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Zaidi S, Park J, Chan JM, Roudier MP, Zhao JL, Gopalan A, Wadosky KM, Patel RA, Sayar E, Karthaus WR, Kates DH, Chaudhary O, Xu T, Masilionis I, Mazutis L, Chaligné R, Obradovic A, Linkov I, Barlas A, Jungbluth AA, Rekhtman N, Silber J, Manova-Todorova K, Watson PA, True LD, Morrissey C, Scher HI, Rathkopf DE, 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. Proc Natl Acad Sci U S A 2024; 121:e2322203121. [PMID: 38968122 PMCID: PMC11252802 DOI: 10.1073/pnas.2322203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/09/2024] [Indexed: 07/07/2024] Open
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 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 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 current and future antigen-directed therapies, its delineation may yield signatures for patient selection in clinical trials, potentially across distinct cancer types.
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MESH Headings
- Male
- Humans
- Single-Cell Analysis/methods
- Animals
- Mice
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Prostatic Neoplasms/drug therapy
- Antigens, Surface/metabolism
- Antigens, Surface/genetics
- Antigens, Neoplasm/metabolism
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/genetics
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Adenocarcinoma/metabolism
- Adenocarcinoma/drug therapy
- Carcinoma, Neuroendocrine/genetics
- Carcinoma, Neuroendocrine/pathology
- Carcinoma, Neuroendocrine/metabolism
- Carcinoma, Neuroendocrine/drug therapy
- Gene Expression Regulation, Neoplastic
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Prostatic Neoplasms, Castration-Resistant/pathology
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/drug therapy
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Affiliation(s)
- Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Jooyoung Park
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul02841, Korea
| | - Joseph M. Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | | | | | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Kristine M. Wadosky
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY14263
| | - Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Wouter R. Karthaus
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne1015, Switzerland
| | - D. Henry Kates
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ojasvi Chaudhary
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Tianhao Xu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ignas Masilionis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Linas Mazutis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ronan Chaligné
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Aleksandar Obradovic
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY10032
| | - Irina Linkov
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Afsar Barlas
- Molecular Cytology Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New YorkNY10065
| | - Achim A. Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Joachim Silber
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Katia Manova-Todorova
- Molecular Cytology Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New YorkNY10065
| | - Philip A. Watson
- Research Outreach and Compliance, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA98195
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA98195
| | - Howard I. Scher
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Dana E. Rathkopf
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Michael J. Morris
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - David W. Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY14263
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul02841, Korea
- Department of Genetics, Yale University School of Medicine, New Haven, CT06510
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA98195
| | - Charles L. Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY10065
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2
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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.
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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
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Gopalan A. Treatment-related Neuroendocrine Prostate Carcinoma-Diagnostic and Molecular Correlates. Adv Anat Pathol 2024; 31:70-79. [PMID: 38223983 DOI: 10.1097/pap.0000000000000431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Treatment-related neuroendocrine prostate cancer is a distinctive category of prostate cancer that arises after intensive suppression of the androgen receptor by next-generation therapeutic inhibition of androgen receptor signaling. The biological processes that set in motion the series of events resulting in transformation of adenocarcinoma to neuroendocrine carcinoma include genomic (loss of tumor suppressors TP53 and RB1, amplification of oncogenes N-MYC and Aurora Kinase A, dysregulation of transcription factors SOX2, achaete-scute-homolog 1, and others) as well as epigenomic (DNA methylation, EZH2 overexpression, and others). Pathologic diagnosis is key to effective therapy for this disease, and this is aided by localizing metastatic lesions for biopsy using radioligand imaging in the appropriate clinical context. As our understanding of biology evolves, there has been increased morphologic recognition and characterization of tumor phenotypes that are present in this advanced post-treatment setting. New and promising biomarkers (delta-like ligand 3 and others) have been discovered, which opens up novel therapeutic avenues including immunotherapy and antibody-drug conjugates for this lethal disease with currently limited treatment options.
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Rao S, Verrill C, Cerundolo L, Alham NK, Kaya Z, O'Hanlon M, Hayes A, Lambert A, James M, Tullis IDC, Niederer J, Lovell S, Omer A, Lopez F, Leslie T, Buffa F, Bryant RJ, Lamb AD, Vojnovic B, Wedge DC, Mills IG, Woodcock DJ, Tomlinson I, Hamdy FC. Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole-genome sequencing with histopathological features. Genome Med 2024; 16:35. [PMID: 38374116 PMCID: PMC10877771 DOI: 10.1186/s13073-024-01302-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Extension of prostate cancer beyond the primary site by local invasion or nodal metastasis is associated with poor prognosis. Despite significant research on tumour evolution in prostate cancer metastasis, the emergence and evolution of cancer clones at this early stage of expansion and spread are poorly understood. We aimed to delineate the routes of evolution and cancer spread within the prostate and to seminal vesicles and lymph nodes, linking these to histological features that are used in diagnostic risk stratification. METHODS We performed whole-genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and lymph nodes of five treatment-naive patients with locally advanced disease. We spatially mapped the clonal composition of cancer across the prostate and the routes of spread of cancer cells within the prostate and to seminal vesicles and lymph nodes in each individual by analysing a total of > 19,000 copy number corrected single nucleotide variants. RESULTS In each patient, we identified sample locations corresponding to the earliest part of the malignancy. In patient 10, we mapped the spread of cancer from the apex of the prostate to the seminal vesicles and identified specific genomic changes associated with the transformation of adenocarcinoma to amphicrine morphology during this spread. Furthermore, we show that the lymph node metastases in this patient arose from specific cancer clones found at the base of the prostate and the seminal vesicles. In patient 15, we observed increased mutational burden, altered mutational signatures and histological changes associated with whole genome duplication. In all patients in whom histological heterogeneity was observed (4/5), we found that the distinct morphologies were located on separate branches of their respective evolutionary trees. CONCLUSIONS Our results link histological transformation with specific genomic alterations and phylogenetic branching. These findings have implications for diagnosis and risk stratification, in addition to providing a rationale for further studies to characterise the genetic changes causally linked to morphological transformation. Our study demonstrates the value of integrating multi-region sequencing with histopathological data to understand tumour evolution and identify mechanisms of prostate cancer spread.
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Affiliation(s)
- Srinivasa Rao
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
- Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK.
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Zeynep Kaya
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Miriam O'Hanlon
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Alicia Hayes
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Adam Lambert
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Martha James
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Jane Niederer
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Shelagh Lovell
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Altan Omer
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Francisco Lopez
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Tom Leslie
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Richard J Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Alastair D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Boris Vojnovic
- Department of Oncology, University of Oxford, Oxford, UK
| | - David C Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
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