1
|
Chambers M, Andre AT, Wright JL, Vakar-Lopez F, Tretiakova M, Reder NP, Haffner MC, True LD. Outcome Analysis of a Series of Mixed-Grade, Non-muscle Invasive, Papillary Carcinomas of the Bladder. Int J Surg Pathol 2024:10668969241246492. [PMID: 38689480 DOI: 10.1177/10668969241246492] [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] [Indexed: 05/02/2024]
Abstract
Introduction. Papillary urothelial carcinomas are currently graded as either low- or high-grade tumors based on World Health Organization (WHO) 2022 guidelines for genitourinary tumors. However, a minority of tumors are mixed-grade tumors, composed predominantly of low-grade cancer with a minor high-grade component. In the 2022 WHO these cancers are recognized as having outcomes comparable to low-grade cancers, although data to date has been limited. Methods. The pathology records of a large academic institution were searched for mixed-grade, non-muscle invasive papillary carcinomas of the bladder and ureter in order to characterize prognosis of these cancers. Results. Of 136 cancers, the majority (n = 104, 76.5%) were solitary, mixed-grade tumors, while 21 (15.4%) had a concurrent low-grade cancer and 11 (8.1%) had multiple mixed-grade tumors at the time of diagnosis. At follow-up (median 48.3 months, range = 1.3 months-18.1 years), 71 cancers recurred (52.2%): 52 (38.2%) as low- or mixed-grade cancers and 18 (13.2%) as high-grade cancers. There were no instances of stage-progression to >pT2. Conclusions. The clinical outcome of mixed-grade carcinomas was similar to what has been reported for low-grade carcinomas. Based on our results, and prior congruent studies of mixed-grade lesions, these lesions may be regarded as a distinct sub-category with a better prognosis than high-grade tumors.
Collapse
Affiliation(s)
- Meagan Chambers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexa T Andre
- University of Washington Medical School, Seattle, WA, USA
| | - Jonathan L Wright
- Department of Urology, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Funda Vakar-Lopez
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Maria Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nicholas P Reder
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Michael C Haffner
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| |
Collapse
|
2
|
Turnham DJ, Mullen MS, Bullock NP, Gilroy KL, Richards AE, Patel R, Quintela M, Meniel VS, Seaton G, Kynaston H, Clarkson RWE, Phesse TJ, Nelson PS, Haffner MC, Staffurth JN, Pearson HB. Development and Characterisation of a New Patient-Derived Xenograft Model of AR-Negative Metastatic Castration-Resistant Prostate Cancer. Cells 2024; 13:673. [PMID: 38667288 PMCID: PMC11049137 DOI: 10.3390/cells13080673] [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: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
As the treatment landscape for prostate cancer gradually evolves, the frequency of treatment-induced neuroendocrine prostate cancer (NEPC) and double-negative prostate cancer (DNPC) that is deficient for androgen receptor (AR) and neuroendocrine (NE) markers has increased. These prostate cancer subtypes are typically refractory to AR-directed therapies and exhibit poor clinical outcomes. Only a small range of NEPC/DNPC models exist, limiting our molecular understanding of this disease and hindering our ability to perform preclinical trials exploring novel therapies to treat NEPC/DNPC that are urgently needed in the clinic. Here, we report the development of the CU-PC01 PDX model that represents AR-negative mCRPC with PTEN/RB/PSMA loss and CTNN1B/TP53/BRCA2 genetic variants. The CU-PC01 model lacks classic NE markers, with only focal and/or weak expression of chromogranin A, INSM1 and CD56. Collectively, these findings are most consistent with a DNPC phenotype. Ex vivo and in vivo preclinical studies revealed that CU-PC01 PDX tumours are resistant to mCRPC standard-of-care treatments enzalutamide and docetaxel, mirroring the donor patient's treatment response. Furthermore, short-term CU-PC01 tumour explant cultures indicate this model is initially sensitive to PARP inhibition with olaparib. Thus, the CU-PC01 PDX model provides a valuable opportunity to study AR-negative mCRPC biology and to discover new treatment avenues for this hard-to-treat disease.
Collapse
Affiliation(s)
- Daniel J. Turnham
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | - Manisha S. Mullen
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | - Nicholas P. Bullock
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | | | - Anna E. Richards
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | - Radhika Patel
- Division of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Marcos Quintela
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | - Valerie S. Meniel
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | - Gillian Seaton
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | - Howard Kynaston
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
- Department of Urology, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Richard W. E. Clarkson
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| | - Toby J. Phesse
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Peter S. Nelson
- Division of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
- Department of Urology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Michael C. Haffner
- Division of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - John N. Staffurth
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Helen B. Pearson
- The European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Hadyn Ellis Building, Cardiff CF24 4HQ, UK
| |
Collapse
|
3
|
Zaidi S, Park J, Chan JM, Roudier MP, Zhao JL, Gopalan A, Wadosky KM, Patel RA, Sayar E, Karthaus WR, Henry Kates D, Chaudhary O, Xu T, Masilionis I, Mazutis L, Chaligné R, Obradovic A, Linkov I, Barlas A, Jungbluth A, Rekhtman N, Silber J, Manova–Todorova K, Watson PA, True LD, Morrissey CM, Scher HI, Rathkopf D, Morris MJ, Goodrich DW, Choi J, Nelson PS, Haffner MC, Sawyers CL. Single Cell Analysis of Treatment-Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies. bioRxiv 2024:2024.04.09.588340. [PMID: 38645034 PMCID: PMC11030323 DOI: 10.1101/2024.04.09.588340] [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] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Targeting cell surface molecules using radioligand and antibody-based therapies has yielded considerable success across cancers. However, it remains unclear how the expression of putative lineage markers, particularly cell surface molecules, varies in the process of lineage plasticity, wherein tumor cells alter their identity and acquire new oncogenic properties. A notable example of lineage plasticity is the transformation of prostate adenocarcinoma (PRAD) to neuroendocrine prostate cancer (NEPC)--a growing resistance mechanism that results in the loss of responsiveness to androgen blockade and portends dismal patient survival. To understand how lineage markers vary across the evolution of lineage plasticity in prostate cancer, we applied single cell analyses to 21 human prostate tumor biopsies and two genetically engineered mouse models, together with tissue microarray analysis (TMA) on 131 tumor samples. Not only did we observe a higher degree of phenotypic heterogeneity in castrate-resistant PRAD and NEPC than previously anticipated, but also found that the expression of molecules targeted therapeutically, namely PSMA, STEAP1, STEAP2, TROP2, CEACAM5, and DLL3, varied within a subset of gene-regulatory networks (GRNs). We also noted that NEPC and small cell lung cancer (SCLC) subtypes shared a set of GRNs, indicative of conserved biologic pathways that may be exploited therapeutically across tumor types. While this extreme level of transcriptional heterogeneity, particularly in cell surface marker expression, may mitigate the durability of clinical responses to novel antigen-directed therapies, its delineation may yield signatures for patient selection in clinical trials, potentially across distinct cancer types.
Collapse
Affiliation(s)
- Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Genitourinary Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jooyoung Park
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Joseph M. Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | | | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kristine M. Wadosky
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Radhika A. Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98195, USA
| | - Erolcan Sayar
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98195, USA
| | - Wouter R. Karthaus
- Swiss Institute for Experimental Cancer Research (ISREC). School of Life Sciences. EPFL, 1015 Lausanne, Switzerland
| | - D. Henry Kates
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ojasvi Chaudhary
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tianhao Xu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ignas Masilionis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Linas Mazutis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronan Chaligné
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aleksandar Obradovic
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Irina Linkov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Afsar Barlas
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Achim Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joachim Silber
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Katia Manova–Todorova
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Philip A. Watson
- Research Outreach and Compliance, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Colm M. Morrissey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Howard I. Scher
- Department of Genitourinary Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Rathkopf
- Department of Genitourinary Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael J. Morris
- Department of Genitourinary Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David W. Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98195, USA
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Charles L. Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
4
|
Li S, Wong A, Sun H, Bhatia V, Javier G, Jana S, Wu Q, Montgomery RB, Wright JL, Lam HM, Hsieh AC, Faltas BM, Haffner MC, Lee JK. A combinatorial genetic strategy for exploring complex genotype-phenotype associations in cancer. Nat Genet 2024; 56:371-376. [PMID: 38424461 PMCID: PMC10937382 DOI: 10.1038/s41588-024-01674-1] [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: 04/17/2023] [Accepted: 01/25/2024] [Indexed: 03/02/2024]
Abstract
Available genetically defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Here, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant bladder and prostate cancer models. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.
Collapse
Affiliation(s)
- Shan Li
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alicia Wong
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Huiyun Sun
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Vipul Bhatia
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Gerardo Javier
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sujata Jana
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Qian Wu
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Robert B Montgomery
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jonathan L Wright
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Hung-Ming Lam
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew C Hsieh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA
| | - Bishoy M Faltas
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Michael C Haffner
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - John K Lee
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA.
- Department of Pathology and Laboratory Medicine, University of Washington School of Medicine, Seattle, WA, USA.
| |
Collapse
|
5
|
Franceschini GM, Quaini O, Mizuno K, Orlando F, Ciani Y, Ku SY, Sigouros M, Rothmann E, Alonso A, Benelli M, Nardella C, Auh J, Freeman D, Hanratty B, Adil M, Elemento O, Tagawa ST, Feng FY, Caffo O, Buttigliero C, Basso U, Nelson PS, Corey E, Haffner MC, Attard G, Aparicio A, Demichelis F, Beltran H. Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation. Cancer Discov 2024; 14:424-445. [PMID: 38197680 PMCID: PMC10905672 DOI: 10.1158/2159-8290.cd-23-0754] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/31/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
Abstract
Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with phenotypic subtypes that drive therapy response and outcome differences. Histologic transformation to castration-resistant neuroendocrine prostate cancer (CRPC-NE) is associated with distinct epigenetic alterations, including changes in DNA methylation. The current diagnosis of CRPC-NE is challenging and relies on metastatic biopsy. We developed a targeted DNA methylation assay to detect CRPC-NE using plasma cell-free DNA (cfDNA). The assay quantifies tumor content and provides a phenotype evidence score that captures diverse CRPC phenotypes, leveraging regions to inform transcriptional state. We tested the design in independent clinical cohorts (n = 222 plasma samples) and qualified it achieving an AUC > 0.93 for detecting pathology-confirmed CRPC-NE (n = 136). Methylation-defined cfDNA tumor content was associated with clinical outcomes in two prospective phase II clinical trials geared towards aggressive variant CRPC and CRPC-NE. These data support the application of targeted DNA methylation for CRPC-NE detection and patient stratification. SIGNIFICANCE Neuroendocrine prostate cancer is an aggressive subtype of treatment-resistant prostate cancer. Early detection is important, but the diagnosis currently relies on metastatic biopsy. We describe the development and validation of a plasma cell-free DNA targeted methylation panel that can quantify tumor fraction and identify patients with neuroendocrine prostate cancer noninvasively. This article is featured in Selected Articles from This Issue, p. 384.
Collapse
Affiliation(s)
- Gian Marco Franceschini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Orsetta Quaini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Kei Mizuno
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Francesco Orlando
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sheng-Yu Ku
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael Sigouros
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Emily Rothmann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alicia Alonso
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | | | - Caterina Nardella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Joonghoon Auh
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brian Hanratty
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mohamed Adil
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Olivier Elemento
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Scott T. Tagawa
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Felix Y. Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Orazio Caffo
- Department of Medical Oncology, Santa Chiara Hospital, Trento, Italy
| | - Consuelo Buttigliero
- Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Turin, Italy
| | - Umberto Basso
- Department of Oncology, Istituto Oncologico Veneto IOV - IRCCS, Padua, Italy
| | | | - Eva Corey
- University of Washington, Seattle, Washington
| | - Michael C. Haffner
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- University of Washington, Seattle, Washington
| | - Gerhardt Attard
- Cancer Institute and University College London Hospitals, University College London, London, United Kingdom
| | - Ana Aparicio
- Department of GU Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| |
Collapse
|
6
|
Mandl A, Jasmine S, Krueger T, Kumar R, Coleman IM, Dalrymple SL, Antony L, Rosen DM, Jing Y, Hanratty B, Patel RA, Jin-Yih L, Dias J, Celatka CA, Tapper AE, Kleppe M, Kanayama M, Speranzini V, Wang YZ, Luo J, Corey E, Sena LA, Casero RA, Lotan T, Trock BJ, Kachhap SK, Denmeade SR, Carducci MA, Mattevi A, Haffner MC, Nelson PS, Rienhoff HY, Isaacs JT, Brennen WN. LSD1 inhibition suppresses ASCL1 and de-represses YAP1 to drive potent activity against neuroendocrine prostate cancer. bioRxiv 2024:2024.01.17.576106. [PMID: 38328141 PMCID: PMC10849473 DOI: 10.1101/2024.01.17.576106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Lysine-specific demethylase 1 (LSD1 or KDM1A ) has emerged as a critical mediator of tumor progression in metastatic castration-resistant prostate cancer (mCRPC). Among mCRPC subtypes, neuroendocrine prostate cancer (NEPC) is an exceptionally aggressive variant driven by lineage plasticity, an adaptive resistance mechanism to androgen receptor axis-targeted therapies. Our study shows that LSD1 expression is elevated in NEPC and associated with unfavorable clinical outcomes. Using genetic approaches, we validated the on-target effects of LSD1 inhibition across various models. We investigated the therapeutic potential of bomedemstat, an orally bioavailable, irreversible LSD1 inhibitor with low nanomolar potency. Our findings demonstrate potent antitumor activity against CRPC models, including tumor regressions in NEPC patient-derived xenografts. Mechanistically, our study uncovers that LSD1 inhibition suppresses the neuronal transcriptional program by downregulating ASCL1 through disrupting LSD1:INSM1 interactions and de-repressing YAP1 silencing. Our data support the clinical development of LSD1 inhibitors for treating CRPC - especially the aggressive NE phenotype. Statement of Significance Neuroendocrine prostate cancer presents a clinical challenge due to the lack of effective treatments. Our research demonstrates that bomedemstat, a potent and selective LSD1 inhibitor, effectively combats neuroendocrine prostate cancer by downregulating the ASCL1- dependent NE transcriptional program and re-expressing YAP1.
Collapse
|
7
|
Dairo O, DePaula Oliveira L, Schaffer E, Vidotto T, Mendes AA, Lu J, Huynh SV, Hicks J, Sowalsky AG, De Marzo AM, Joshu CE, Hanratty B, Sfanos KS, Isaacs WB, Haffner MC, Lotan TL. FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer. Cancer Res Commun 2024; 4:152-163. [PMID: 38112617 PMCID: PMC10795515 DOI: 10.1158/2767-9764.crc-23-0248] [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: 05/31/2023] [Revised: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Fatty acid synthase (FASN) catalyzes the synthesis of long-chain saturated fatty acids and is overexpressed during prostatic tumorigenesis, where it is the therapeutic target in several ongoing trials. However, the mechanism of FASN upregulation in prostate cancer remains unclear. Here, we examine FASN gene CpG methylation pattern by InfiniumEPIC profiling and whole-genome bisulfite sequencing across multiple racially diverse primary and metastatic prostate cancer cohorts, comparing with FASN protein expression as measured by digitally quantified IHC assay and reverse phase protein array analysis or FASN gene expression. We demonstrate that the FASN gene body is hypomethylated and overexpressed in primary prostate tumors compared with benign tissue, and FASN gene methylation is significantly inversely correlated with FASN protein or gene expression in both primary and metastatic prostate cancer. Primary prostate tumors with ERG gene rearrangement have increased FASN expression and we find evidence of FASN hypomethylation in this context. FASN expression is also significantly increased in prostate tumors from carriers of the germline HOXB13 G84E mutation compared with matched controls, consistent with a report that HOXB13 may contribute to epigenetic regulation of FASN in vitro. However, in contrast to previous studies, we find no significant association of FASN expression or methylation with self-identified race in models that include ERG status across two independent primary tumor cohorts. Taken together, these data support a potential epigenetic mechanism for FASN regulation in the prostate which may be relevant for selecting patients responsive to FASN inhibitors. SIGNIFICANCE Here, we leverage multiple independent primary and metastatic prostate cancer cohorts to demonstrate that FASN gene body methylation is highly inversely correlated with FASN gene and protein expression. This finding may shed light on epigenetic mechanisms of FASN regulation in prostate cancer and provides a potentially useful biomarker for selecting patients in future trials of FASN inhibitors.
Collapse
Affiliation(s)
- Oluwademilade Dairo
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Ethan Schaffer
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Thiago Vidotto
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Adrianna A. Mendes
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jiayun Lu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sophie Vo Huynh
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jessica Hicks
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Adam G. Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, NCI, Bethesda, Maryland
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Corrine E. Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Brian Hanratty
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Karen S. Sfanos
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - William B. Isaacs
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland
| |
Collapse
|
8
|
Patel RA, Sayar E, Coleman I, Roudier MP, Hanratty B, Low JY, Jaiswal N, Ajkunic A, Dumpit R, Ercan C, Salama N, O’Brien VP, Isaacs WB, Epstein JI, De Marzo AM, Trock BJ, Luo J, Brennen WN, Tretiakova M, Vakar-Lopez F, True LD, Goodrich DW, Corey E, Morrissey C, Nelson PS, Hurley PJ, Gulati R, Haffner MC. Characterization of HOXB13 expression patterns in localized and metastatic castration-resistant prostate cancer. J Pathol 2024; 262:105-120. [PMID: 37850574 PMCID: PMC10871027 DOI: 10.1002/path.6216] [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: 05/12/2023] [Revised: 08/16/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023]
Abstract
HOXB13 is a key lineage homeobox transcription factor that plays a critical role in the differentiation of the prostate gland. Several studies have suggested that HOXB13 alterations may be involved in prostate cancer development and progression. Despite its potential biological relevance, little is known about the expression of HOXB13 across the disease spectrum of prostate cancer. To this end, we validated a HOXB13 antibody using genetic controls and investigated HOXB13 protein expression in murine and human developing prostates, localized prostate cancers, and metastatic castration-resistant prostate cancers. We observed that HOXB13 expression increases during later stages of murine prostate development. All localized prostate cancers showed HOXB13 protein expression. Interestingly, lower HOXB13 expression levels were observed in higher-grade tumors, although no significant association between HOXB13 expression and recurrence or disease-specific survival was found. In advanced metastatic prostate cancers, HOXB13 expression was retained in the majority of tumors. While we observed lower levels of HOXB13 protein and mRNA levels in tumors with evidence of lineage plasticity, 84% of androgen receptor-negative castration-resistant prostate cancers and neuroendocrine prostate cancers (NEPCs) retained detectable levels of HOXB13. Notably, the reduced expression observed in NEPCs was associated with a gain of HOXB13 gene body CpG methylation. In comparison to the commonly used prostate lineage marker NKX3.1, HOXB13 showed greater sensitivity in detecting advanced metastatic prostate cancers. Additionally, in a cohort of 837 patients, 383 with prostatic and 454 with non-prostatic tumors, we found that HOXB13 immunohistochemistry had a 97% sensitivity and 99% specificity for prostatic origin. Taken together, our studies provide valuable insight into the expression pattern of HOXB13 during prostate development and cancer progression. Furthermore, our findings support the utility of HOXB13 as a diagnostic biomarker for prostate cancer, particularly to confirm the prostatic origin of advanced metastatic castration-resistant tumors. © 2023 The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Neha Jaiswal
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Azra Ajkunic
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ruth Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Caner Ercan
- Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Nina Salama
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Valerie P. O’Brien
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - William B. Isaacs
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Jonathan I. Epstein
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Pathology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Angelo M. De Marzo
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Pathology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Bruce J. Trock
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Jun Luo
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - W Nathaniel Brennen
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Maria Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Funda Vakar-Lopez
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - David W. Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paula J. Hurley
- Departments of Medicine and Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| |
Collapse
|
9
|
Ajkunic A, Sayar E, Roudier MP, Patel RA, Coleman IM, De Sarkar N, Hanratty B, Adil M, Zhao J, Zaidi S, True LD, Sperger JM, Cheng HH, Yu EY, Montgomery RB, Hawley JE, Ha G, Lee JK, Harmon SA, Corey E, Lang JM, Sawyers CL, Morrissey C, Schweizer MT, Gulati R, Nelson PS, Haffner MC. ASSESSMENT OF CELL SURFACE TARGETS IN METASTATIC PROSTATE CANCER: EXPRESSION LANDSCAPE AND MOLECULAR CORRELATES. Res Sq 2023:rs.3.rs-3745991. [PMID: 38196594 PMCID: PMC10775381 DOI: 10.21203/rs.3.rs-3745991/v1] [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] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Therapeutic approaches targeting proteins on the surface of cancer cells have emerged as an important strategy for precision oncology. To fully capitalize on the potential impact of drugs targeting surface proteins, detailed knowledge about the expression patterns of the target proteins in tumor tissues is required. In castration-resistant prostate cancer (CRPC), agents targeting prostate-specific membrane antigen (PSMA) have demonstrated clinical activity. However, PSMA expression is lost in a significant number of CRPC tumors, and the identification of additional cell surface targets is necessary in order to develop new therapeutic approaches. Here, we performed a comprehensive analysis of the expression and co-expression patterns of trophoblast cell-surface antigen 2 (TROP2), delta-like ligand 3 (DLL3), and carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) in CRPC samples from a rapid autopsy cohort. We show that DLL3 and CEACAM5 exhibit the highest expression in neuroendocrine prostate cancer (NEPC), while TROP2 is expressed across different CRPC molecular subtypes, except for NEPC. We observed variable intra-tumoral and inter-tumoral heterogeneity and no dominant metastatic site predilections for TROP2, DLL3, and CEACAM5. We further show that AR amplifications were associated with higher expression of PSMA and TROP2 but lower DLL3 and CEACAM5 levels. Conversely, PSMA and TROP2 expression was lower in RB1-altered tumors. In addition to genomic alterations, we demonstrate a tight correlation between epigenetic states, particularly histone H3 lysine 27 methylation (H3K27me3) at the transcriptional start site and gene body of TACSTD2 (encoding TROP2), DLL3, and CEACAM5, and their respective protein expression in CRPC patient-derived xenografts. Collectively, these findings provide novel insights into the patterns and determinants of expression of TROP2, DLL3, and CEACAM5 with important implications for the clinical development of cell surface targeting agents in CRPC.
Collapse
Affiliation(s)
- Azra Ajkunic
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Radhika A Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ilsa M Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
- Department of Pathology, Medical College of Wisconsin, WI, USA
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mohamed Adil
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jimmy Zhao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Heather H Cheng
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Evan Y Yu
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Robert B Montgomery
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jessica E Hawley
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Gavin Ha
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Stephanie A Harmon
- Artificial Intelligence Resource, Molecular Imaging Branch, NCI, NIH, Bethesda, MD, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | | | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Michael T Schweizer
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Roman Gulati
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| |
Collapse
|
10
|
Ghali F, Vakar-Lopez F, Roudier MP, Garcia J, Arora S, Cheng HH, Schweizer MT, Haffner MC, Lee JK, Yu EY, Grivas P, Montgomery B, Hsieh AC, Wright JL, Lam HM. Metastatic Bladder Cancer Expression and Subcellular Localization of Nectin-4 and Trop-2 in Variant Histology: A Rapid Autopsy Study. Clin Genitourin Cancer 2023; 21:669-678. [PMID: 37344281 PMCID: PMC10674028 DOI: 10.1016/j.clgc.2023.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/07/2023] [Revised: 05/18/2023] [Accepted: 05/21/2023] [Indexed: 06/23/2023]
Abstract
BACKGROUND Nectin-4 and Trop-2 are transmembrane targets of FDA-approved antibody-drug conjugates (ADC) Enfortumab-vedotin (EV) and Sacituzumab govitecan (SG), respectively, for the treatment of metastatic urothelial carcinoma (mUC). The expression and role of Nectin-4 and Trop-2 in mUC variant histology is poorly described. MATERIALS AND METHODS We evaluate membranous and cytoplasmic protein expression, and mRNA levels of Nectin-4 and Trop-2 within matched primary and metastatic mUC samples to determine heterogeneity of ADC targets in mUC variants. RESULTS Patients with mUC were consented for rapid autopsy immediately after death. Tissues from matched primary and metastatic lesions were collected. A total of 67 specimens from 20 patients were analyzed: 27 were UC, 17 plasmacytoid (PUC), 18 UC with squamous differentiation (UCSD), and 5 neuroendocrine (NE); 10 from primary and 57 from metastatic sites. All histology except NE expressed moderate-high levels of Nectin-4 and Trop-2 by both immunohistochemistry and RNAseq. Nectin-4 demonstrated prominent cytoplasmic staining in metastatic PUC and UCSD. Trop-2 demonstrated strong cytoplasmic and membrane staining in primary and metastatic tumors. Interestingly, Nectin-4 and Trop-2 expression are positively correlated at both mRNA and protein levels. CONCLUSION UC and non-NE variants express notable level of Nectin-4 and Trop-2 in both primary and metastatic lesions. Membrane staining of Nectin-4 and Trop-2 is present but cytoplasmic staining is a more common event in both mUC and mUC variant histology. These findings support evaluation of EV and SG in heavily treated variant histology BC and urge attention on the clinical relevance of cytoplasmic localization of ADC targets.
Collapse
Affiliation(s)
- Fady Ghali
- Department of Urology, University of Washington School of Medicine, Seattle, WA
| | - Funda Vakar-Lopez
- Department of Pathology, University of Washington School of Medicine, Seattle, WA
| | - Martine P Roudier
- Department of Urology, University of Washington School of Medicine, Seattle, WA
| | - Jose Garcia
- Department of Urology, University of Washington School of Medicine, Seattle, WA
| | - Sonali Arora
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
| | - Heather H Cheng
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Michael T Schweizer
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA; Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Evan Y Yu
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Petros Grivas
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Bruce Montgomery
- Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Andrew C Hsieh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA; Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Jonathan L Wright
- Department of Urology, University of Washington School of Medicine, Seattle, WA; Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA.
| | - Hung-Ming Lam
- Department of Urology, University of Washington School of Medicine, Seattle, WA.
| |
Collapse
|
11
|
Liao SY, Rudoy D, Frank SB, Phan LT, Klezovitch O, Kwan J, Coleman I, Haffner MC, Li D, Nelson PS, Emili A, Vasioukhin V. SND1 binds to ERG and promotes tumor growth in genetic mouse models of prostate cancer. Nat Commun 2023; 14:7435. [PMID: 37973913 PMCID: PMC10654515 DOI: 10.1038/s41467-023-43245-8] [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: 08/21/2022] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
SND1 and MTDH are known to promote cancer and therapy resistance, but their mechanisms and interactions with other oncogenes remain unclear. Here, we show that oncoprotein ERG interacts with SND1/MTDH complex through SND1's Tudor domain. ERG, an ETS-domain transcription factor, is overexpressed in many prostate cancers. Knocking down SND1 in human prostate epithelial cells, especially those overexpressing ERG, negatively impacts cell proliferation. Transcriptional analysis shows substantial overlap in genes regulated by ERG and SND1. Mechanistically, we show that ERG promotes nuclear localization of SND1/MTDH. Forced nuclear localization of SND1 prominently increases its growth promoting function irrespective of ERG expression. In mice, prostate-specific Snd1 deletion reduces cancer growth and tumor burden in a prostate cancer model (PB-Cre/Ptenflox/flox/ERG mice), Moreover, we find a significant overlap between prostate transcriptional signatures of ERG and SND1. These findings highlight SND1's crucial role in prostate tumorigenesis, suggesting SND1 as a potential therapeutic target in prostate cancer.
Collapse
Affiliation(s)
- Sheng-You Liao
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Dmytro Rudoy
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sander B Frank
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Luan T Phan
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Olga Klezovitch
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Julian Kwan
- Center for Network Systems Biology, Departments of Biochemistry & Biology, Boston University, Boston, MA, USA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Dapei Li
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Emili
- Center for Network Systems Biology, Departments of Biochemistry & Biology, Boston University, Boston, MA, USA
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Valeri Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
| |
Collapse
|
12
|
Hawley JE, Obradovic AZ, Dallos MC, Lim EA, Runcie K, Ager CR, McKiernan J, Anderson CB, Decastro GJ, Weintraub J, Virk R, Lowy I, Hu J, Chaimowitz MG, Guo XV, Zhang Y, Haffner MC, Worley J, Stein MN, Califano A, Drake CG. Anti-PD-1 immunotherapy with androgen deprivation therapy induces robust immune infiltration in metastatic castration-sensitive prostate cancer. Cancer Cell 2023; 41:1972-1988.e5. [PMID: 37922910 DOI: 10.1016/j.ccell.2023.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/19/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
When compared to other malignancies, the tumor microenvironment (TME) of primary and castration-resistant prostate cancer (CRPC) is relatively devoid of immune infiltrates. While androgen deprivation therapy (ADT) induces a complex immune infiltrate in localized prostate cancer, the composition of the TME in metastatic castration-sensitive prostate cancer (mCSPC), and the effects of ADT and other treatments in this context are poorly understood. Here, we perform a comprehensive single-cell RNA sequencing (scRNA-seq) profiling of metastatic sites from patients participating in a phase 2 clinical trial (NCT03951831) that evaluated standard-of-care chemo-hormonal therapy combined with anti-PD-1 immunotherapy. We perform a longitudinal, protein activity-based analysis of TME subpopulations, revealing immune subpopulations conserved across multiple metastatic sites. We also observe dynamic changes in these immune subpopulations in response to treatment and a correlation with clinical outcomes. Our study uncovers a therapy-resistant, transcriptionally distinct tumor subpopulation that expands in cell number in treatment-refractory patients.
Collapse
Affiliation(s)
- Jessica E Hawley
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Aleksandar Z Obradovic
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Matthew C Dallos
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Emerson A Lim
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Karie Runcie
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Casey R Ager
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - James McKiernan
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Christopher B Anderson
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Guarionex J Decastro
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Joshua Weintraub
- Department of Interventional Radiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Renu Virk
- Department of Pathology, Columbia University Irving Medical Center, New York, NY, USA
| | - Israel Lowy
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Jianhua Hu
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matthew G Chaimowitz
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Xinzheng V Guo
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ya Zhang
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mark N Stein
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032 USA; Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032 USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032 USA; J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032 USA.
| | - Charles G Drake
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA; Department of Interventional Radiology, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
13
|
Crowell PD, Giafaglione JM, Jones AE, Nunley NM, Hashimoto T, Delcourt AML, Petcherski A, Agrawal R, Bernard MJ, Diaz JA, Heering KY, Huang RR, Low JY, Matulionis N, Navone NM, Ye H, Zoubeidi A, Christofk HR, Rettig MB, Reiter RE, Haffner MC, Boutros PC, Shirihai OS, Divakaruni AS, Goldstein AS. MYC is a regulator of androgen receptor inhibition-induced metabolic requirements in prostate cancer. Cell Rep 2023; 42:113221. [PMID: 37815914 DOI: 10.1016/j.celrep.2023.113221] [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: 02/13/2023] [Revised: 08/17/2023] [Accepted: 09/20/2023] [Indexed: 10/12/2023] Open
Abstract
Advanced prostate cancers are treated with therapies targeting the androgen receptor (AR) signaling pathway. While many tumors initially respond to AR inhibition, nearly all develop resistance. It is critical to understand how prostate tumor cells respond to AR inhibition in order to exploit therapy-induced phenotypes prior to the outgrowth of treatment-resistant disease. Here, we comprehensively characterize the effects of AR blockade on prostate cancer metabolism using transcriptomics, metabolomics, and bioenergetics approaches. The metabolic response to AR inhibition is defined by reduced glycolysis, robust elongation of mitochondria, and increased reliance on mitochondrial oxidative metabolism. We establish DRP1 activity and MYC signaling as mediators of AR-blockade-induced metabolic phenotypes. Rescuing DRP1 phosphorylation after AR inhibition restores mitochondrial fission, while rescuing MYC restores glycolytic activity and prevents sensitivity to complex I inhibition. Our study provides insight into the regulation of treatment-induced metabolic phenotypes and vulnerabilities in prostate cancer.
Collapse
Affiliation(s)
- Preston D Crowell
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jenna M Giafaglione
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas M Nunley
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Takao Hashimoto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amelie M L Delcourt
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anton Petcherski
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Raag Agrawal
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew J Bernard
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Johnny A Diaz
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kylie Y Heering
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rong Rong Huang
- Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nedas Matulionis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nora M Navone
- Department of GU Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huihui Ye
- Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amina Zoubeidi
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Heather R Christofk
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew B Rettig
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert E Reiter
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Paul C Boutros
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Orian S Shirihai
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of Endocrinology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Clinical Biochemistry, School of Medicine, Ben Gurion University of The Negev, Beer-Sheva, Israel
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew S Goldstein
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
14
|
Duplaquet L, Li Y, Booker MA, Xie Y, Olsen SN, Patel RA, Hong D, Hatton C, Denize T, Walton E, Laimon YN, Li R, Jiang Y, Bronson RT, Southard J, Li S, Signoretti S, Qiu X, Cejas P, Armstrong SA, Long HW, Tolstorukov MY, Haffner MC, Oser MG. KDM6A epigenetically regulates subtype plasticity in small cell lung cancer. Nat Cell Biol 2023; 25:1346-1358. [PMID: 37591951 PMCID: PMC10546329 DOI: 10.1038/s41556-023-01210-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 07/26/2022] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Small cell lung cancer (SCLC) exists broadly in four molecular subtypes: ASCL1, NEUROD1, POU2F3 and Inflammatory. Initially, SCLC subtypes were thought to be mutually exclusive, but recent evidence shows intra-tumoural subtype heterogeneity and plasticity between subtypes. Here, using a CRISPR-based autochthonous SCLC genetically engineered mouse model to study the consequences of KDM6A/UTX inactivation, we show that KDM6A inactivation induced plasticity from ASCL1 to NEUROD1 resulting in SCLC tumours that express both ASCL1 and NEUROD1. Mechanistically, KDM6A normally maintains an active chromatin state that favours the ASCL1 subtype with its loss decreasing H3K4me1 and increasing H3K27me3 at enhancers of neuroendocrine genes leading to a cell state that is primed for ASCL1-to-NEUROD1 subtype switching. This work identifies KDM6A as an epigenetic regulator that controls ASCL1 to NEUROD1 subtype plasticity and provides an autochthonous SCLC genetically engineered mouse model to model ASCL1 and NEUROD1 subtype heterogeneity and plasticity, which is found in 35-40% of human SCLCs.
Collapse
Affiliation(s)
- Leslie Duplaquet
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yixiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew A Booker
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Naomi Olsen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Radhika A Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Deli Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Walton
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yasmin N Laimon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roderick T Bronson
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Jackson Southard
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA, USA.
| |
Collapse
|
15
|
Nyquist MD, Coleman IM, Lucas JM, Li D, Hanratty B, Meade H, Mostaghel EA, Plymate SR, Corey E, Haffner MC, Nelson PS. Supraphysiological Androgens Promote the Tumor Suppressive Activity of the Androgen Receptor through cMYC Repression and Recruitment of the DREAM Complex. Cancer Res 2023; 83:2938-2951. [PMID: 37352376 PMCID: PMC10472100 DOI: 10.1158/0008-5472.can-22-2613] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/24/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
The androgen receptor (AR) pathway regulates key cell survival programs in prostate epithelium. The AR represents a near-universal driver and therapeutic vulnerability in metastatic prostate cancer, and targeting AR has a remarkable therapeutic index. Though most approaches directed toward AR focus on inhibiting AR signaling, laboratory and now clinical data have shown that high dose, supraphysiological androgen treatment (SPA) results in growth repression and improved outcomes in subsets of patients with prostate cancer. A better understanding of the mechanisms contributing to SPA response and resistance could help guide patient selection and combination therapies to improve efficacy. To characterize SPA signaling, we integrated metrics of gene expression changes induced by SPA together with cistrome data and protein-interactomes. These analyses indicated that the dimerization partner, RB-like, E2F, and multivulval class B (DREAM) complex mediates growth repression and downregulation of E2F targets in response to SPA. Notably, prostate cancers with complete genomic loss of RB1 responded to SPA treatment, whereas loss of DREAM complex components such as RBL1/2 promoted resistance. Overexpression of MYC resulted in complete resistance to SPA and attenuated the SPA/AR-mediated repression of E2F target genes. These findings support a model of SPA-mediated growth repression that relies on the negative regulation of MYC by AR leading to repression of E2F1 signaling via the DREAM complex. The integrity of MYC signaling and DREAM complex assembly may consequently serve as determinants of SPA responses and as pathways mediating SPA resistance. SIGNIFICANCE Determining the molecular pathways by which supraphysiological androgens promote growth arrest and treatment responses in prostate cancer provides opportunities for biomarker-selected clinical trials and the development of strategies to augment responses.
Collapse
Affiliation(s)
- Michael D. Nyquist
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ilsa M. Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jared M. Lucas
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Dapei Li
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Brian Hanratty
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Hannah Meade
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Elahe A. Mostaghel
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, Washington
| | - Stephen R. Plymate
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
| |
Collapse
|
16
|
Tolkach Y, Ovtcharov V, Pryalukhin A, Eich ML, Gaisa NT, Braun M, Radzhabov A, Quaas A, Hammerer P, Dellmann A, Hulla W, Haffner MC, Reis H, Fahoum I, Samarska I, Borbat A, Pham H, Heidenreich A, Klein S, Netto G, Caie P, Buettner R. An international multi-institutional validation study of the algorithm for prostate cancer detection and Gleason grading. NPJ Precis Oncol 2023; 7:77. [PMID: 37582946 PMCID: PMC10427608 DOI: 10.1038/s41698-023-00424-6] [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: 02/14/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
Pathologic examination of prostate biopsies is time consuming due to the large number of slides per case. In this retrospective study, we validate a deep learning-based classifier for prostate cancer (PCA) detection and Gleason grading (AI tool) in biopsy samples. Five external cohorts of patients with multifocal prostate biopsy were analyzed from high-volume pathology institutes. A total of 5922 H&E sections representing 7473 biopsy cores from 423 patient cases (digitized using three scanners) were assessed concerning tumor detection. Two tumor-bearing datasets (core n = 227 and 159) were graded by an international group of pathologists including expert urologic pathologists (n = 11) to validate the Gleason grading classifier. The sensitivity, specificity, and NPV for the detection of tumor-bearing biopsies was in a range of 0.971-1.000, 0.875-0.976, and 0.988-1.000, respectively, across the different test cohorts. In several biopsy slides tumor tissue was correctly detected by the AI tool that was initially missed by pathologists. Most false positive misclassifications represented lesions suspicious for carcinoma or cancer mimickers. The quadratically weighted kappa levels for Gleason grading agreement for single pathologists was 0.62-0.80 (0.77 for AI tool) and 0.64-0.76 (0.72 for AI tool) for the two grading datasets, respectively. In cases where consensus for grading was reached among pathologists, kappa levels for AI tool were 0.903 and 0.855. The PCA detection classifier showed high accuracy for PCA detection in biopsy cases during external validation, independent of the institute and scanner used. High levels of agreement for Gleason grading were indistinguishable between experienced genitourinary pathologists and the AI tool.
Collapse
Affiliation(s)
- Yuri Tolkach
- Institute of Pathology, University Hospital Cologne, Cologne, Germany.
| | | | - Alexey Pryalukhin
- Institute of Pathology, Landesklinikum Wiener Neustadt, Wiener Neustadt, Austria
| | - Marie-Lisa Eich
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Martin Braun
- Institute of Pathology Troisdorf, Troisdorf, Germany
| | | | - Alexander Quaas
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Peter Hammerer
- Urology Clinic, Municipal Clinic of Brunswick, Brunswick, Germany
| | - Ansgar Dellmann
- Institute of Pathology, Municipal Clinic of Brunswick, Brunswick, Germany
| | - Wolfgang Hulla
- Institute of Pathology, Landesklinikum Wiener Neustadt, Wiener Neustadt, Austria
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Henning Reis
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ibrahim Fahoum
- Department of Pathology, Sourasky Medical Center, Tel Aviv, Israel
| | - Iryna Samarska
- Department of Pathology, University Hospital Maastricht, Maastricht, The Netherlands
| | - Artem Borbat
- Department of Pathology, Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - Hoa Pham
- Department of Pathology, Bach Mai Hospital, Hanoi, Vietnam
- Department of Pathology, University of Nagasaki, Nagasaki, Japan
| | - Axel Heidenreich
- Clinic of Urology, University Hospital Cologne, Cologne, Germany
| | - Sebastian Klein
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - George Netto
- Department of Pathology, University of Alabama, Birmingham, AL, USA
| | | | - Reinhard Buettner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| |
Collapse
|
17
|
Quintanal-Villalonga A, Durani V, Sabet A, Redin E, Kawasaki K, Shafer M, Karthaus WR, Zaidi S, Zhan YA, Manoj P, Sridhar H, Shah NS, Chow A, Bhanot UK, Linkov I, Asher M, Yu HA, Qiu J, de Stanchina E, Patel RA, Morrissey C, Haffner MC, Koche RP, Sawyers CL, Rudin CM. Exportin 1 inhibition prevents neuroendocrine transformation through SOX2 down-regulation in lung and prostate cancers. Sci Transl Med 2023; 15:eadf7006. [PMID: 37531417 PMCID: PMC10777207 DOI: 10.1126/scitranslmed.adf7006] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/12/2023] [Indexed: 08/04/2023]
Abstract
In lung and prostate adenocarcinomas, neuroendocrine (NE) transformation to an aggressive derivative resembling small cell lung cancer (SCLC) is associated with poor prognosis. We previously described dependency of SCLC on the nuclear transporter exportin 1. Here, we explored the role of exportin 1 in NE transformation. We observed up-regulated exportin 1 in lung and prostate pretransformation adenocarcinomas. Exportin 1 was up-regulated after genetic inactivation of TP53 and RB1 in lung and prostate adenocarcinoma cell lines, accompanied by increased sensitivity to the exportin 1 inhibitor selinexor in vitro. Exportin 1 inhibition prevented NE transformation in different TP53/RB1-inactivated prostate adenocarcinoma xenograft models that acquire NE features upon treatment with the aromatase inhibitor enzalutamide and extended response to the EGFR inhibitor osimertinib in a lung cancer transformation patient-derived xenograft (PDX) model exhibiting combined adenocarcinoma/SCLC histology. Ectopic SOX2 expression restored the enzalutamide-promoted NE phenotype on adenocarcinoma-to-NE transformation xenograft models despite selinexor treatment. Selinexor sensitized NE-transformed lung and prostate small cell carcinoma PDXs to standard cytotoxics. Together, these data nominate exportin 1 inhibition as a potential therapeutic target to constrain lineage plasticity and prevent or treat NE transformation in lung and prostate adenocarcinoma.
Collapse
Affiliation(s)
- Alvaro Quintanal-Villalonga
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vidushi Durani
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amin Sabet
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Esther Redin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kenta Kawasaki
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Moniquetta Shafer
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wouter R. Karthaus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yingqian A. Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Parvathy Manoj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harsha Sridhar
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nisargbhai S. Shah
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew Chow
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Umesh K. Bhanot
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Irina Linkov
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marina Asher
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Helena A. Yu
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Juan Qiu
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Radhika A. Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 19024, USA
| | - Colm Morrissey
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 19024, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charles L. Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charles M. Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| |
Collapse
|
18
|
Jana S, Brahma S, Arora S, Wladyka CL, Hoang P, Blinka S, Hough R, Horn JL, Liu Y, Wang LJ, Depeille P, Smith E, Montgomery RB, Lee JK, Haffner MC, Vakar-Lopez F, Grivas P, Wright JL, Lam HM, Black PC, Roose JP, Ryazanov AG, Subramaniam AR, Henikoff S, Hsieh AC. Transcriptional-translational conflict is a barrier to cellular transformation and cancer progression. Cancer Cell 2023; 41:853-870.e13. [PMID: 37084735 PMCID: PMC10208629 DOI: 10.1016/j.ccell.2023.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/31/2023] [Accepted: 03/24/2023] [Indexed: 04/23/2023]
Abstract
We uncover a tumor-suppressive process in urothelium called transcriptional-translational conflict caused by deregulation of the central chromatin remodeling component ARID1A. Loss of Arid1a triggers an increase in a nexus of pro-proliferation transcripts, but a simultaneous inhibition of the eukaryotic elongation factor 2 (eEF2), which results in tumor suppression. Resolution of this conflict through enhancing translation elongation speed enables the efficient and precise synthesis of a network of poised mRNAs resulting in uncontrolled proliferation, clonogenic growth, and bladder cancer progression. We observe a similar phenomenon in patients with ARID1A-low tumors, which also exhibit increased translation elongation activity through eEF2. These findings have important clinical implications because ARID1A-deficient, but not ARID1A-proficient, tumors are sensitive to pharmacologic inhibition of protein synthesis. These discoveries reveal an oncogenic stress created by transcriptional-translational conflict and provide a unified gene expression model that unveils the importance of the crosstalk between transcription and translation in promoting cancer.
Collapse
Affiliation(s)
- Sujata Jana
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sandipan Brahma
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Cynthia L Wladyka
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Patrick Hoang
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Steven Blinka
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rowan Hough
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jessie L Horn
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yuzhen Liu
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Li-Jie Wang
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Philippe Depeille
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eric Smith
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - John K Lee
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Michael C Haffner
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Funda Vakar-Lopez
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Petros Grivas
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jonathan L Wright
- Department of Urology, University of Washington, Seattle, WA 98915, USA
| | - Hung-Ming Lam
- Department of Urology, University of Washington, Seattle, WA 98915, USA
| | - Peter C Black
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexey G Ryazanov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | | | - Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew C Hsieh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA; Genome Sciences, University of Washington, Seattle, WA 98915, USA.
| |
Collapse
|
19
|
Graham LS, Haffner MC, Sayar E, Gawne A, Schweizer MT, Pritchard CC, Coleman I, Nelson PS, Yu EY. Clinical, pathologic, and molecular features of amphicrine prostate cancer. Prostate 2023; 83:641-648. [PMID: 36779357 PMCID: PMC11023623 DOI: 10.1002/pros.24497] [Citation(s) in RCA: 2] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/13/2022] [Accepted: 01/23/2023] [Indexed: 02/14/2023]
Abstract
BACKGROUND Amphicrine prostate carcinoma (AMPC) is a poorly defined subset of prostate cancer in which cells co-express luminal prostate epithelial and neuroendocrine markers. The optimal treatment strategy is unknown. We sought to further characterize the clinical, histomorphologic, and molecular characteristics of AMPC and to identify areas of potential future treatment investigations. METHODS We retrospectively identified 17 cases of AMPC at a single institution, defined as synaptophysin expression in >70% of cells and co-expression of androgen receptor (AR) signaling markers (either AR, PSA, or NKX3.1) in >50% of cells. Clinical and histologic features of AMPC cases as well as response to treatment and clinical outcomes were described. RESULTS Five AMPC cases arose de novo in the absence of prior systemic treatment and behaved distinctly from cases that were treatment-emergent. In these de novo cases, despite expression of neuroendocrine markers, prognosis appeared more favorable than high-grade neuroendocrine carcinoma, with two (40%) patients with de novo metastatic disease, universal response to androgen deprivation therapy, and no deaths at a median follow-up of 12.3 months. Treatment-emergent AMPC arose a median of 41.1 months after androgen deprivation therapy initiation and was associated with poor response to therapy. CONCLUSIONS We show that amphicrine prostate cancer is a unique entity and differs in clinical and molecular features from high-grade neuroendocrine carcinomas of the prostate. Our study highlights the need to recognize AMPC as a unique molecularly defined subgroup of prostate cancer.
Collapse
Affiliation(s)
- Laura S. Graham
- Division of Medical Oncology, Department of Internal Medicine, University of Colorado, Aurora, CO
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Erolcan Sayar
- Divisions of Human Biology and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Agnes Gawne
- Divisions of Human Biology and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Michael T. Schweizer
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA
| | - Evan Y. Yu
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| |
Collapse
|
20
|
Li S, Wong A, Sun H, Bhatia V, Javier G, Jana S, Montgomery RB, Wright JL, Lam HM, Hsieh AC, Faltas BM, Haffner MC, Lee JK. Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations. bioRxiv 2023:2023.04.12.536652. [PMID: 37609344 PMCID: PMC10441433 DOI: 10.1101/2023.04.12.536652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Available genetically-defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Herein, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant bladder and prostate cancer models. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.
Collapse
|
21
|
Bhatia V, Kamat NV, Pariva TE, Wu LT, Tsao A, Sasaki K, Sun H, Javier G, Nutt S, Coleman I, Hitchcock L, Zhang A, Rudoy D, Gulati R, Patel RA, Roudier MP, True LD, Srivastava S, Morrissey CM, Haffner MC, Nelson PS, Priceman SJ, Ishihara J, Lee JK. Targeting advanced prostate cancer with STEAP1 chimeric antigen receptor T cell and tumor-localized IL-12 immunotherapy. Nat Commun 2023; 14:2041. [PMID: 37041154 PMCID: PMC10090190 DOI: 10.1038/s41467-023-37874-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/04/2023] [Indexed: 04/13/2023] Open
Abstract
Six transmembrane epithelial antigen of the prostate 1 (STEAP1) is a cell surface antigen for therapeutic targeting in prostate cancer. Here, we report broad expression of STEAP1 relative to prostate-specific membrane antigen (PSMA) in lethal metastatic prostate cancers and the development of a STEAP1-directed chimeric antigen receptor (CAR) T cell therapy. STEAP1 CAR T cells demonstrate reactivity in low antigen density, antitumor activity across metastatic prostate cancer models, and safety in a human STEAP1 knock-in mouse model. STEAP1 antigen escape is a recurrent mechanism of treatment resistance and is associated with diminished tumor antigen processing and presentation. The application of tumor-localized interleukin-12 (IL-12) therapy in the form of a collagen binding domain (CBD)-IL-12 fusion protein combined with STEAP1 CAR T cell therapy enhances antitumor efficacy by remodeling the immunologically cold tumor microenvironment of prostate cancer and combating STEAP1 antigen escape through the engagement of host immunity and epitope spreading.
Collapse
Affiliation(s)
- Vipul Bhatia
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Nikhil V Kamat
- Division of Medical Oncology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - Tiffany E Pariva
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Li-Ting Wu
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Annabelle Tsao
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Koichi Sasaki
- Department of Bioengineering, Imperial College London, 86 Wood Lane, London, W12 0BZ, UK
| | - Huiyun Sun
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Gerardo Javier
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Sam Nutt
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Ilsa Coleman
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Lauren Hitchcock
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Ailin Zhang
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Dmytro Rudoy
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Roman Gulati
- Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Radhika A Patel
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Martine P Roudier
- Department of Urology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - Lawrence D True
- Department of Pathology and Laboratory Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - Shivani Srivastava
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Colm M Morrissey
- Department of Urology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - Michael C Haffner
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Pathology and Laboratory Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Peter S Nelson
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Division of Medical Oncology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Urology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Department of Pathology and Laboratory Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Saul J Priceman
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
- Department of Immuno-Oncology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Jun Ishihara
- Department of Bioengineering, Imperial College London, 86 Wood Lane, London, W12 0BZ, UK.
| | - John K Lee
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
- Division of Medical Oncology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- Department of Pathology and Laboratory Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
| |
Collapse
|
22
|
Sayar E, Patel RA, Coleman IM, Roudier MP, Zhang A, Mustafi P, Low JY, Hanratty B, Ang LS, Bhatia V, Adil M, Bakbak H, Quigley DA, Schweizer MT, Hawley JE, Kollath L, True LD, Feng FY, Bander NH, Corey E, Lee JK, Morrissey C, Gulati R, Nelson PS, Haffner MC. Reversible epigenetic alterations mediate PSMA expression heterogeneity in advanced metastatic prostate cancer. JCI Insight 2023; 8:e162907. [PMID: 36821396 PMCID: PMC10132157 DOI: 10.1172/jci.insight.162907] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 06/21/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Prostate-specific membrane antigen (PSMA) is an important cell surface target in prostate cancer. There are limited data on the heterogeneity of PSMA tissue expression in metastatic castration-resistant prostate cancer (mCRPC). Furthermore, the mechanisms regulating PSMA expression (encoded by the FOLH1 gene) are not well understood. Here, we demonstrate that PSMA expression is heterogeneous across different metastatic sites and molecular subtypes of mCRPC. In a rapid autopsy cohort in which multiple metastatic sites per patient were sampled, we found that 13 of 52 (25%) cases had no detectable PSMA and 23 of 52 (44%) cases showed heterogeneous PSMA expression across individual metastases, with 33 (63%) cases harboring at least 1 PSMA-negative site. PSMA-negative tumors displayed distinct transcriptional profiles with expression of druggable targets such as MUC1. Loss of PSMA was associated with epigenetic changes of the FOLH1 locus, including gain of CpG methylation and loss of histone 3 lysine 27 (H3K27) acetylation. Treatment with histone deacetylase (HDAC) inhibitors reversed this epigenetic repression and restored PSMA expression in vitro and in vivo. Collectively, these data provide insights into the expression patterns and regulation of PSMA in mCRPC and suggest that epigenetic therapies - in particular, HDAC inhibitors - can be used to augment PSMA levels.
Collapse
Affiliation(s)
- Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Ilsa M. Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Martine P. Roudier
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
| | - Ailin Zhang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Pallabi Mustafi
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lisa S. Ang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Vipul Bhatia
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Mohamed Adil
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Hasim Bakbak
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David A. Quigley
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Michael T. Schweizer
- Division of Medical Oncology, Department of Medicine, UW, Seattle, Washington, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jessica E. Hawley
- Division of Medical Oncology, Department of Medicine, UW, Seattle, Washington, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lori Kollath
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, UW, Seattle, Washington, USA
| | - Felix Y. Feng
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Neil H. Bander
- Department of Urology, Weill Cornell Medicine, New York, New York, USA
| | - Eva Corey
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
| | - John K. Lee
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Urology, Weill Cornell Medicine, New York, New York, USA
| | - Colm Morrissey
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
- Division of Medical Oncology, Department of Medicine, UW, Seattle, Washington, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, UW, Seattle, Washington, USA
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, UW, Seattle, Washington, USA
| |
Collapse
|
23
|
Duplaquet L, Li Y, Booker MA, Xie Y, Patel RA, Hong D, Denize T, Walton E, Laimon YN, Bronson R, Southard J, Li S, Signoretti S, Tolstorukov MY, Cejas P, Long HW, Haffner MC, Oser MG. Abstract 5774: Small cell lung cancer subtype plasticity is regulated by KDM6A. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5774] [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
Small cell lung cancer (SCLC) is a high-grade neuroendocrine cancer that accounts for ~15% of lung cancers. While nearly all SCLCs are genetically driven by near universal loss of function (LOF) mutations in RB1 and TP53; several recent studies show that there are different phenotypic SCLC molecular subtypes characterized by expression of lineage transcription factors. These include the neuroendocrine ASCL1 and NEUROD1 subtypes which together comprise ~70-80% of SCLCs. Initially subtypes were thought to be mutually exclusive, but recent evidence shows intra-tumoral subtype heterogeneity and plasticity between subtypes. A recent study found that 35-40% of human SCLCs express both ASCL1 and NEUROD1, but the mechanisms driving ASCL1 and NEUROD1 intra-tumoral heterogeneity are not well understood. My laboratory previously developed an autochthonous CRISPR-based SCLC genetically-engineered mouse model (GEMM) generated by intratracheally injecting adenoviruses encoding Cre recombinase and sgRNAs targeting Rb1, Trp53, and Rbl2. Cre turns on Cas9 expression and allows for CRISPR/Cas9 editing of Rb1, Trp53, and Rbl2 in somatic cells in the lungs. The unique advantage of this model is that it allows the inclusion of sgRNAs targeting additional genes of interest in the same adenovirus. Using this CRISPR-based autochthonous SCLC GEMM approach, we studied the consequences of inactivating the epigenetic modifier KDM6A during SCLC tumorigenesis. KDM6A functions as an H3K27 histone demethylase and also exists in the COMPASS complex with KMT2C/D to promote H3K4 mono-/di-methylation at enhancers. KDM6A along with its protein binding partner KMT2D are mutated in SCLC and KDM6A has been implicated in controlling differentiation in other lineages. Strikingly, we found that KDM6A inactivation in SCLC GEMMs induced plasticity from ASCL1 to NEUROD1 resulting in SCLC tumors that expressed both ASCL1 and NEUROD1. ATAC-sequencing showed open chromatin at the promoters of NEUROD1 and NEUROD1 target genes in KDM6A inactivated tumors. Interestingly, KDM6A inactivated tumors showed a spectrum of ASCL1 to NEUROD1 heterogeneity where some KDM6A inactivated tumors completely lost ASCL1 and solely expressed NEUROD1, some tumors expressed ASCL1 and NEUROD1 in a mutually exclusive manner, while others primarily expressed ASCL1 with very few NEUROD1 positive cells. Mechanistically, KDM6A binds and maintains ASCL1 target genes in an active chromatin state with its loss increasing H3K27me3 near both promoters and enhancers, and decreasing H3K4me1/2 at enhancers together leading to a cell state primed for ASCL1 to NEUROD1 subtype switching. This work identifies KDM6A as an epigenetic regulator that controls ASCL1 to NEUROD1 subtype plasticity and provides an autochthonous SCLC GEMM to model ASCL1 and NEUROD1 subtype heterogeneity, which is found in 35-40% of human SCLCs.
Citation Format: Leslie Duplaquet, Yixiang Li, Matthew A. Booker, Yingtian Xie, Radhika A. Patel, Deli Hong, Thomas Denize, Emily Walton, Yasmin N. Laimon, Roderick Bronson, Jackson Southard, Shuqiang Li, Sabina Signoretti, Michael Y. Tolstorukov, Paloma Cejas, Henry W. Long, Michael C. Haffner, Matthew G. Oser. Small cell lung cancer subtype plasticity is regulated by KDM6A. [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 5774.
Collapse
Affiliation(s)
| | - Yixiang Li
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | - Deli Hong
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Yamamoto A, Huang Y, Krajina BA, McBirney M, Doak AE, Qu S, Wang CL, Haffner MC, Cheung KJ. Metastasis from the tumor interior and necrotic core formation are regulated by breast cancer-derived angiopoietin-like 7. Proc Natl Acad Sci U S A 2023; 120:e2214888120. [PMID: 36853945 PMCID: PMC10013750 DOI: 10.1073/pnas.2214888120] [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: 08/31/2022] [Accepted: 01/06/2023] [Indexed: 03/01/2023] Open
Abstract
Necrosis in the tumor interior is a common feature of aggressive cancers that is associated with poor clinical prognosis and the development of metastasis. How the necrotic core promotes metastasis remains unclear. Here, we report that emergence of necrosis inside the tumor is correlated temporally with increased tumor dissemination in a rat breast cancer model and in human breast cancer patients. By performing spatially focused transcriptional profiling, we identified angiopoietin-like 7 (Angptl7) as a tumor-specific factor localized to the perinecrotic zone. Functional studies showed that Angptl7 loss normalizes central necrosis, perinecrotic dilated vessels, metastasis, and reduces circulating tumor cell counts to nearly zero. Mechanistically, Angptl7 promotes vascular permeability and supports vascular remodeling in the perinecrotic zone. Taken together, these findings show that breast tumors actively produce factors controlling central necrosis formation and metastatic dissemination from the tumor core.
Collapse
Affiliation(s)
- Ami Yamamoto
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA98195
| | - Yin Huang
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Brad A. Krajina
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Margaux McBirney
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Andrea E. Doak
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA98195
| | - Sixuan Qu
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Carolyn L. Wang
- Department of Radiology, University of Washington School of Medicine, Seattle, WA98195
| | - Michael C. Haffner
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98109
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Kevin J. Cheung
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| |
Collapse
|
25
|
De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G. Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes. Cancer Discov 2023; 13:632-653. [PMID: 36399432 PMCID: PMC9976992 DOI: 10.1158/2159-8290.cd-22-0692] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/01/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Advanced prostate cancers comprise distinct phenotypes, but tumor classification remains clinically challenging. Here, we harnessed circulating tumor DNA (ctDNA) to study tumor phenotypes by ascertaining nucleosome positioning patterns associated with transcription regulation. We sequenced plasma ctDNA whole genomes from patient-derived xenografts representing a spectrum of androgen receptor active (ARPC) and neuroendocrine (NEPC) prostate cancers. Nucleosome patterns associated with transcriptional activity were reflected in ctDNA at regions of genes, promoters, histone modifications, transcription factor binding, and accessible chromatin. We identified the activity of key phenotype-defining transcriptional regulators from ctDNA, including AR, ASCL1, HOXB13, HNF4G, and GATA2. To distinguish NEPC and ARPC in patient plasma samples, we developed prediction models that achieved accuracies of 97% for dominant phenotypes and 87% for mixed clinical phenotypes. Although phenotype classification is typically assessed by IHC or transcriptome profiling from tumor biopsies, we demonstrate that ctDNA provides comparable results with diagnostic advantages for precision oncology. SIGNIFICANCE This study provides insights into the dynamics of nucleosome positioning and gene regulation associated with cancer phenotypes that can be ascertained from ctDNA. New methods for classification in phenotype mixtures extend the utility of ctDNA beyond assessments of somatic DNA alterations with important implications for molecular classification and precision oncology. This article is highlighted in the In This Issue feature, p. 517.
Collapse
Affiliation(s)
- Navonil De Sarkar
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pathology and Prostate Cancer Center of Excellence, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Robert D. Patton
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Anna-Lisa Doebley
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington
- Medical Scientist Training Program, University of Washington, Seattle, Washington
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Mohamed Adil
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Adam J. Kreitzman
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jay F. Sarthy
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Minjeong Ko
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sandipan Brahma
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael P. Meers
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Derek H. Janssens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Lisa S. Ang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ilsa M. Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Arnab Bose
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ruth F. Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jared M. Lucas
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Talina A. Nunez
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Holly M. Nguyen
- Department of Urology, University of Washington, Seattle, Washington
| | | | - Colin C. Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Michael T. Schweizer
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sylvan C. Baca
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Matthew L. Freedman
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - R. Bruce Montgomery
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
| |
Collapse
|
26
|
Schweizer MT, Gulati R, Yezefski T, Cheng HH, Mostaghel E, Haffner MC, Patel RA, De Sarkar N, Ha G, Dumpit R, Woo B, Lin A, Panlasigui P, McDonald N, Lai M, Nega K, Hammond J, Grivas P, Hsieh A, Montgomery B, Nelson PS, Yu EY. Bipolar androgen therapy plus olaparib in men with metastatic castration-resistant prostate cancer. Prostate Cancer Prostatic Dis 2023; 26:194-200. [PMID: 36564459 PMCID: PMC10286318 DOI: 10.1038/s41391-022-00636-0] [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: 10/03/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Bipolar androgen therapy (BAT) results in rapid fluctuation of testosterone (T) between near-castrate and supraphysiological levels and has shown promise in metastatic castration-resistant prostate cancer (mCRPC). Its clinical effects may be mediated through induction of DNA damage, and preclinical studies suggest synergy with PARP inhibitors. PATIENTS AND METHODS This was a single-center, Phase II trial testing olaparib plus BAT (T cypionate/enanthate 400 mg every 28 days) with ongoing androgen deprivation. Planned recruitment was 30 subjects (equal proportions with/without homologous recombination repair [HRR] gene mutations) with mCRPC post abiraterone and/or enzalutamide. The primary objective was to determine PSA50 response (PSA decline ≥50% from baseline) rate at 12-weeks. The primary analysis utilized the entire (intent-to-treat [ITT]) cohort, with those dropping out early counted as non-responders. Secondary/exploratory analyses were in those treated beyond 12-weeks (response-evaluable cohort). RESULTS Thirty-six patients enrolled and 6 discontinued prior to response assessment. In the ITT cohort, PSA50 response rate at 12-weeks was 11/36 (31%; 95% CI 17-48%), and 16/36 (44%, 95% CI 28-62%) had a PSA50 response at any time on-study. After a median follow-up of 19 months, the median clinical/radiographic progression-free survival in the ITT cohort was 13.0 months (95% CI 7-17). Clinical outcomes were similar regardless of HRR gene mutational status. CONCLUSIONS BAT plus olaparib is associated with high response rates and long PFS. Clinical benefit was observed regardless of HRR gene mutational status.
Collapse
Affiliation(s)
- Michael T Schweizer
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Roman Gulati
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Todd Yezefski
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Heather H Cheng
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elahe Mostaghel
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- VA Puget Sound Health Care System, Seattle, WA, USA
| | - Michael C Haffner
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Radhika A Patel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ruth Dumpit
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brianna Woo
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aaron Lin
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Patrick Panlasigui
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Nerina McDonald
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael Lai
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Katie Nega
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jeannette Hammond
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Petros Grivas
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Hsieh
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- VA Puget Sound Health Care System, Seattle, WA, USA
| | - Peter S Nelson
- Department of Medicine, University of Washington, Seattle, WA, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Evan Y Yu
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| |
Collapse
|
27
|
Watanabe R, Sugihara N, Kono R, Arai O, Kakuda T, Noda T, Nishimura K, Fukumoto T, Miura N, Kurata M, Miyauchi Y, Kitazawa R, Haffner MC, Kikugawa T, Saika T. Detection of intraductal carcinoma of the prostate (IDCP) cases focusing on high-grade prostatic intraepithelial neoplasia (PIN) findings regarding invasive carcinoma of the prostate. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.6_suppl.379] [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: 03/18/2023] Open
Abstract
379 Background: Intraductal carcinoma of the prostate (IDCP) is a pathological pattern that involves atypical cells proliferating within the normal gland where basal cells are preserved. These exhibit cribriform morphology, a finding associated with poor prognosis. In addition to the TMPRSS2-ERG fusion gene, TP53, RB1, and PTEN deletions, and SPOP and HRR gene mutations, such as a BRCA mutations, are frequently detected in patients with IDCP. The National Comprehensive Cancer Network (NCCN) guidelines suggest that early genetic testing should be considered. However, IDCP recognition is notably low, and diagnosis requires skill. Methods: We selected 98 cases with "prostate cancer with high-grade prostatic intraepithelial neoplasia (PIN) in the background" by referring to the pathology reports of cases who underwent total prostatectomy for prostate cancer at our hospital between November 2011 and November 2021. Twelve cases were narrowed down to those that were considered suggestive of IDCP based on the pathology reports and reviewed by three pathologists to determine the presence of IDCP. These were additionally reviewed by three pathologists for the presence or absence of IDCP and a gene test of prostatectomy specimens was submitted for the relevant cases to determine the presence or absence of HRR gene mutations. Results: Five of the twelve cases were determined to be IDCP positive. The Gleason score of background prostate cancer was 4+3 in 3 cases, 4+4 in 1 case, and 4+5 in 1 case. Median postoperative follow-up was 37 months (22- 45 months); 3 of the 5 patients had no recurrence, 1 had recurrence at 2 years and 3 months resulting in additional local radio therapy (RT), and 1 patient died of other causes. Pathology genetic testing identified HRR-related genetic abnormalities, including BRCA mutations. Conclusions: We were able to establish IDCP cases from past high-grade PIN cases. As a number of HRR gene mutations of unknown pathological significance were detected, IDCP cases could be retrieved from past cases and genetic abnormalities could be identified efficiently. The findings of the study provide a possible approach to diagnose prostate cancer cases with genetic mutations at an early stage.
Collapse
Affiliation(s)
| | - Naoya Sugihara
- Department of Urology, Ehime University Hospital, Toon, Japan
| | - Reina Kono
- Department of Urology, Ehime University Hospital, Toon, Japan
| | - Osuke Arai
- Department of Urology, Ehime University Hospital, Toon, Japan
| | - Toshio Kakuda
- Department of Urology, Ehime University Hospital, Toon, Japan
| | - Terutaka Noda
- Department of Urology, Ehime University Hospital, Toon, Japan
| | | | | | - Noriyoshi Miura
- Department of Urology, Ehime University Hospital, Toon, Japan
| | - Mie Kurata
- Department of Pathology, Ehime University Graduate School of Medicine and Proteo-Science Center, Ehime, Japan
| | - Yuki Miyauchi
- Department of Urology, Ehime University Hospital, Toon, Japan
| | - Riko Kitazawa
- Division of Diagnostic Pathology, Ehime University Hospital, Toon, Japan
| | | | - Tadahiko Kikugawa
- Department of Urology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Takashi Saika
- Department of Urology, Ehime University Hospital, Toon, Japan
| |
Collapse
|
28
|
Yamamoto A, Huang Y, Krajina BA, McBirney M, Doak AE, Wang CL, Haffner MC, Cheung KJ. Abstract B049: Breast cancer-derived angiopoietin-like 7 regulates necrotic core formation and metastasis from the tumor interior. Cancer Res 2023. [DOI: 10.1158/1538-7445.metastasis22-b049] [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: 01/19/2023]
Abstract
Abstract
Necrosis in the tumor interior is a common feature of aggressive cancers that is associated with poor clinical prognosis and the development of metastasis. However, how the necrotic core promotes tumor cell dissemination and metastasis remains unclear. Foundational models for cancer metastasis research include mouse, zebrafish, and chick embryo, but identifying tumor cells in transit is painstaking. Here we used a rat model of breast cancer metastasis to increase detection of dissemination events. Owing to the large size and higher blood volume of rats, we collected 10 times more circulating tumor cells (CTCs) than from mice. In the rat model, tumor dissemination was temporally correlated with the emergence of necrosis in the tumor interior. These findings were corroborated by longitudinal study of CTC abundance and tissue necrosis markers in blood plasma from patients with metastatic breast cancer. Further, we observed that dilated blood vessels were located next to necrotic regions of the tumor and that their increase was concurrent with the initiation of intratumoral necrosis and increase in CTC abundance. Bulk RNA sequencing of mouse-to-rat xenograft tumor necrotic core compared to the non-necrotic rim revealed distinct tumor-specific and host-specific transcripts in the necrotic interior. We identified angiopoietin-like 7 (Angptl7) as a tumor-specific factor localized to the peri-necrotic zone. Functional studies showed that Angptl7 loss normalizes central necrosis, peri-necrotic dilated vessels, metastasis, and reduces circulating tumor cell counts to nearly zero. Mechanistically, Angptl7 promoted vascular permeability and supported vascular remodeling in the peri-necrotic zone. Taken together, these findings show that breast tumors actively produce factors controlling central necrosis formation and metastatic dissemination from the tumor core. Tumor dissemination events are localized spatially to dilated peri-necrotic vessels in the tumor interior, and tumor dissemination is dependent functionally on the expression of a factor, Angptl7, produced by peri-necrotic tumor cells. Our findings in breast cancer models, in conjunction with recent clinical observations, provide strong evidence for tumor dissemination from the tumor interior.
Citation Format: Ami Yamamoto, Yin Huang, Brad A. Krajina, Margaux McBirney, Andrea E. Doak, Carolyn L. Wang, Michael C. Haffner, Kevin J. Cheung. Breast cancer-derived angiopoietin-like 7 regulates necrotic core formation and metastasis from the tumor interior [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr B049.
Collapse
Affiliation(s)
| | - Yin Huang
- 2Fred Hutchinson Cancer Center, Seattle, WA,
| | | | | | | | | | | | | |
Collapse
|
29
|
Low JY, Ko M, Hanratty B, Patel RA, Bhamidipati A, Heaphy CM, Sayar E, Lee JK, Li S, De Marzo AM, Nelson WG, Gupta A, Yegnasubramanian S, Ha G, Epstein JI, Haffner MC. Genomic Characterization of Prostatic Basal Cell Carcinoma. Am J Pathol 2023; 193:4-10. [PMID: 36309102 PMCID: PMC9768679 DOI: 10.1016/j.ajpath.2022.09.010] [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: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
Basal cell carcinoma (BCC) of the prostate is a rare tumor. Compared with the more common acinar adenocarcinoma (AAC) of the prostate, BCCs show features of basal cell differentiation and are thought to be biologically distinct from AAC. The spectrum of molecular alterations of BCC has not been comprehensively described, and genomic studies are lacking. Herein, whole genome sequencing was performed on archival formalin-fixed, paraffin-embedded specimens of two cases with BCC. Prostatic BCCs were characterized by an overall low copy number and mutational burden. Recurrent copy number loss of chromosome 16 was observed. In addition, putative driver gene alterations in KIT, DENND3, PTPRU, MGA, and CYLD were identified. Mechanistically, depletion of the CYLD protein resulted in increased proliferation of prostatic basal cells in vitro. Collectively, these studies show that prostatic BCC displays distinct genomic alterations from AAC and highlight a potential role for loss of chromosome 16 in the pathogenesis of this rare tumor type.
Collapse
Affiliation(s)
- Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Minjeong Ko
- Division of Public Health Science, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Radhika A Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Akshay Bhamidipati
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher M Heaphy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington; Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Shan Li
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Angelo M De Marzo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - William G Nelson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anuj Gupta
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Gavin Ha
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington; Division of Public Health Science, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jonathan I Epstein
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington.
| |
Collapse
|
30
|
Bakbak H, Sayar E, Kaur HB, Salles DC, Patel RA, Hicks J, Lotan TL, De Marzo AM, Gulati R, Epstein JI, Haffner MC. Clonal relationships of adjacent Gleason pattern 3 and Gleason pattern 5 lesions in Gleason Scores 3+5=8 and 5+3=8. Hum Pathol 2022; 130:18-24. [PMID: 36309296 PMCID: PMC10542864 DOI: 10.1016/j.humpath.2022.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/04/2022]
Abstract
Genomic studies have demonstrated a high level of intra-tumoral heterogeneity in prostate cancer. There is strong evidence suggesting that individual tumor foci can arise as genetically distinct, clonally independent lesions. However, recent studies have also demonstrated that adjacent Gleason pattern (GP) 3 and GP4 lesions can originate from the same clone but follow divergent genetic and morphologic evolution. The clonal relationship of adjacent GP3 and GP5 lesions has thus far not been investigated. Here we analyzed a cohort of 14 cases-11 biopsy and 3 radical prostatectomy specimens-with a Gleason score of 3 + 5 = 8 or 5 + 3 = 8 present in the same biopsy or in a single dominant tumor nodule at radical prostatectomy. Clonal and subclonal relationships between GP3 and GP5 lesions were assessed using genetically validated immunohistochemical assays for ERG, PTEN, and P53. 9/14 (64%) cases showed ERG reactivity in both GP3 and GP5 lesions. Only 1/14 (7%) cases showed a discordant pattern with ERG staining present only in GP3. PTEN expression was lost in 2/14 (14%) cases with perfect concordance between GP5 and GP3. P53 nuclear reactivity was present in 1/14 (7%) case in both GP5 and GP3. This study provides first evidence that the majority of adjacent GP3 and GP5 lesions share driver alterations and are clonally related. In addition, we observed a lower-than-expected rate of PTEN loss in GP5 in the context of Gleason score 3 + 5 = 8 or 5 + 3 = 8 tumors.
Collapse
Affiliation(s)
- Hasim Bakbak
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Harsimar B Kaur
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Daniela C Salles
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Radhika A Patel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Jessica Hicks
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Tamara L Lotan
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA; Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Angelo M De Marzo
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA; Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Jonathan I Epstein
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA; Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA; Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98195, WA, USA.
| |
Collapse
|
31
|
Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res 2022; 82:3888-3902. [PMID: 36251389 PMCID: PMC9627125 DOI: 10.1158/0008-5472.can-22-1123] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 07/29/2022] [Indexed: 02/03/2023]
Abstract
Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
Collapse
Affiliation(s)
- Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI
- William S. Middleton Memorial Veterans' Hospital, Madison, WI
| | | | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Corinne Maurice-Dror
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver, BC, Canada
| | - Ashutosh Maheshwari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wenbin Ye
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Jessica Petricca
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Marc D Perry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - William S Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Alicia K Morgans
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Robert E Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
| | - Matthew B Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Anders Bjartell
- Department of Translational Medicine, Medical Faculty, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin-Madison, Madison, WI
| | | | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
- Department of Urologic Surgery, University of California Davis, Sacramento, CA
| | - Phuoc T Tran
- Department of Radiation Oncology, University of Maryland, College Park, Baltimore, MD
| | - Edwin M Posadas
- Urologic Oncology Program & Uro-Oncology Research Laboratories, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Arc Institute, Palo Alto, CA
| | - Christopher A Maher
- Siteman Cancer Center, Washington University, St. Louis, MO
- McDonnell Genome Institute, Washington University, St. Louis, MO
- Department of Internal Medicine, Washington University, St. Louis, MO
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - 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
- Jonsson Comprehensive Cancer Center, Departments of Human Genetics and Urology, University of California Los Angeles, Los Angeles, CA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
| |
Collapse
|
32
|
Sowalsky AG, Plymate SR, Haffner MC, de Bono JS, Sharp A. Re: Heng Li, Yucong Zhang, Dong Li, et al. Androgen Receptor Splice Variant 7 Predicts Shorter Response in Patients with Metastatic Hormone-sensitive Prostate Cancer Receiving Androgen Deprivation Therapy. Eur Urol 2021;79:879-86 AR-V7 is Rare in Hormone-sensitive Prostate Cancer: AR-V7 is Rare in Hormone-sensitive Prostate Cancer. Eur Urol 2022; 82:e135-e136. [PMID: 36038450 DOI: 10.1016/j.eururo.2022.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/25/2022] [Indexed: 11/04/2022]
Affiliation(s)
- Adam G Sowalsky
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Stephen R Plymate
- University of Washington, Seattle, WA, USA; Geriatrics Research, Education and Clinical Center, VAPSHCS, Seattle, WA, USA
| | - Michael C Haffner
- University of Washington, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Johann S de Bono
- Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - Adam Sharp
- Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| |
Collapse
|
33
|
Lowe AW, Macura KJ, Kates M, Lotan T, Haffner MC, Rowe SP. Prostate multi-parametric magnetic resonance imaging appearance of diffuse adenosis of the peripheral zone (DAPZ). Urol Case Rep 2022; 45:102178. [PMID: 35968526 PMCID: PMC9363943 DOI: 10.1016/j.eucr.2022.102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022] Open
Abstract
Imaging specialists must recognize potential mimics of prostate cancer (PCa) on multi-parametric magnetic resonance imaging (mpMRI). We describe the appearance of diffuse adenosis of the peripheral zone (DAPZ) on mpMRI. The features of DAPZ parallel those of diffuse PCa, with low signal on T2-weighted images, rapid enhancement on dynamic contrast-enhanced sequences, and restricted diffusion. DAPZ is typically encountered in younger men with elevated prostate specific antigen (PSA) levels and portends an increased risk of the development of PCa. Recognition of the imaging appearance of DAPZ may reassure patients with concordant pathologic findings and may aid in selecting patients for follow-up.
Collapse
|
34
|
Pattwell SS, Arora S, Nuechterlein N, Zager M, Loeb KR, Cimino PJ, Holland NC, Reche-Ley N, Bolouri H, Almiron Bonnin DA, Szulzewsky F, Phadnis VV, Ozawa T, Wagner MJ, Haffner MC, Cao J, Shendure J, Holland EC. Oncogenic role of a developmentally regulated NTRK2 splice variant. Sci Adv 2022; 8:eabo6789. [PMID: 36206341 PMCID: PMC9544329 DOI: 10.1126/sciadv.abo6789] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Temporally regulated alternative splicing choices are vital for proper development, yet the wrong splice choice may be detrimental. Here, we highlight a previously unidentified role for the neurotrophin receptor splice variant TrkB.T1 in neurodevelopment, embryogenesis, transformation, and oncogenesis across multiple tumor types in humans and mice. TrkB.T1 is the predominant NTRK2 isoform across embryonic organogenesis, and forced overexpression of this embryonic pattern causes multiple solid and nonsolid tumors in mice in the context of tumor suppressor loss. TrkB.T1 also emerges as the predominant NTRK isoform expressed in a wide range of adult and pediatric tumors, including those harboring tropomyosin receptor kinase fusions. Affinity purification-mass spectrometry proteomic analysis reveals distinct interactors with known developmental and oncogenic signaling pathways such as Wnt, transforming growth factor-β, Sonic Hedgehog, and Ras. From alterations in splicing factors to changes in gene expression, the discovery of isoform specific oncogenes with embryonic ancestry has the potential to shape the way we think about developmental systems and oncology.
Collapse
Affiliation(s)
- Siobhan S. Pattwell
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Division of Pediatrics, Department Hematology/Oncology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
| | - Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Michael Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Keith R. Loeb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 325 9th Avenue, Box 359791, Seattle, WA 98104, USA
| | - Patrick J. Cimino
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 325 9th Avenue, Box 359791, Seattle, WA 98104, USA
| | - Nikolas C. Holland
- Center for Neural Science, New York University, 4 Washington Place, #809, New York, NY 10003, USA
- Department of Psychiatry, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | | | - Hamid Bolouri
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA 98101, USA
| | - Damian A. Almiron Bonnin
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
| | | | - Tatsuya Ozawa
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Michael J. Wagner
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
- Division of Medical Oncology, University of Washington, 825 Eastlake Ave E., Seattle, WA 98109, USA
| | - Michael C. Haffner
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 325 9th Avenue, Box 359791, Seattle, WA 98104, USA
| | - Junyue Cao
- Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| |
Collapse
|
35
|
Westbrook TC, Guan X, Rodansky E, Flores D, Liu CJ, Udager AM, Patel RA, Haffner MC, Hu YM, Sun D, Beer TM, Foye A, Aggarwal R, Quigley DA, Youngren JF, Ryan CJ, Gleave M, Wang Y, Huang J, Coleman I, Morrissey C, Nelson PS, Evans CP, Lara P, Reiter RE, Witte O, Rettig M, Wong CK, Weinstein AS, Uzunangelov V, Stuart JM, Thomas GV, Feng FY, Small EJ, Yates JA, Xia Z, Alumkal JJ. Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity. Nat Commun 2022; 13:5345. [PMID: 36109521 PMCID: PMC9477876 DOI: 10.1038/s41467-022-32701-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 03/14/2022] [Accepted: 08/11/2022] [Indexed: 11/08/2022] Open
Abstract
The androgen receptor (AR) signaling inhibitor enzalutamide (enza) is one of the principal treatments for metastatic castration-resistant prostate cancer (CRPC). Several emergent enza clinical resistance mechanisms have been described, including lineage plasticity in which the tumors manifest reduced dependency on the AR. To improve our understanding of enza resistance, herein we analyze the transcriptomes of matched biopsies from men with metastatic CRPC obtained prior to treatment and at progression (n = 21). RNA-sequencing analysis demonstrates that enza does not induce marked, sustained changes in the tumor transcriptome in most patients. However, three patients' progression biopsies show evidence of lineage plasticity. The transcription factor E2F1 and pathways linked to tumor stemness are highly activated in baseline biopsies from patients whose tumors undergo lineage plasticity. We find a gene signature enriched in these baseline biopsies that is strongly associated with poor survival in independent patient cohorts and with risk of castration-induced lineage plasticity in patient-derived xenograft models, suggesting that tumors harboring this gene expression program may be at particular risk for resistance mediated by lineage plasticity and poor outcomes.
Collapse
Affiliation(s)
- Thomas C Westbrook
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Xiangnan Guan
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Eva Rodansky
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Diana Flores
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Chia Jen Liu
- Department of Pathology, Michigan Center for Translational Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Aaron M Udager
- Department of Pathology, Michigan Center for Translational Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Radhika A Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ya-Mei Hu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Duanchen Sun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, 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
- 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 Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jack F Youngren
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles J Ryan
- Masonic Cancer Center, University of Minnesota; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Martin Gleave
- Department of Urological Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Department of Urological Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Experimental Therapeutics, BC Cancer, University of British Columbia, Vancouver, BC, Canada
| | | | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Primo Lara
- University of California Davis, Davis, CA, USA
| | | | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Matthew Rettig
- University of California Los Angeles, Los Angeles, CA, USA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Christopher K Wong
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Alana S Weinstein
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Vlado Uzunangelov
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Josh M Stuart
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - George V Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Joel A Yates
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Zheng Xia
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Joshi J Alumkal
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
36
|
Rodems TS, Heninger E, Stahlfeld CN, Gilsdorf CS, Carlson KN, Kircher MR, Singh A, Krueger TEG, Beebe DJ, Jarrard DF, McNeel DG, Haffner MC, Lang JM. Reversible epigenetic alterations regulate class I HLA loss in prostate cancer. Commun Biol 2022; 5:897. [PMID: 36050516 PMCID: PMC9437063 DOI: 10.1038/s42003-022-03843-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 11/02/2021] [Accepted: 08/15/2022] [Indexed: 11/09/2022] Open
Abstract
Downregulation of HLA class I (HLA-I) impairs immune recognition and surveillance in prostate cancer and may underlie the ineffectiveness of checkpoint blockade. However, the molecular mechanisms regulating HLA-I loss in prostate cancer have not been fully explored. Here, we conducted a comprehensive analysis of HLA-I genomic, epigenomic and gene expression alterations in primary and metastatic human prostate cancer. Loss of HLA-I gene expression was associated with repressive chromatin states including DNA methylation, histone H3 tri-methylation at lysine 27, and reduced chromatin accessibility. Pharmacological DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibition decreased DNA methylation and increased H3 lysine 27 acetylation and resulted in re-expression of HLA-I on the surface of tumor cells. Re-expression of HLA-I on LNCaP cells by DNMT and HDAC inhibition increased activation of co-cultured prostate specific membrane antigen (PSMA)27-38-specific CD8+ T-cells. HLA-I expression is epigenetically regulated by functionally reversible DNA methylation and chromatin modifications in human prostate cancer. Methylated HLA-I was detected in HLA-Ilow circulating tumor cells (CTCs), which may serve as a minimally invasive biomarker for identifying patients who would benefit from epigenetic targeted therapies.
Collapse
Affiliation(s)
- Tamara S Rodems
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Erika Heninger
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Charlotte N Stahlfeld
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Cole S Gilsdorf
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Kristin N Carlson
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Madison R Kircher
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Anupama Singh
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Timothy E G Krueger
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - David J Beebe
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Biomedical Engineering, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Pathology, University of Wisconsin, Madison, 3170 UW Medical Foundation Centennial Building, 1685 Highland Ave., Madison, WI, 53705, USA
| | - David F Jarrard
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Urology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Douglas G McNeel
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, N., Seattle, WA, 98109, USA.,Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA.,Department of Pathology, Johns Hopkins School of Medicine, 600N Wolfe St., Baltimore, MD, 21287, USA
| | - Joshua M Lang
- University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.
| |
Collapse
|
37
|
Sowalsky AG, Figueiredo I, Lis RT, Coleman I, Gurel B, Bogdan D, Yuan W, Russo JW, Bright JR, Whitlock NC, Trostel SY, Ku AT, Patel RA, True LD, Welti J, Jimenez-Vacas JM, Rodrigues DN, Riisnaes R, Neeb A, Sprenger CT, Swain A, Wilkinson S, Karzai F, Dahut WL, Balk SP, Corey E, Nelson PS, Haffner MC, Plymate SR, de Bono JS, Sharp A. Assessment of Androgen Receptor Splice Variant-7 as a Biomarker of Clinical Response in Castration-Sensitive Prostate Cancer. Clin Cancer Res 2022; 28:3509-3525. [PMID: 35695870 PMCID: PMC9378683 DOI: 10.1158/1078-0432.ccr-22-0851] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/17/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Therapies targeting the androgen receptor (AR) have improved the outcome for patients with castration-sensitive prostate cancer (CSPC). Expression of the constitutively active AR splice variant-7 (AR-V7) has shown clinical utility as a predictive biomarker of AR-targeted therapy resistance in castration-resistant prostate cancer (CRPC), but its importance in CSPC remains understudied. EXPERIMENTAL DESIGN We assessed different approaches to quantify AR-V7 mRNA and protein in prostate cancer cell lines, patient-derived xenograft (PDX) models, publicly available cohorts, and independent institutional clinical cohorts, to identify reliable approaches for detecting AR-V7 mRNA and protein and its association with clinical outcome. RESULTS In CSPC and CRPC cohorts, AR-V7 mRNA was much less abundant when detected using reads across splice boundaries than when considering isoform-specific exonic reads. The RM7 AR-V7 antibody had increased sensitivity and specificity for AR-V7 protein detection by immunohistochemistry (IHC) in CRPC cohorts but rarely identified AR-V7 protein reactivity in CSPC cohorts, when compared with the EPR15656 AR-V7 antibody. Using multiple CRPC PDX models, we demonstrated that AR-V7 expression was exquisitely sensitive to hormonal manipulation. In CSPC institutional cohorts, AR-V7 protein quantification by either assay was associated neither with time to development of castration resistance nor with overall survival, and intense neoadjuvant androgen-deprivation therapy did not lead to significant AR-V7 mRNA or staining following treatment. Neither pre- nor posttreatment AR-V7 levels were associated with volumes of residual disease after therapy. CONCLUSIONS This study demonstrates that further analytical validation and clinical qualification are required before AR-V7 can be considered for clinical use in CSPC as a predictive biomarker.
Collapse
Affiliation(s)
| | | | - Rosina T. Lis
- Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Ilsa Coleman
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Bora Gurel
- Institute of Cancer Research, London, UK
| | | | - Wei Yuan
- Institute of Cancer Research, London, UK
| | | | - John R. Bright
- Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | | | - Anson T. Ku
- Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | | | | | | | | | | | - Antje Neeb
- Institute of Cancer Research, London, UK
| | | | | | | | - Fatima Karzai
- Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | - Steven P. Balk
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Eva Corey
- University of Washington, Seattle, Washington
| | - Peter S. Nelson
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- University of Washington, Seattle, Washington
| | - Michael C. Haffner
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- University of Washington, Seattle, Washington
| | - Stephen R. Plymate
- University of Washington, Seattle, Washington
- Geriatrics Research, Education and Clinical Center, VAPSHCS, Seattle, Washington
| | - Johann S. de Bono
- Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Adam Sharp
- Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| |
Collapse
|
38
|
Coleman IM, DeSarkar N, Morrissey C, Xin L, Roudier MP, Sayar E, Li D, Corey E, Haffner MC, Nelson PS. Therapeutic Implications for Intrinsic Phenotype Classification of Metastatic Castration-Resistant Prostate Cancer. Clin Cancer Res 2022; 28:3127-3140. [PMID: 35552660 PMCID: PMC9365375 DOI: 10.1158/1078-0432.ccr-21-4289] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/18/2022] [Accepted: 05/09/2022] [Indexed: 01/09/2023]
Abstract
PURPOSE To determine whether metastatic castration-resistant prostate cancers (mCRPC) partition into molecular phenotypes corresponding to intrinsic differentiation states and ascertain whether these subtypes exhibit specific druggable features and associate with treatment outcomes. EXPERIMENTAL DESIGN We used RNAseq, digital spatial profiling, and histological assessments from metastatic biopsies and patient-derived xenografts to segregate mCRPCs into subtypes defined by the PAM50 breast cancer classification algorithm. Subtype associations with treatment responses in preclinical models and patients were determined. RESULTS Using the PAM50 algorithm, we partitioned 270 mCRPC tumors into LumA (42%), LumB (24%), and Basal (34%) subtypes with classification largely driven by proliferation rates and androgen receptor (AR) activity. Most neuroendocrine tumors classified as Basal. Pathways enriched in the LumA subtype include TGFß and NOTCH signaling. LumB subtype tumors were notable for elevated MYC activity. Basal subtype tumors exhibited elevated IL6-STAT3 signaling and features of adult stem cell states. In patients where multiple tumors were evaluated, the majority had concordant PAM50 subtype determination, though a subset exhibited marked inter- and intratumor heterogeneity, including divergent classifications between primary and metastatic sites. In preclinical models, LumA subtype tumors were highly responsive to androgen deprivation and docetaxel chemotherapy whereas Basal tumors were largely resistant. In clinical cohorts patients with Basal subtype tumors demonstrated a shorter time on treatment with AR signaling inhibitors and docetaxel relative to patients with luminal subtypes. CONCLUSIONS Subtyping of mCRPC based on cell differentiation states has potential clinical utility for identifying patients with divergent expression of treatment targets and responses to systemic therapy.
Collapse
Affiliation(s)
- Ilsa M. Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
| | - Navonil DeSarkar
- Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Li Xin
- Department of Urology, University of Washington, Seattle, Washington
| | | | | | - Dapei Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
| |
Collapse
|
39
|
Pham MT, Gupta A, Gupta H, Vaghasia A, Skaist A, Garrison MA, Coulter JB, Haffner MC, Zheng SL, Xu J, DeStefano Shields C, Isaacs WB, Wheelan SJ, Nelson WG, Yegnasubramanian S. Identifying Phased Mutations and Complex Rearrangements in Human Prostate Cancer Cell Lines through Linked-Read Whole-Genome Sequencing. Mol Cancer Res 2022; 20:1013-1020. [PMID: 35452513 PMCID: PMC9262859 DOI: 10.1158/1541-7786.mcr-21-0683] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/19/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
A limited number of cell lines have fueled the majority of preclinical prostate cancer research, but their genomes remain incompletely characterized. Here, we utilized whole-genome linked-read sequencing for comprehensive characterization of phased mutations and rearrangements in the most commonly used cell lines in prostate cancer research including PC3, LNCaP, DU145, CWR22Rv1, VCaP, LAPC4, MDA-PCa-2b, RWPE-1, and four derivative castrate-resistant (CR) cell lines LNCaP_Abl, LNCaP_C42b, VCaP-CR, and LAPC4-CR. Phasing of mutations allowed determination of "gene-level haplotype" to assess whether genes harbored heterozygous mutations in one or both alleles. Phased structural variant analysis allowed identification of complex rearrangement chains consistent with chromothripsis and chromoplexy. In addition, comparison of parental and derivative CR lines revealed previously known and novel genomic alterations associated with the CR phenotype. IMPLICATIONS This study therefore comprehensively characterized phased genomic alterations in the commonly used prostate cancer cell lines, providing a useful resource for future prostate cancer research.
Collapse
Affiliation(s)
- Minh-Tam Pham
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anuj Gupta
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harshath Gupta
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ajay Vaghasia
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alyza Skaist
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - McKinzie A. Garrison
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jonathan B. Coulter
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael C. Haffner
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Division of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Pathology, University of Washington, Seattle, Washington
| | - S. Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Christina DeStefano Shields
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - William B. Isaacs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah J. Wheelan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - William G. Nelson
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
40
|
Pham MTN, Haffner MC, Wick HC, Coulter JB, Gupta A, Chikarmane RV, Gupta H, Wheelan S, Nelson WG, Yegnasubramanian S. Abstract 680: Topoisomerase 2 beta facilitates chromatin reorganization during Androgen Receptor induced transcription and contributes to chromoplexy in prostate cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-680] [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
Prostate cancer (PCa) is the most common malignancy and second leading cause of cancer death in American men. Androgen Receptor (AR) mediated transcriptional program is central to normal prostate homeostasis and drives PCa growth and survival. Chromoplexy, a highly complex genomic architecture with several intra- and inter-chromosomal segments joined in a chain, is among the most prominent genetic alterations that drive both prostate cancer initiation and progression, and often involves sites of AR transcription. Previous studies have shown that AR induced, topoisomerase 2 beta (TOP2B) mediated double strand breaks were recombinogenic and led to de novo formation of TMPRSS2-ERG fusion gene, shedding light on the potential role of TOP2B in chromoplexy formation. However, the precise role of TOP2B in AR transcription was not well understood. Here, we hypothesize that TOP2B is recruited to resolve topological constraints arising during induction of AR transcriptional programs, and its catalytic activity is required to facilitate or maintain chromosomal interactions optimal for transcriptional induction. We performed Chromosomal Conformation Capture related techniques (3C and HiC) on LNCaP cells before and after androgen stimulation and observed an increase in chromatin interactions within 15kb from promoters of AR target genes upon androgen induction. These interactions depended on TOP2B, as TOP2B catalytic inhibition or knockdown reduced them significantly. Furthermore, TOP2B Hi-CHIP revealed that TOP2B is involved in key enhancer-promoter looping and in several interactions among gene body, enhancers, promoters of AR target genes, and nearby topological associated domain borders. We went on to isolate which steps during AR transcription induction required TOP2B by examining chromatin localization of the key factors, including AR, cohesin (SMC1A), CTCF, histone 3 lysine 27 acetylation (H3K27ac), and total and phosphorylated RNA Polymerase II (RNAPII) using ChIP-seq. These experiments revealed that TOP2B was not required for AR binding nor for localization of H3K27ac marks. However, it was required for recruitment of cohesin to AR binding sites as well as to AR target gene promoters and gene bodies, for displacement of CTCF near AR target genes, and for localization and phosphorylation of RNAPII at AR target genes. These data nominate TOP2B as a key AR coactivator, assisting in the proper assembly of cohesin during transcription induction, and maintaining chromosomal interactions optimal for binding and activation of RNAPII. Intriguingly, sites of binding of TOP2B, as well as of cohesin, were highly associated with sites of chromoplexy complex rearrangements in human prostate cancers. Taken together, this work elucidates the role of TOP2B in AR-induced transcription, and implicates its involvement in chromoplexy formation in PCa.
Citation Format: Minh-Tam N. Pham, Michael C. Haffner, Heather C. Wick, Jonathan B. Coulter, Anuj Gupta, Roshan V. Chikarmane, Harshath Gupta, Sarah Wheelan, William G. Nelson, Srinivasan Yegnasubramanian. Topoisomerase 2 beta facilitates chromatin reorganization during Androgen Receptor induced transcription and contributes to chromoplexy in prostate cancer [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 680.
Collapse
Affiliation(s)
| | | | | | | | - Anuj Gupta
- 1Johns Hopkins School of Medicine, Baltimore, MD
| | | | | | | | | | | |
Collapse
|
41
|
Qiu X, Brown LG, Conner JL, Nguyen HM, Boufaied N, Abou Alaiwi S, Seo JH, El Zarif T, Bell C, O’Connor E, Hanratty B, Pomerantz M, Freedman ML, Brown M, Haffner MC, Nelson PS, Feng FY, Labbé DP, Long HW, Corey E. Response to supraphysiological testosterone is predicted by a distinct androgen receptor cistrome. JCI Insight 2022; 7:157164. [PMID: 35603787 PMCID: PMC9220831 DOI: 10.1172/jci.insight.157164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The androgen receptor (AR) is a master transcription factor that regulates prostate cancer (PC) development and progression. Inhibition of AR signaling by androgen deprivation is the first-line therapy with initial efficacy for advanced and recurrent PC. Paradoxically, supraphysiological levels of testosterone (SPT) also inhibit PC progression. However, as with any therapy, not all patients show a therapeutic benefit, and responses differ widely in magnitude and duration. In this study, we evaluated whether differences in the AR cistrome before treatment can distinguish between SPT-responding (R) and -nonresponding (NR) tumors. We provide the first preclinical evidence to our knowledge that SPT-R tumors exhibit a distinct AR cistrome when compared with SPT-NR tumors, indicating a differential biological role of the AR. We applied an integrated analysis of ChIP-Seq and RNA-Seq to the pretreatment tumors and identified an SPT-R signature that distinguishes R and NR tumors. Because transcriptomes of SPT-treated clinical specimens are not available, we interrogated available castration-resistant PC (CRPC) transcriptomes and showed that the SPT-R signature is associated with improved survival and has the potential to identify patients who would respond to SPT. These findings provide an opportunity to identify the subset of patients with CRPC who would benefit from SPT therapy.
Collapse
Affiliation(s)
- Xintao Qiu
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Lisha G. Brown
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Jennifer L. Conner
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Holly M. Nguyen
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Nadia Boufaied
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sarah Abou Alaiwi
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ji-Heui Seo
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Talal El Zarif
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Connor Bell
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Edward O’Connor
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian Hanratty
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Mark Pomerantz
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew L. Freedman
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Felix Y. Feng
- University of California at San Francisco, San Francisco, California, USA
| | - David P. Labbé
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Surgery, Division of Urology, McGill University, Montréal, Québec, Canada
| | - Henry W. Long
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington, USA
| |
Collapse
|
42
|
Patel RA, Coleman I, Roudier MP, Konnick EQ, Hanratty B, Dumpit R, Lucas JM, Ang LS, Low JY, Tretiakova MS, Ha G, Lee JK, True LD, De Marzo AM, Nelson PS, Morrissey C, Pritchard CC, Haffner MC. Comprehensive assessment of anaplastic lymphoma kinase in localized and metastatic prostate cancer reveals targetable alterations. Cancer Res Commun 2022; 2:277-285. [PMID: 36337169 PMCID: PMC9635400 DOI: 10.1158/2767-9764.crc-21-0156] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 06/16/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is a tyrosine kinase with genomic and expression changes in many solid tumors. ALK inhibition is first line therapy for lung cancers with ALK alterations, and an effective therapy in other tumor types, but has not been well-studied in prostate cancer. Here, we aim to delineate the role of ALK genomic and expression changes in primary and metastatic prostate cancer. We determined ALK expression by immunohistochemistry and RNA-Seq, and genomic alterations by NGS. We assessed functional consequences of ALK overexpression and pharmacological ALK inhibition by cell proliferation and cell viability assays. Among 372 primary prostate cancer cases we identified one case with uniformly high ALK protein expression. Genomic analysis revealed a SLC45A3-ALK fusion which promoted oncogenesis in in vitro assays. We observed ALK protein expression in 5/52 (9%) of metastatic prostate cancer cases, of which 4 of 5 had neuroendocrine features. ALK-expressing neuroendocrine prostate cancer had a distinct transcriptional program, and earlier disease progression. An ALK-expressing neuroendocrine prostate cancer model was sensitive to pharmacological ALK inhibition. In summary, we found that ALK overexpression is rare in primary prostate cancer, but more frequent in metastatic prostate cancers with neuroendocrine differentiation. Further, ALK fusions similar to lung cancer are an occasional driver in prostate cancer. Our data suggest that ALK-directed therapies could be an option in selected patients with advanced prostate cancer.
Collapse
Affiliation(s)
- Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Eric Q. Konnick
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- The Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ruth Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jared M. Lucas
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lisa S. Ang
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Maria S. Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Gavin Ha
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
- The Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - John K. Lee
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Angelo M. De Marzo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- The Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Colin C. Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- The Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
43
|
Rodems TS, Juang DS, Stahlfeld CN, Gilsdorf CS, Krueger TEG, Heninger E, Zhao SG, Sperger JM, Beebe DJ, Haffner MC, Lang JM. SEEMLIS: a flexible semi-automated method for enrichment of methylated DNA from low-input samples. Clin Epigenetics 2022; 14:37. [PMID: 35272673 PMCID: PMC8908705 DOI: 10.1186/s13148-022-01252-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/18/2022] [Indexed: 01/02/2023] Open
Abstract
Background DNA methylation alterations have emerged as hallmarks of cancer and have been proposed as screening, prognostic, and predictive biomarkers. Traditional approaches for methylation analysis have relied on bisulfite conversion of DNA, which can damage DNA and is not suitable for targeted gene analysis in low-input samples. Here, we have adapted methyl-CpG-binding domain protein 2 (MBD2)-based DNA enrichment for use on a semi-automated exclusion-based sample preparation (ESP) platform for robust and scalable enrichment of methylated DNA from low-input samples, called SEEMLIS. Results We show that combining methylation-sensitive enzyme digestion with ESP-based MBD2 enrichment allows for single gene analysis with high sensitivity for GSTP1 in highly impure, heterogenous samples. We also show that ESP-based MBD2 enrichment coupled with targeted pre-amplification allows for analysis of multiple genes with sensitivities approaching the single cell level in pure samples for GSTP1 and RASSF1 and sensitivity down to 14 cells for these genes in highly impure samples. Finally, we demonstrate the potential clinical utility of SEEMLIS by successful detection of methylated gene signatures in circulating tumor cells (CTCs) from patients with prostate cancer with varying CTC number and sample purity. Conclusions SEEMLIS is a robust assay for targeted DNA methylation analysis in low-input samples, with flexibility at multiple steps. We demonstrate the feasibility of this assay to analyze DNA methylation in prostate cancer cells using CTCs from patients with prostate cancer as a real-world example of a low-input analyte of clinical importance. In summary, this novel assay provides a platform for determining methylation signatures in rare cell populations with broad implications for research as well as clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01252-4.
Collapse
Affiliation(s)
- Tamara S Rodems
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Duane S Juang
- Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - Charlotte N Stahlfeld
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Cole S Gilsdorf
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Tim E G Krueger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Erika Heninger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Jamie M Sperger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - David J Beebe
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Pathology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, N., Seattle, WA, 98109, USA.,Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA.,Department of Pathology, Johns Hopkins School of Medicine, 600 N Wolfe St., Baltimore, MD, 21287, USA
| | - Joshua M Lang
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,7151 WI Institutes for Medical Research, 1111 Highland Ave., Madison, WI, 53705, USA.
| |
Collapse
|
44
|
Abstract
Metastatic prostate cancer remains uncurable. In this issue of Cell Reports Medicine, Rice et al. present an assessment of a compound (SU086) demonstrating activity in prostate cancer models through heat shock protein 90 inhibition and cell metabolism changes.
Collapse
Affiliation(s)
- Stephen R. Plymate
- Department of Medicine, University of Washington, Seattle, WA, USA
- Puget Sound VA Health Care System, Geriatric Research Education and Clinical Center, Seattle, WA, USA
| | - Cynthia Sprenger
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Corresponding author
| |
Collapse
|
45
|
Biles MJ, Haffner MC, Hanratty B, Pierorazio PM. Whole Genome Sequencing Reveals Independent Clonal Origin of Bilateral Testicular Germ Cell Tumors in Two Patients with Pure Seminoma. Urology 2022; 165:184-186. [DOI: 10.1016/j.urology.2022.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/22/2021] [Accepted: 01/13/2022] [Indexed: 10/19/2022]
|
46
|
De Sarkar N, Dasgupta S, Chatterjee P, Coleman I, Ha G, Ang LS, Kohlbrenner EA, Frank SB, Nunez TA, Salipante SJ, Corey E, Morrissey C, Van Allen E, Schweizer MT, Haffner MC, Patel R, Hanratty B, Lucas JM, Dumpit RF, Pritchard CC, Montgomery RB, Nelson PS. Genomic attributes of homology-directed DNA repair deficiency in metastatic prostate cancer. JCI Insight 2021; 6:152789. [PMID: 34877933 PMCID: PMC8675196 DOI: 10.1172/jci.insight.152789] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023] Open
Abstract
Cancers with homology-directed DNA repair (HRR) deficiency exhibit high response rates to poly(ADP-ribose) polymerase inhibitors (PARPi) and platinum chemotherapy. Though mutations disrupting BRCA1 and BRCA2 associate with HRR deficiency (HRRd), patterns of genomic aberrations and mutation signatures may be more sensitive and specific indicators of compromised repair. Here, we evaluated whole-exome sequences from 418 metastatic prostate cancers (mPCs) and determined that one-fifth exhibited genomic characteristics of HRRd that included Catalogue Of Somatic Mutations In Cancer mutation signature 3. Notably, a substantial fraction of tumors with genomic features of HRRd lacked biallelic loss of a core HRR-associated gene, such as BRCA2. In this subset, HRRd associated with loss of chromodomain helicase DNA binding protein 1 but not with mutations in serine-protein kinase ATM, cyclin dependent kinase 12, or checkpoint kinase 2. HRRd genomic status was strongly correlated with responses to PARPi and platinum chemotherapy, a finding that supports evaluating biomarkers reflecting functional HRRd for treatment allocation.
Collapse
Affiliation(s)
| | | | | | | | - Gavin Ha
- Divisions of Human Biology.,Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lisa S Ang
- Divisions of Human Biology.,Clinical Research
| | | | | | | | | | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington, USA
| | | | - Michael T Schweizer
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | | | | | | | | | | | - Robert B Montgomery
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter S Nelson
- Divisions of Human Biology.,Clinical Research.,Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology and.,Department of Urology, University of Washington, Seattle, Washington, USA.,Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington, USA
| |
Collapse
|
47
|
Asrani K, Torres AFC, Woo J, Vidotto T, Tsai HK, Luo J, Corey E, Hanratty B, Coleman I, Yegnasubramanian S, De Marzo AM, Nelson PS, Haffner MC, Lotan TL. Reciprocal YAP1 loss and INSM1 expression in neuroendocrine prostate cancer. J Pathol 2021; 255:425-437. [PMID: 34431104 PMCID: PMC8599638 DOI: 10.1002/path.5781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/30/2021] [Accepted: 08/19/2021] [Indexed: 12/13/2022]
Abstract
Neuroendocrine prostate cancer (NEPC) is a rare but aggressive histologic variant of prostate cancer that responds poorly to androgen deprivation therapy. Hybrid NEPC-adenocarcinoma (AdCa) tumors are common, often eluding accurate pathologic diagnosis and requiring ancillary markers for classification. We recently performed an outlier-based meta-analysis across a number of independent gene expression microarray datasets to identify novel markers that differentiate NEPC from AdCa, including up-regulation of insulinoma-associated protein 1 (INSM1) and loss of Yes-associated protein 1 (YAP1). Here, using diverse cancer gene expression datasets, we show that Hippo pathway-related genes, including YAP1, are among the top down-regulated gene sets with expression of the neuroendocrine transcription factors, including INSM1. In prostate cancer cell lines, transgenic mouse models, and human prostate tumor cohorts, we confirm that YAP1 RNA and YAP1 protein expression are silenced in NEPC and demonstrate that the inverse correlation of INSM1 and YAP1 expression helps to distinguish AdCa from NEPC. Mechanistically, we find that YAP1 loss in NEPC may help to maintain INSM1 expression in prostate cancer cell lines and we further demonstrate that YAP1 silencing likely occurs epigenetically, via CpG hypermethylation near its transcriptional start site. Taken together, these data nominate two additional markers to distinguish NEPC from AdCa and add to data from other tumor types suggesting that Hippo signaling is tightly reciprocally regulated with neuroendocrine transcription factor expression. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Kaushal Asrani
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Alba F. C. Torres
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Juhyung Woo
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Thiago Vidotto
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Harrison K. Tsai
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Current address: Boston Children’s Hospital, Boston, MA
| | - Jun Luo
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA
| | - Brian Hanratty
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA
| | - Srinivasan Yegnasubramanian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA
| | - Michael C. Haffner
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| |
Collapse
|
48
|
Haffner MC, Bhamidipati A, Tsai HK, Esopi DM, Vaghasia AM, Low JY, Patel RA, Guner G, Pham MT, Castagna N, Hicks J, Wyhs N, Aebersold R, De Marzo AM, Nelson WG, Guo T, Yegnasubramanian S. Phenotypic characterization of two novel cell line models of castration-resistant prostate cancer. Prostate 2021; 81:1159-1171. [PMID: 34402095 PMCID: PMC8460612 DOI: 10.1002/pros.24210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/22/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND Resistance to androgen deprivation therapies is a major driver of mortality in advanced prostate cancer. Therefore, there is a need to develop new preclinical models that allow the investigation of resistance mechanisms and the assessment of drugs for the treatment of castration-resistant prostate cancer. METHODS We generated two novel cell line models (LAPC4-CR and VCaP-CR) which were derived by passaging LAPC4 and VCaP cells in vivo and in vitro under castrate conditions. We performed detailed transcriptomic (RNA-seq) and proteomic analyses (SWATH-MS) to delineate expression differences between castration-sensitive and castration-resistant cell lines. Furthermore, we characterized the in vivo and in vitro growth characteristics of these novel cell line models. RESULTS The two cell line derivatives LAPC4-CR and VCaP-CR showed castration-resistant growth in vitro and in vivo which was only minimally inhibited by AR antagonists, enzalutamide, and bicalutamide. High-dose androgen treatment resulted in significant growth arrest of VCaP-CR but not in LAPC4-CR cells. Both cell lines maintained AR expression, but exhibited distinct expression changes on the mRNA and protein level. Integrated analyses including data from LNCaP and the previously described castration-resistant LNCaP-abl cells revealed an expression signature of castration resistance. CONCLUSIONS The two novel cell line models LAPC4-CR and VCaP-CR and their comprehensive characterization on the RNA and protein level represent important resources to study the molecular mechanisms of castration resistance.
Collapse
Affiliation(s)
- Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Akshay Bhamidipati
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Harrison K. Tsai
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - David M. Esopi
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Ajay M. Vaghasia
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Jin-Yih Low
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Radhika A. Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gunes Guner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Hacettepe University Faculty of Medicine, Department of Pathology, Ankara, Turkey
| | - Minh-Tam Pham
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Nicole Castagna
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Jessica Hicks
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Nicolas Wyhs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zürich, Switzerland
- Faculty of Science, University of Zürich, Zürich. Switzerland
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William G. Nelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zürich, Switzerland
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Srinivasan Yegnasubramanian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| |
Collapse
|
49
|
Cejas P, Xie Y, Font-Tello A, Lim K, Syamala S, Qiu X, Tewari AK, Shah N, Nguyen HM, Patel RA, Brown L, Coleman I, Hackeng WM, Brosens L, Dreijerink KMA, Ellis L, Alaiwi SA, Seo JH, Baca S, Beltran H, Khani F, Pomerantz M, Dall'Agnese A, Crowdis J, Van Allen EM, Bellmunt J, Morrisey C, Nelson PS, DeCaprio J, Farago A, Dyson N, Drapkin B, Liu XS, Freedman M, Haffner MC, Corey E, Brown M, Long HW. Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer. Nat Commun 2021; 12:5775. [PMID: 34599169 PMCID: PMC8486778 DOI: 10.1038/s41467-021-26042-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/07/2021] [Indexed: 12/30/2022] Open
Abstract
Neuroendocrine carcinomas (NEC) are tumors expressing markers of neuronal differentiation that can arise at different anatomic sites but have strong histological and clinical similarities. Here we report the chromatin landscapes of a range of human NECs and show convergence to the activation of a common epigenetic program. With a particular focus on treatment emergent neuroendocrine prostate cancer (NEPC), we analyze cell lines, patient-derived xenograft (PDX) models and human clinical samples to show the existence of two distinct NEPC subtypes based on the expression of the neuronal transcription factors ASCL1 and NEUROD1. While in cell lines and PDX models these subtypes are mutually exclusive, single-cell analysis of human clinical samples exhibits a more complex tumor structure with subtypes coexisting as separate sub-populations within the same tumor. These tumor sub-populations differ genetically and epigenetically contributing to intra- and inter-tumoral heterogeneity in human metastases. Overall, our results provide a deeper understanding of the shared clinicopathological characteristics shown by NECs. Furthermore, the intratumoral heterogeneity of human NEPCs suggests the requirement of simultaneous targeting of coexisting tumor populations as a therapeutic strategy. Neuroendocrine carcinomas (NECs) arise from different anatomic sites, but have similar histological and clinical features. Here, the authors show that the epigenetic landscape of a range of NECs converges towards a common epigenetic state, while distinct subtypes occur within neuroendocrine prostate cancer contributing to intratumor heterogeneity in clinical samples.
Collapse
Affiliation(s)
- Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ) and CIBERONC, La Paz University Hospital, Madrid, Spain.
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudeepa Syamala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neel Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Radhika A Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wenzel M Hackeng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lodewijk Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Leigh Ellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Sylvan Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Francesca Khani
- Weill Cornell Medical Center, Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, New York, NY, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | - Jett Crowdis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joaquim Bellmunt
- Beth Israel Deaconess Medical Center and PSMAR-IMIM Lab. Harvard Medical School, Boston, Massachusetts, USA
| | - Colm Morrisey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Anna Farago
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Nicholas Dyson
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Benjamin Drapkin
- Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
50
|
Etzioni R, Haffner MC, Gulati R. Divining Harm-Benefit Tradeoffs of Magnetic Resonance Imaging-targeted Biopsy. Eur Urol 2021; 80:573-574. [PMID: 34479754 DOI: 10.1016/j.eururo.2021.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/13/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Ruth Etzioni
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Pathology, University of Washington, Seattle, WA, USA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| |
Collapse
|