann Arbor.,Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine (T.E., T.J.G., W.E.R.), University of Michigan, Ann Arbor
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