1
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Praharaj M, Shen F, Lee AJ, Zhao L, Nirschl TR, Theodros D, Singh AK, Wang X, Adusei KM, Lombardo KA, Williams RA, Sena LA, Thompson EA, Tam A, Yegnasubramanian S, Pearce EJ, Leone RD, Alt J, Rais R, Slusher BS, Pardoll DM, Powell JD, Zarif JC. Metabolic reprogramming of tumor-associated macrophages using glutamine antagonist JHU083 drives tumor immunity in myeloid-rich prostate and bladder cancer tumors. Cancer Immunol Res 2024:745149. [PMID: 38701369 DOI: 10.1158/2326-6066.cir-23-1105] [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] [Received: 12/27/2023] [Revised: 04/10/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024]
Abstract
Glutamine metabolism in tumor microenvironments critically regulates anti-tumor immunity. Using glutamine-antagonist prodrug JHU083, we report potent tumor growth inhibition in urologic tumors by JHU083-reprogrammed tumor-associated macrophages (TAMs) and tumor-infiltrating monocytes (TIMs). We show JHU083-mediated glutamine antagonism in tumor microenvironments induces TNF, pro-inflammatory, and mTORC1 signaling in intratumoral TAM clusters. JHU083-reprogrammed TAMs also exhibit increased tumor cell phagocytosis and diminished pro-angiogenic capacities. In vivo inhibition of TAM glutamine consumption resulted in increased glycolysis, a broken TCA cycle, and purine metabolism disruption. Although the anti-tumor effect of glutamine antagonism on tumor-infiltrating T cells was moderate, JHU083 promoted a stem cell-like phenotype in CD8+ T cells and decreased Treg abundance. Finally, JHU083 caused a ubiquitous shutdown in glutamine utilizing metabolic pathways in tumor cells, leading to reduced HIF-1alpha, c-MYC phosphorylation, and induction of tumor cell apoptosis, all key anti-tumor features.
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Affiliation(s)
- Monali Praharaj
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Fan Shen
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alex J Lee
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Liang Zhao
- Complete Omics (United States), Baltimore, MD, United States
| | - Thomas R Nirschl
- Johns Hopkins University School of Medicine, Balitmore, MD, United States
| | - Debebe Theodros
- Johns Hopkins University School of Medicine, Baltimore, United States
| | - Alok K Singh
- Johns Hopkins University School of Medicine, Baltimore, United States
| | | | - Kenneth M Adusei
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Raekwon A Williams
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Laura A Sena
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Ada Tam
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Edward J Pearce
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Jesse Alt
- Johns Hopkins University, Baltimore, Maryland, United States
| | - Rana Rais
- Johns Hopkins School of Medicine, Baltimore, MD, United States
| | | | - Drew M Pardoll
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Jelani C Zarif
- Johns Hopkins University School of Medicine, Baltimore, United States
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2
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Mori JO, Elhussin I, Brennen WN, Graham MK, Lotan TL, Yates CC, De Marzo AM, Denmeade SR, Yegnasubramanian S, Nelson WG, Denis GV, Platz EA, Meeker AK, Heaphy CM. Prognostic and therapeutic potential of senescent stromal fibroblasts in prostate cancer. Nat Rev Urol 2024; 21:258-273. [PMID: 37907729 PMCID: PMC11058122 DOI: 10.1038/s41585-023-00827-x] [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] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
The stromal component of the tumour microenvironment in primary and metastatic prostate cancer can influence and promote disease progression. Within the prostatic stroma, fibroblasts are one of the most prevalent cell types associated with precancerous and cancerous lesions; they have a vital role in the structural composition, organization and integrity of the extracellular matrix. Fibroblasts within the tumour microenvironment can undergo cellular senescence, which is a stable arrest of cell growth and a phenomenon that is emerging as a recognized hallmark of cancer. Supporting the idea that cellular senescence has a pro-tumorigenic role, a subset of senescent cells exhibits a senescence-associated secretory phenotype (SASP), which, along with increased inflammation, can promote prostate cancer cell growth and survival. These cellular characteristics make targeting senescent cells and/or modulating SASP attractive as a potential preventive or therapeutic option for prostate cancer.
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Affiliation(s)
- Joakin O Mori
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Isra Elhussin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - W Nathaniel Brennen
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mindy K Graham
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tamara L Lotan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Clayton C Yates
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Angelo M De Marzo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Samuel R Denmeade
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William G Nelson
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gerald V Denis
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA
- Department of Pharmacology and Experimental Therapeutics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Elizabeth A Platz
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alan K Meeker
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher M Heaphy
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA.
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
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3
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Caramella-Pereira F, Zheng Q, Hicks JL, Roy S, Jones T, Pomper M, Antony L, Meeker AK, Yegnasubramanian S, De Marzo AM, Brennen WN. Overexpression of Fibroblast Activation Protein (FAP) in stroma of proliferative inflammatory atrophy (PIA) and primary adenocarcinoma of the prostate. medRxiv 2024:2024.04.04.24305338. [PMID: 38633791 PMCID: PMC11023661 DOI: 10.1101/2024.04.04.24305338] [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: 04/19/2024]
Abstract
Fibroblast activation protein (FAP) is a serine protease upregulated at sites of tissue remodeling and cancer that represents a promising therapeutic and molecular imaging target. In prostate cancer, studies of FAP expression using tissue microarrays are conflicting, such that its clinical potential is unclear. Furthermore, little is known regarding FAP expression in benign prostatic tissues. Here we demonstrated, using a novel iterative multiplex IHC assay in standard tissue sections, that FAP was nearly absent in normal regions, but was increased consistently in regions of proliferative inflammatory atrophy (PIA). In carcinoma, FAP was expressed in all cases, but was highly heterogeneous. High FAP levels were associated with increased pathological stage and cribriform morphology. We verified that FAP levels in cancer correlated with CD163+ M2 macrophage density. In this first report to quantify FAP protein in benign prostate and primary tumors, using standard large tissue sections, we clarify that FAP is present in all primary prostatic carcinomas, supporting its potential clinical relevance. The finding of high levels of FAP within PIA supports the injury/regeneration model for its pathogenesis and suggests that it harbors a protumorigenic stroma. Yet, high levels of FAP in benign regions could lead to false positive FAP-based molecular imaging results in clinically localized prostate cancer.
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4
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Stangis MM, Chen Z, Min J, Glass SE, Jackson JO, Radyk MD, Hoi XP, Brennen WN, Yu M, Dinh HQ, Coffey RJ, Shrubsole MJ, Chan KS, Grady WM, Yegnasubramanian S, Lyssiotis CA, Maitra A, Halberg RB, Dey N, Lau KS. The Hallmarks of Precancer. Cancer Discov 2024; 14:683-689. [PMID: 38571435 DOI: 10.1158/2159-8290.cd-23-1550] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Research on precancers, as defined as at-risk tissues and early lesions, is of high significance given the effectiveness of early intervention. We discuss the need for risk stratification to prevent overtreatment, an emphasis on the role of genetic and epigenetic aging when considering risk, and the importance of integrating macroenvironmental risk factors with molecules and cells in lesions and at-risk normal tissues for developing effective intervention and health policy strategies.
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Affiliation(s)
- Mary M Stangis
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Gastroenterology Division, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Zhengyi Chen
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jimin Min
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah E Glass
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jordan O Jackson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Megan D Radyk
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xen Ping Hoi
- Department of Urology, Houston Methodist Research Institute, Houston, Texas
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - W Nathaniel Brennen
- Genitourinary Cancer Disease Division, Department of Oncology, Johns Hopkins Medicine, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, Johns Hopkins Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins Medicine, Baltimore, Maryland
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Martha J Shrubsole
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Keith S Chan
- Department of Urology, Houston Methodist Research Institute, Houston, Texas
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - William M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Srinivasan Yegnasubramanian
- Genitourinary Cancer Disease Division, Department of Oncology, Johns Hopkins Medicine, Baltimore, Maryland
- Molecular Radiation Science Division, Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, Maryland
- Kidney-Urologic Pathology Division, Department of Pathology, Johns Hopkins Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
- Division of Gastroenterology, Internal Medicine, University of Washington, Seattle, Washington
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Anirban Maitra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard B Halberg
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Gastroenterology Division, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Neelendu Dey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
| | - Ken S Lau
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
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5
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Markowski MC, Taplin ME, Aggarwal R, Sena LA, Wang H, Qi H, Lalji A, Sinibaldi V, Carducci MA, Paller CJ, Marshall CH, Eisenberger MA, Sanin DE, Yegnasubramanian S, Gomes-Alexandre C, Ozbek B, Jones T, De Marzo AM, Denmeade SR, Antonarakis ES. Bipolar androgen therapy plus nivolumab for patients with metastatic castration-resistant prostate cancer: the COMBAT phase II trial. Nat Commun 2024; 15:14. [PMID: 38167882 PMCID: PMC10762051 DOI: 10.1038/s41467-023-44514-2] [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: 07/05/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
Cyclic high-dose testosterone administration, known as bipolar androgen therapy (BAT), is a treatment strategy for patients with metastatic castration-resistant prostate cancer (mCRPC). Here, we report the results of a multicenter, single arm Phase 2 study (NCT03554317) enrolling 45 patients with heavily pretreated mCRPC who received BAT (testosterone cypionate, 400 mg intramuscularly every 28 days) with the addition of nivolumab (480 mg intravenously every 28 days) following three cycles of BAT monotherapy. The primary endpoint of a confirmed PSA50 response rate was met and estimated at 40% (N = 18/45, 95% CI: 25.7-55.7%, P = 0.02 one-sided against the 25% null hypothesis). Sixteen of the PSA50 responses were achieved before the addition of nivolumab. Secondary endpoints included objective response rate (ORR), median PSA progression-free survival, radiographic progression-free survival (rPFS), overall survival (OS), and safety/tolerability. The ORR was 24% (N = 10/42). Three of the objective responses occurred following the addition of nivolumab. After a median follow-up of 17.9 months, the median rPFS was 5.6 (95% CI: 5.4-6.8) months, and median OS was 24.4 (95% CI: 17.6-31.1) months. BAT/nivolumab was well tolerated, resulting in only five (11%) drug related, grade-3 adverse events. In a predefined exploratory analysis, clinical response rates correlated with increased baseline levels of intratumoral PD-1 + T cells. In paired metastatic tumor biopsies, BAT induced pro-inflammatory gene expression changes that were restricted to patients achieving a clinical response. These data suggest that BAT may augment antitumor immune responses that are further potentiated by immune checkpoint blockade.
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Affiliation(s)
- Mark C Markowski
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Laura A Sena
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hao Wang
- Division of Quantitative Sciences, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Hanfei Qi
- Division of Quantitative Sciences, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Aliya Lalji
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Victoria Sinibaldi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Michael A Carducci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Channing J Paller
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Catherine H Marshall
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Mario A Eisenberger
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - David E Sanin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Busra Ozbek
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tracy Jones
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Angelo M De Marzo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Samuel R Denmeade
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Emmanuel S Antonarakis
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Masonic Cancer Center, University of Minnesota Medical Center, Minneapolis, MN, USA
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6
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Chen J, Zheng Q, Hicks JL, Trabzonlu L, Ozbek B, Jones T, Vaghasia AM, Larman TC, Wang R, Markowski MC, Denmeade SR, Pienta KJ, Hruban RH, Antonarakis ES, Gupta A, Dang CV, Yegnasubramanian S, De Marzo AM. MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression. JCI Insight 2023; 8:e169868. [PMID: 37971875 PMCID: PMC10807718 DOI: 10.1172/jci.insight.169868] [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: 02/20/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
Increased mitochondrial function may render some cancers vulnerable to mitochondrial inhibitors. Since mitochondrial function is regulated partly by mitochondrial DNA copy number (mtDNAcn), accurate measurements of mtDNAcn could help reveal which cancers are driven by increased mitochondrial function and may be candidates for mitochondrial inhibition. However, prior studies have employed bulk macrodissections that fail to account for cell type-specific or tumor cell heterogeneity in mtDNAcn. These studies have often produced unclear results, particularly in prostate cancer. Herein, we developed a multiplex in situ method to spatially quantify cell type-specific mtDNAcn. We show that mtDNAcn is increased in luminal cells of high-grade prostatic intraepithelial neoplasia (HGPIN), is increased in prostatic adenocarcinomas (PCa), and is further elevated in metastatic castration-resistant prostate cancer. Increased PCa mtDNAcn was validated by 2 orthogonal methods and is accompanied by increases in mtRNAs and enzymatic activity. Mechanistically, MYC inhibition in prostate cancer cells decreases mtDNA replication and expression of several mtDNA replication genes, and MYC activation in the mouse prostate leads to increased mtDNA levels in the neoplastic prostate cells. Our in situ approach also revealed elevated mtDNAcn in precancerous lesions of the pancreas and colon/rectum, demonstrating generalization across cancer types using clinical tissue samples.
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Affiliation(s)
- Jiayu Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Qizhi Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jessica L. Hicks
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Levent Trabzonlu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Busra Ozbek
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tracy Jones
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Tatianna C. Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Sam R. Denmeade
- Department of Oncology and
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenneth J. Pienta
- Department of Oncology and
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ralph H. Hruban
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Emmanuel S. Antonarakis
- Department of Oncology and
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Chi V. Dang
- Department of Oncology and
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology and
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology and
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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7
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Lee E, Coulter J, Mishra A, Caramella-Pereira F, Demarzo A, Rudek M, Hu C, Han M, DeWeese TL, Yegnasubramanian S, Song DY. Induction of double-strand breaks with the non-steroidal androgen receptor ligand flutamide in patients on androgen suppression: a study protocol for a randomized, double-blind prospective trial. Trials 2023; 24:809. [PMID: 38104131 PMCID: PMC10725600 DOI: 10.1186/s13063-023-07838-4] [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: 01/03/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Prostate cancer remains the most prevalent malignancy and the second-leading cause of cancer-related death in men in the USA. Radiation therapy, typically with androgen suppression, remains a mainstay in the treatment of intermediate- and high-risk, potentially lethal prostate cancers. However, local recurrence and treatment failure remain common. Basic and translational research has determined the potential for using androgen receptor (AR) ligands (e.g., dihydrotestosterone and flutamide) in the context of androgen-deprived prostate cancer to induce AR- and TOP2B-mediated DNA double-strand breaks (DSBs) and thereby synergistically enhance the effect of radiation therapy (RT). The primary aim of this study is to carry out pharmacodynamic translation of these findings to humans. METHODS Patients with newly diagnosed, biopsy-confirmed localized prostatic adenocarcinoma will be recruited. Flutamide, an oral non-steroidal androgen receptor ligand, will be administered orally 6-12 h prior to prostate biopsy (performed under anesthesia prior to brachytherapy seed implantation). Key study parameters will include the assessment of DNA double-strand breaks by γH2A.x foci and AR localization to the nucleus. The initial 6 patients will be treated in a single-arm run-in phase to assess futility by establishing whether at least 2 subjects from this group develop γH2A.x foci in prostate cancer cells. If this criterion is met, the study will advance to a two-arm, randomized controlled phase in which 24 participants will be randomized 2:1 to either flutamide intervention or placebo standard-of-care (with all patients receiving definitive brachytherapy). The key pharmacodynamic endpoint will be to assess whether the extent of γH2A.x foci (proportion of cancer cells positive and number of foci per cancer cell) is greater in patients receiving flutamide versus placebo. Secondary outcomes of this study include an optional, exploratory analysis that will (a) describe cancer-specific methylation patterns of cell-free DNA in plasma and urine and (b) assess the utility of serum and urine samples as a DNA-based biomarker for tracking therapeutic response. DISCUSSION This study will confirm in humans the pharmacodynamic effect of AR ligands to induce transient double-strand breaks when administered in the context of androgen deprivation as a novel therapy for prostate cancer. The findings of this study will permit the development of a larger trial evaluating flutamide pulsed-dose sequencing in association with fractionated external beam RT (+/- brachytherapy). The study is ongoing, and preliminary data collection and recruitment are underway; analysis has yet to be performed. TRIAL REGISTRATION ClinicalTrials.gov NCT03507608. Prospectively registered on 25 April 2018.
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Affiliation(s)
- Emerson Lee
- Johns Hopkins University School of Medicine, Baltimore, USA
| | | | - Alok Mishra
- Department of Oncology, Johns Hopkins University, Baltimore, USA
| | | | - Angelo Demarzo
- Oncology Pathology, Johns Hopkins University, Baltimore, USA
| | - Michelle Rudek
- Department of Oncology, Johns Hopkins University, Baltimore, USA
| | - Chen Hu
- Department of Biostatistics, Johns Hopkins University, Baltimore, USA
| | - Misop Han
- Department of Urology, Johns Hopkins University, Baltimore, USA
| | - Theodore L DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, USA
| | - Srinivasan Yegnasubramanian
- Department of Urology, Johns Hopkins University, Baltimore, USA
- Department of Oncology, Johns Hopkins University, Baltimore, USA
| | - Daniel Y Song
- Department of Urology, Johns Hopkins University, Baltimore, USA.
- Department of Oncology, Johns Hopkins University, Baltimore, USA.
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, USA.
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8
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Huff AL, Longway G, Mitchell JT, Andaloori L, Davis-Marcisak E, Chen F, Lyman MR, Wang R, Mathew J, Barrett B, Rahman S, Leatherman J, Yarchoan M, Azad NS, Yegnasubramanian S, Kagohara LT, Fertig EJ, Jaffee EM, Armstrong TD, Zaidi N. CD4 T cell-activating neoantigens enhance personalized cancer vaccine efficacy. JCI Insight 2023; 8:e174027. [PMID: 38063199 PMCID: PMC10795827 DOI: 10.1172/jci.insight.174027] [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: 07/18/2023] [Accepted: 10/17/2023] [Indexed: 12/18/2023] Open
Abstract
Personalized cancer vaccines aim to activate and expand cytotoxic antitumor CD8+ T cells to recognize and kill tumor cells. However, the role of CD4+ T cell activation in the clinical benefit of these vaccines is not well defined. We previously established a personalized neoantigen vaccine (PancVAX) for the pancreatic cancer cell line Panc02, which activates tumor-specific CD8+ T cells but required combinatorial checkpoint modulators to achieve therapeutic efficacy. To determine the effects of neoantigen-specific CD4+ T cell activation, we generated a vaccine (PancVAX2) targeting both major histocompatibility complex class I- (MHCI-) and MHCII-specific neoantigens. Tumor-bearing mice vaccinated with PancVAX2 had significantly improved control of tumor growth and long-term survival benefit without concurrent administration of checkpoint inhibitors. PancVAX2 significantly enhanced priming and recruitment of neoantigen-specific CD8+ T cells into the tumor with lower PD-1 expression after reactivation compared with the CD8+ vaccine alone. Vaccine-induced neoantigen-specific Th1 CD4+ T cells in the tumor were associated with decreased Tregs. Consistent with this, PancVAX2 was associated with more proimmune myeloid-derived suppressor cells and M1-like macrophages in the tumor, demonstrating a less immunosuppressive tumor microenvironment. This study demonstrates the biological importance of prioritizing and including CD4+ T cell-specific neoantigens for personalized cancer vaccine modalities.
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Affiliation(s)
- Amanda L. Huff
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gabriella Longway
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jacob T. Mitchell
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Lalitya Andaloori
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Emily Davis-Marcisak
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Fangluo Chen
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Melissa R. Lyman
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rulin Wang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jocelyn Mathew
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Benjamin Barrett
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sabahat Rahman
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - James Leatherman
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mark Yarchoan
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nilofer S. Azad
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- inHealth Precision Medicine Program
| | - Luciane T. Kagohara
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Applied Mathematics and Statistics, and
| | - Elana J. Fertig
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Applied Mathematics and Statistics, and
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Todd D. Armstrong
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Neeha Zaidi
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
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9
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Singh AK, Wang R, Lombardo KA, Praharaj M, Bullen CK, Um P, Gupta M, Srikrishna G, Davis S, Komm O, Illei PB, Ordonez AA, Bahr M, Huang J, Gupta A, Psoter KJ, Creisher PS, Li M, Pekosz A, Klein SL, Jain SK, Bivalacqua TJ, Yegnasubramanian S, Bishai WR. Intravenous BCG vaccination reduces SARS-CoV-2 severity and promotes extensive reprogramming of lung immune cells. iScience 2023; 26:107733. [PMID: 37674985 PMCID: PMC10477068 DOI: 10.1016/j.isci.2023.107733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/31/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023] Open
Abstract
Bacillus Calmette-Guérin (BCG) confers heterologous immune protection against viral infections and has been proposed as vaccine against SARS-CoV-2 (SCV2). Here, we tested intravenous BCG vaccination against COVID-19 using the golden Syrian hamster model. BCG vaccination conferred a modest reduction on lung SCV2 viral load, bronchopneumonia scores, and weight loss, accompanied by a reversal of SCV2-mediated T cell lymphopenia, and reduced lung granulocytes. BCG uniquely recruited immunoglobulin-producing plasma cells to the lung suggesting accelerated local antibody production. BCG vaccination also recruited elevated levels of Th1, Th17, Treg, CTLs, and Tmem cells, with a transcriptional shift away from exhaustion markers and toward antigen presentation and repair. Similarly, BCG enhanced recruitment of alveolar macrophages and reduced key interstitial macrophage subsets, that show reduced IFN-associated gene expression. Our observations indicate that BCG vaccination protects against SCV2 immunopathology by promoting early lung immunoglobulin production and immunotolerizing transcriptional patterns among key myeloid and lymphoid populations.
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Affiliation(s)
- Alok K. Singh
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Rulin Wang
- Sydney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Kara A. Lombardo
- Johns Hopkins University, School of Medicine, Department of Urology, Baltimore, MD, USA
| | - Monali Praharaj
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD, USA
| | - C. Korin Bullen
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Peter Um
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Manish Gupta
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Geetha Srikrishna
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Stephanie Davis
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Oliver Komm
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Peter B. Illei
- Johns Hopkins University, School of Medicine, Department of Pathology, Baltimore, MD, USA
| | - Alvaro A. Ordonez
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, USA
| | - Melissa Bahr
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, USA
| | - Joy Huang
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Anuj Gupta
- Sydney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Kevin J. Psoter
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of General Pediatrics, Baltimore, MD, USA
| | - Patrick S. Creisher
- Johns Hopkins University, Bloomberg School of Public Health, The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Baltimore, MD, USA
| | - Maggie Li
- Johns Hopkins University, Bloomberg School of Public Health, The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Baltimore, MD, USA
| | - Andrew Pekosz
- Johns Hopkins University, Bloomberg School of Public Health, The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Baltimore, MD, USA
| | - Sabra L. Klein
- Johns Hopkins University, Bloomberg School of Public Health, The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Baltimore, MD, USA
| | - Sanjay K. Jain
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, USA
| | - Trinity J. Bivalacqua
- Perelman School of Medicine at the University of Pennsylvania, Division of Urology, Department of Surgery, Philadelphia, PA, USA
| | | | - William R. Bishai
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
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10
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Graham MK, Wang R, Chikarmane R, Wodu B, Vaghasia A, Gupta A, Zheng Q, Hicks J, Sysa-Shah P, Pan X, Castagna N, Liu J, Meyers J, Skaist A, Zhang Y, Schuebel K, Simons BW, Bieberich CJ, Nelson WG, Lupold SE, DeWeese TL, De Marzo AM, Yegnasubramanian S. Convergent alterations in the tumor microenvironment of MYC-driven human and murine prostate cancer. bioRxiv 2023:2023.09.07.553268. [PMID: 37905029 PMCID: PMC10614732 DOI: 10.1101/2023.09.07.553268] [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: 11/02/2023]
Abstract
The tissue microenvironment in prostate cancer is profoundly altered. While such alterations have been implicated in driving prostate cancer initiation and progression to aggressive disease, how prostate cancer cells and their precursors mediate those changes is unclear, in part due to the inability to longitudinally study the disease evolution in human tissues. To overcome this limitation, we performed extensive single-cell RNA-sequencing (scRNA-seq) and rigorous molecular pathology of the comparative biology between human prostate cancer and key time points in the disease evolution of a genetically engineered mouse model (GEMM) of prostate cancer. Our studies of human tissues, with validation in a large external data set, revealed that cancer cell-intrinsic activation of MYC signaling was the top up-regulated pathway in human cancers, representing a common denominator across the well-known molecular and pathological heterogeneity of human prostate cancer. Likewise, numerous non-malignant cell states in the tumor microenvironment (TME), including non-cancerous epithelial, immune, and fibroblast cell compartments, were conserved across individuals, raising the possibility that these cell types may be a sequelae of the convergent MYC activation in the cancer cells. To test this hypothesis, we employed a GEMM of prostate epithelial cell-specific MYC activation in two mouse strains. Cell communication network and pathway analyses suggested that MYC oncogene-expressing neoplastic cells, directly and indirectly, reprogrammed the TME during carcinogenesis, leading to the emergence of cascading cell state alterations in neighboring epithelial, immune, and fibroblast cell types that paralleled key findings in human prostate cancer. Importantly, among these changes, the progression from a precursor-enriched to invasive-cancer-enriched state was accompanied by a cell-intrinsic switch from pro-immunogenic to immunosuppressive transcriptional programs with coinciding enrichment of immunosuppressive myeloid and Treg cells in the immune microenvironment. These findings implicate activation of MYC signaling in reshaping convergent aspects of the TME of prostate cancer as a common denominator across the otherwise well-documented molecular heterogeneity of human prostate cancer.
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11
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Graham MK, Mao S, Viswanathan AN, Wang R, Wodu B, Gupta A, Vaghasia A, Leitzel J, Lowe K, Pasquale SD, Kaplin D, DeWeese TL, Yegnasubramanian S. Defining the Transcriptional Landscapes of the Tumor Microenvironment of Cervical and Vaginal Cancers at Single-Cell Resolution. Int J Radiat Oncol Biol Phys 2023; 117:e531. [PMID: 37785648 DOI: 10.1016/j.ijrobp.2023.06.1813] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Malignancies found within vaginal tissue are often diagnosed as cancers of the cervix, vulva, or urethra and are clinically treated with similar modalities. However, the rarity of vaginal cancer may be an artifice of categorization; current treatment paradigms do not take into account tissue-specific mutations and differences in mechanistic pathways intracellularly. Understanding the shared and distinctly different transcriptional profiles of vaginal and cervical tumors at a single-cell resolution will provide insights in vaginal tumor biology and will open avenues for future clinical interventions. MATERIALS/METHODS Biopsies of tumor and adjacent normal tissue from 9 patients (3 adenocarcinomas (ADC), 3 squamous cell carcinomas (SCC) from the cervix, and 3 vaginal SCC) were collected and analyzed by single-cell RNA sequencing (scRNA-seq) to compare the tumor, immune, and stromal features of cervical and vaginal cancers. RESULTS Collectively, over 50,000 cells were analyzed by scRNA-seq in this study. We performed dimensionality reduction and clustering analysis of the single-cell transcriptomes to identify the major cell types composing the vaginal and cervical tumor tissues. Compared to Cervical SCC, Vaginal SCC tissues showed reduced fractions of macrophages (-2.7 log2-fold; padj < 0.02) and T cells (-3.7 log2-fold; padj < 0.02) by differential cell proportion analysis (RAISIN). Likewise, the vaginal SCC epithelial cell compartments showed downregulation of inflammatory pathways including TNF signaling via NFKB (NES = -5.7, padj = 5.0 × 10-19), IL2 STAT5 signaling (NES = -4.5, padj = 1.6 × 10-12), and interferon gamma response (NES = -4.3, padj = 9.4 × 10-12), among the Hallmark pathway collection. On the other hand, vaginal SCC epithelial cells showed significant upregulation of oxidative phosphorylation (NES = 4.8, padj = 1.7 × 10-17), p53 pathway (NES = 4.2, padj = 1.8 × 10-13), mTORC1 signaling (NES = 4.2, padj = 1.9 × 10-13), and estrogen early and late response (NES = 4.0, padj < 7.5 × 10-12) compared to cervical SCC. CONCLUSION These results highlight distinct differences in the cell type composition and cancer epithelial pathways in vaginal vs. cervical SCC. Among upregulated pathways in vaginal SCC, ER and mTORC1 pathway activation may represent targets for therapeutic intervention worthy of further investigation.
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Affiliation(s)
- M K Graham
- Department of Urology, Northwestern University, Chicago, IL; Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - S Mao
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - A N Viswanathan
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - R Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - B Wodu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - A Gupta
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - A Vaghasia
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - J Leitzel
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - K Lowe
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - S Di Pasquale
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - D Kaplin
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - T L DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - S Yegnasubramanian
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
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12
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McCammack E, Alcorn SR, LaVigne A, Wright JL, DeWeese TL, Yegnasubramanian S, Deville C. Stereotactic Radiotherapy Deserts are Under-Represented among Radiation Oncology Alternative Payment Model Sites. Int J Radiat Oncol Biol Phys 2023; 117:e605. [PMID: 37785824 DOI: 10.1016/j.ijrobp.2023.06.1973] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) In bundled payment models including the proposed Radiation Oncology Alternative Payment Model (RO-APM), reimbursement favors shorter treatment paradigms like stereotactic radiotherapy (SRT). However, SRT requires specialized equipment, staff, and quality assurance procedures not available across the US. To understand the geospatial distribution of SRT and its impact on bundled payment models, we investigated the interplay between SRT resources with sociodemographic characteristics and oncologic outcomes for an index site of prostate cancer (PC). MATERIALS/METHODS We constructed an ecologic study model using data from the HRSA Area Health Resources, AMA Physician Masterfile, USDA Agriculture Economic Research Service, Medicare Provider and Service Files, and NIH Cancer State Profiles. SRT use was operationalized as the presence of Medicare SRT billing codes. Sociodemographic variables included county racial distributions, %poverty, and rural vs. urban classification. Provider to patient at risk density (PPRD) was defined as number of radiation oncologists per 100,000 males ≥65 years. PC incidence and death rates were evaluated. Uni- and multivariable logistic regressions examined links between SRT use, proposed RO-APM status, PPRD, sociodemographic variables, and PC oncologic outcomes at the US county level. All listed statistics demonstrated p <0.05. RESULTS SRT use was identified in 13% of all 3140 counties and in 49% of counties with documented RO providers. In univariable analyses, odds of SRT use was higher in counties that were metro [odds ratio (OR) 19.9] and with higher %Black constituents (OR 6.95); odds decreased with higher %poverty (OR 0.92). Among counties with RO providers, odds of SRT use increased with higher PPRD (OR 1.01). Odds of SRT use was associated with higher PC incidence (1.01) but lower death rates (OR 0.99). SRT use was more common in participating RO-APM counties (OR 2.66); moreover, magnitude and direction of associations between sociodemographic variables and RO-APM participation were similar to those for SRT use. In multivariable analysis, SRT use remained significantly associated with metro status, %Black constituents, PPRD, and PC death rates. CONCLUSION Both SRT use and proposed RO-APM participation were most prevalent in metro counties with higher PPRD and %Black populations, likely reflecting presence of densely populated cities with high health resources. If SRT is incentivized in future reimbursement models, then rural, lower resource communities without SRT may be disadvantaged. Lack of association between SRT and PC incidence indicates the presence of "SRT deserts"-counties with high oncologic need but no SRT. To enable visualization of SRT deserts and encourage interventions aimed at reducing disparities in SRT access, our results will be included in an interactive web platform (bit.ly/density maps).
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Affiliation(s)
| | - S R Alcorn
- Department of Radiation Oncology, University of Minnesota Medical School, Minneapolis, MN
| | - A LaVigne
- Johns Hopkins University School of Medicine, Baltimore, MA
| | - J L Wright
- Johns Hopkins Medicine, Department of Radiation Oncology, Baltimore, MD
| | - T L DeWeese
- Johns Hopkins University School of Medicine, Department of Radiation Oncology and Molecular Radiation Sciences, Baltimore, MD
| | - S Yegnasubramanian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - C Deville
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
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13
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Rajeh A, Cornman HL, Gupta A, Szeto MD, Kambala A, Oladipo O, Parthasarathy V, Deng J, Wheelan S, Pritchard T, Kwatra MM, Semenov YR, Gusev A, Yegnasubramanian S, Kwatra SG. Somatic mutations reveal hyperactive Notch signaling and racial disparities in prurigo nodularis. medRxiv 2023:2023.09.25.23295810. [PMID: 37808834 PMCID: PMC10557842 DOI: 10.1101/2023.09.25.23295810] [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: 10/10/2023]
Abstract
Prurigo nodularis (PN) is a chronic inflammatory skin disease that disproportionately affects African Americans and is characterized by pruritic skin nodules of unknown etiology. Little is known about genetic alterations in PN pathogenesis, especially relating to somatic events which are often implicated in inflammatory conditions. We thus performed whole-exome sequencing on 54 lesional and nonlesional skin biopsies from 17 PN patients and 10 atopic dermatitis (AD) patients for comparison. Somatic mutational analysis revealed that PN lesional skin harbors pervasive somatic mutations in fibrotic, neurotropic, and cancer-associated genes. Nonsynonymous mutations were most frequent in NOTCH1 and the Notch signaling pathway, a regulator of cellular proliferation and tissue fibrosis, and NOTCH1 mutations were absent in AD. Somatic copy-number analysis, combined with expression data, showed that recurrently deleted and downregulated genes in PN lesional skin are associated with axonal guidance and extension. Follow-up immunofluorescence validation demonstrated increased NOTCH1 expression in PN lesional skin fibroblasts and increased Notch signaling in PN lesional dermis. Finally, multi-center data revealed a significantly increased risk of NOTCH1-associated diseases in PN patients. In characterizing the somatic landscape of PN, we uncover novel insights into its pathophysiology and identify a role for dysregulated Notch signaling in PN.
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Affiliation(s)
- Ahmad Rajeh
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hannah L Cornman
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anuj Gupta
- The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Mindy D Szeto
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anusha Kambala
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olusola Oladipo
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Varsha Parthasarathy
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Junwen Deng
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Wheelan
- Present affiliation: National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
| | - Thomas Pritchard
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madan M Kwatra
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander Gusev
- Division of Genetics, Brigham & Women's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Srinivasan Yegnasubramanian
- The Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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14
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Dykema AG, Zhang J, Cheung LS, Connor S, Zhang B, Zeng Z, Cherry CM, Li T, Caushi JX, Nishimoto M, Munoz AJ, Ji Z, Hou W, Zhan W, Singh D, Zhang T, Rashid R, Mitchell-Flack M, Bom S, Tam A, Ionta N, Aye THK, Wang Y, Sawosik CA, Tirado LE, Tomasovic LM, VanDyke D, Spangler JB, Anagnostou V, Yang S, Spicer J, Rayes R, Taube J, Brahmer JR, Forde PM, Yegnasubramanian S, Ji H, Pardoll DM, Smith KN. Lung tumor-infiltrating T reg have divergent transcriptional profiles and function linked to checkpoint blockade response. Sci Immunol 2023; 8:eadg1487. [PMID: 37713507 PMCID: PMC10629528 DOI: 10.1126/sciimmunol.adg1487] [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: 12/08/2022] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
Regulatory T cells (Treg) are conventionally viewed as suppressors of endogenous and therapy-induced antitumor immunity; however, their role in modulating responses to immune checkpoint blockade (ICB) is unclear. In this study, we integrated single-cell RNA-seq/T cell receptor sequencing (TCRseq) of >73,000 tumor-infiltrating Treg (TIL-Treg) from anti-PD-1-treated and treatment-naive non-small cell lung cancers (NSCLC) with single-cell analysis of tumor-associated antigen (TAA)-specific Treg derived from a murine tumor model. We identified 10 subsets of human TIL-Treg, most of which have high concordance with murine TIL-Treg subsets. Only one subset selectively expresses high levels of TNFRSF4 (OX40) and TNFRSF18 (GITR), whose engangement by cognate ligand mediated proliferative programs and NF-κB activation, as well as multiple genes involved in Treg suppression, including LAG3. Functionally, the OX40hiGITRhi subset is the most highly suppressive ex vivo, and its higher representation among total TIL-Treg correlated with resistance to PD-1 blockade. Unexpectedly, in the murine tumor model, we found that virtually all TIL-Treg-expressing T cell receptors that are specific for TAA fully develop a distinct TH1-like signature over a 2-week period after entry into the tumor, down-regulating FoxP3 and up-regulating expression of TBX21 (Tbet), IFNG, and certain proinflammatory granzymes. Transfer learning of a gene score from the murine TAA-specific TH1-like Treg subset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1-responding tumors. These findings demonstrate that TIL-Treg partition into multiple distinct transcriptionally defined subsets with potentially opposing effects on ICB-induced antitumor immunity and suggest that TAA-specific TIL-Treg may positively contribute to antitumor responses.
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Affiliation(s)
- Arbor G. Dykema
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jiajia Zhang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Laurene S. Cheung
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sydney Connor
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Boyang Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Zhen Zeng
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Taibo Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Justina X. Caushi
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marni Nishimoto
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew J. Munoz
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Wenpin Hou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wentao Zhan
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dipika Singh
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tianbei Zhang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rufiaat Rashid
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marisa Mitchell-Flack
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sadhana Bom
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ada Tam
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nick Ionta
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thet H. K. Aye
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yi Wang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Camille A. Sawosik
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lauren E. Tirado
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Luke M. Tomasovic
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Derek VanDyke
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie B. Spangler
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Valsamo Anagnostou
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephen Yang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Roni Rayes
- Department of Surgery, McGill University, Montreal, Canada
| | - Janis Taube
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Julie R. Brahmer
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Patrick M. Forde
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Srinivasan Yegnasubramanian
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Drew M. Pardoll
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kellie N. Smith
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
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15
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Gupta H, Inoue H, Nakai Y, Nakayama M, Jones T, Hicks JL, Kumar B, Gurel M, Nelson WG, Marzo AMD, Yegnasubramanian S. Progressive Spreading of DNA Methylation in the GSTP1 Promoter CpG Island across Transitions from Precursors to Invasive Prostate Cancer. Cancer Prev Res (Phila) 2023; 16:449-460. [PMID: 37347938 PMCID: PMC10529302 DOI: 10.1158/1940-6207.capr-22-0485] [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: 12/26/2022] [Revised: 06/08/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023]
Abstract
Glutathione S-transferase pi 1 (GSTP1) is lowly expressed in normal prostate luminal cells and becomes induced in most proliferative inflammatory atrophy (PIA) lesions. GSTP1 becomes silenced in prostatic intraepithelial neoplasia (PIN) and prostate adenocarcinoma (CaP) via cytosine-phospho-guanine (CpG) island promoter hypermethylation. However, GSTP1 methylation patterns in PIA and PIN, and their relationship to patterns in CaP are poorly understood. We used bisulfite genomic sequencing to examine patterns of GSTP1 promoter CpG island methylation in laser capture microdissected benign, PIA, PIN, and CaP regions from 32 subjects that underwent radical prostatectomy. We analyzed 908 sequence clones across 24 normal epithelium, 37 PIA, 18 PIN, and 23 CaP regions, allowing assessment of 34,863 CpG sites with allelic phasing. Normal and PIA lesions were mostly unmethylated with 0.52 and 1.3% of total CpG sites methylated, respectively. PIN and CaP lesions had greater methylation with 24% and 51% of total CpG sites methylated, respectively. The degree of GSTP1 methylation showed progression from PIA << PIN < CaP. PIN lesions showed more partial methylation compared with CaP lesions. Partially methylated lesions were enriched for methylation changes at AP1 and SP1 transcription factor binding sites. These results demonstrate that methylation density in the GSTP1 CpG island in PIN was intermediate relative to that in normal prostate epithelium/PIA and CaP lesions. These results are consistent with gradual spreading of DNA methylation centered at the SP1/AP1 transcription factor binding sites in precursor lesions, with subsequent spreading of methylation across the entire CpG island in transition to CaP. PREVENTION RELEVANCE DNA hypermethylation at the GSTP1 promoter progressively spreads from being unmethylated in normal prostate to intermediate levels in precursor lesions to extensive methylation in cancer. This molecular progression of GSTP1 promoter methylation patterns in early prostate carcinogenesis could be useful for identification and interception of prostate cancer precursors.
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Affiliation(s)
| | - Hitoshi Inoue
- Sidney Kimmel Comprehensive Cancer Center
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Ikeda Municipal Hospital, Japan
| | - Yasutomo Nakai
- Sidney Kimmel Comprehensive Cancer Center
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Osaka International Cancer Institute, Japan
| | - Masashi Nakayama
- Sidney Kimmel Comprehensive Cancer Center
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Osaka International Cancer Institute, Japan
| | - Tracy Jones
- Sidney Kimmel Comprehensive Cancer Center
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jessica L. Hicks
- Sidney Kimmel Comprehensive Cancer Center
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Meltem Gurel
- Sidney Kimmel Comprehensive Cancer Center
- Department of Urology, Ikeda Municipal Hospital, Japan
- BenevolentAI, London, UK
| | - William G. Nelson
- Sidney Kimmel Comprehensive Cancer Center
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology; Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Angelo M. De Marzo
- Sidney Kimmel Comprehensive Cancer Center
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology; Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology; Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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16
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Kagan AB, Garrison DA, Anders NM, Webster J, Baker SD, Yegnasubramanian S, Rudek MA. DNA methyltransferase inhibitor exposure-response: Challenges and opportunities. Clin Transl Sci 2023; 16:1309-1322. [PMID: 37345219 PMCID: PMC10432879 DOI: 10.1111/cts.13548] [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: 02/22/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Although DNA methyltransferase inhibitors (DNMTis), such as azacitidine and decitabine, are used extensively in the treatment of myelodysplastic syndromes and acute myeloid leukemia, there remain unanswered questions about DNMTi's mechanism of action and predictors of clinical response. Because patients often remain on single-agent DNMTis or DNMTi-containing regimens for several months before knowing whether clinical benefit can be achieved, the development and clinical validation of response-predictive biomarkers represents an important unmet need in oncology. In this review, we will summarize the clinical studies that led to the approval of azacitidine and decitabine, as well as the real-world experience with these drugs. We will then focus on biomarker development for DNMTis-specifically, efforts at determining exposure-response relationships and challenges that remain impacting the broader clinical translation of these methods. We will highlight recent progress in liquid-chromatography tandem mass spectrometry technology that has allowed for the simultaneous measurement of decitabine genomic incorporation and global DNA methylation, which has significant potential as a mechanism-of-action based biomarker in patients on DNMTis. Last, we will cover important research questions that need to be addressed in order to optimize this potential biomarker for clinical use.
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Affiliation(s)
- Amanda B. Kagan
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Dominique A. Garrison
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Nicole M. Anders
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Jonathan A. Webster
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Sharyn D. Baker
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Srinivasan Yegnasubramanian
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Michelle A. Rudek
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
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17
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Obradovic A, Ager C, Turunen M, Nirschl T, Khosravi-Maharlooei M, Iuga A, Jackson CM, Yegnasubramanian S, Tomassoni L, Fernandez EC, McCann P, Rogava M, DeMarzo AM, Kochel CM, Allaf M, Bivalacqua T, Lim M, Realubit R, Karan C, Drake CG, Califano A. Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators. Cancer Cell 2023; 41:933-949.e11. [PMID: 37116491 PMCID: PMC10193511 DOI: 10.1016/j.ccell.2023.04.003] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/13/2022] [Accepted: 04/06/2023] [Indexed: 04/30/2023]
Abstract
Due to their immunosuppressive role, tumor-infiltrating regulatory T cells (TI-Tregs) represent attractive immuno-oncology targets. Analysis of TI vs. peripheral Tregs (P-Tregs) from 36 patients, across four malignancies, identified 17 candidate master regulators (MRs) as mechanistic determinants of TI-Treg transcriptional state. Pooled CRISPR-Cas9 screening in vivo, using a chimeric hematopoietic stem cell transplant model, confirmed the essentiality of eight MRs in TI-Treg recruitment and/or retention without affecting other T cell subtypes, and targeting one of the most significant MRs (Trps1) by CRISPR KO significantly reduced ectopic tumor growth. Analysis of drugs capable of inverting TI-Treg MR activity identified low-dose gemcitabine as the top prediction. Indeed, gemcitabine treatment inhibited tumor growth in immunocompetent but not immunocompromised allografts, increased anti-PD-1 efficacy, and depleted MR-expressing TI-Tregs in vivo. This study provides key insight into Treg signaling, specifically in the context of cancer, and a generalizable strategy to systematically elucidate and target MR proteins in immunosuppressive subpopulations.
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Affiliation(s)
- Aleksandar Obradovic
- Columbia Center for Translational Immunology, Irving Medical Center, New York, NY, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Casey Ager
- Columbia Center for Translational Immunology, Irving Medical Center, New York, NY, USA; Department of Hematology Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mikko Turunen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Thomas Nirschl
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Alina Iuga
- Department of Pathology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Christopher M Jackson
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Lorenzo Tomassoni
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ester Calvo Fernandez
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Patrick McCann
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Meri Rogava
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Angelo M DeMarzo
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christina M Kochel
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mohamad Allaf
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Trinity Bivalacqua
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Lim
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, CA, USA
| | - Ronald Realubit
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; J.P. Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Karan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; J.P. Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles G Drake
- Columbia Center for Translational Immunology, Irving Medical Center, New York, NY, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; J.P. Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
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18
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Skinner NE, Ogega CO, Frumento N, Clark KE, Paul H, Yegnasubramanian S, Schuebel K, Meyers J, Gupta A, Wheelan S, Cox AL, Crowe JE, Ray SC, Bailey JR. Corrigendum: Convergent antibody responses are associated with broad neutralization of hepatitis C virus. Front Immunol 2023; 14:1201033. [PMID: 37180140 PMCID: PMC10167485 DOI: 10.3389/fimmu.2023.1201033] [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: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2023.1135841.].
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Affiliation(s)
- Nicole E. Skinner
- Center for Vaccines and Immunity, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Medicine, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Clinton O. Ogega
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Nicole Frumento
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kaitlyn E. Clark
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Harry Paul
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Kornel Schuebel
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jennifer Meyers
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Anuj Gupta
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sarah Wheelan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrea L. Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - James E. Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Stuart C. Ray
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Justin R. Bailey
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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19
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Alexandre CG, Hicks J, Jones T, Isaacs JT, Bowers K, Skist A, Sena L, Meyers J, Antonarakis E, Sanin D, Qi H, Denmeade S, Markowski M, Yegnasubramanian S, De Marzo A. Abstract 4345: Molecular pathology studies reveal PD1+ CD8 T cell density correlates with response to supraphysiological testosterone treatment in pre-treatment biopsies and MYC mRNA and protein correlate with response after treatment. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4345] [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
While most patients with metastatic prostatic adenocarcinoma respond initially, nearly all develop resistance to multiple lines of androgen deprivation therapies. This is related to overexpression of the androgen receptor (AR), which is frequently driven by AR amplification. In some patients, increased AR renders tumor cells sensitive to high dose androgens which paradoxically inhibits their growth. Bipolar Androgen Therapy (BAT) was introduced in which patients with castration resistant prostate cancer (CRPC) are treated intermittently with high dose testosterone. This produces biochemical and objective responses, and may re-sensitize prostate cancer to subsequent second generation AR inhibitors. This study utilizes samples from a recently performed clinical trial for patients with CRPC that included sequential biopsies of soft tissue metastases before BAT and after 3 cycles of BAT and before patients were treated with nivolumab.Tumor cells were present in FFPE blocks for both the pretreatment and C4D1 time points for 24 of the patients. These FFPE samples were stained using a recently validated iterative multiplex IHC assay containing 6 antibodies including: CD3 (T cells), CD4 (Helper T Cells), CD8 (Cytotoxic T Cells), PD1 (T Cell Checkpoint), FOXP3 (T-Reg cells), and Keratin 8 (epithelial cell marker). Biopsy slides were scanned after each round of staining and whole slide scans were imported into the HALO image analysis where they underwent color deconvolution, image registration and fusion. Regions of tumor were demarcated manually, and computerized automated image analysis was used to determine cell densities for 8 cell phenotypes (total CD3+, CD3+CD4+, CD3+CD8+, CD3+CD4+Foxp3+, CD3+CD4+PD1+, CD3+CD8+PD1+, CD3+CD4+PD1-, CD3+CD8+PD1-). There was a higher density of CD3+CD8+PD1+ cells in the pretreatment biopsies of men who responded (R) (to BAT) as compared with those who did not respond (NR)(p=0.015 Wilcoxon rank-sum test; mean 92.7 [R] vs 13.9 [NR]). The difference in R vs. NR was less and not significant in the CD3+CD8+PD1- population. There was a trend towards a higher density of CD3+CD4+PD1+ cells in the pretreatment samples in responders, but less so in the CD3+CD4+PD1- population. In the C4D1 biopsies, only CD3+ total cells were significantly higher in the R vs. NR (P=0.02), but the other phenotypes were not. We conclude that increased density of CD3+C8+PD1+, but not CD3+CD8+PD1- cells was present in pre-treatment biopsies in responders as compared with non-responders to BAT. These results indicate that men who are likely to respond to high dose testosterone treatment harbor tumors that are immunologically distinct prior to treatment than those men unlikely to respond. Additional spatial analysis and comparisons with RNAseq data will be presented.
Citation Format: Carolina Gomes Alexandre, Jessica Hicks, Tracy Jones, John T Isaacs, Kiara Bowers, Alyza Skist, Laura Sena, Jennifer Meyers, Emmanuel Antonarakis, David Sanin, Hanfei Qi, Samuel Denmeade, Mark Markowski, Srinivasan Yegnasubramanian, Angelo De Marzo. Molecular pathology studies reveal PD1+ CD8 T cell density correlates with response to supraphysiological testosterone treatment in pre-treatment biopsies and MYC mRNA and protein correlate with response after treatment. [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 4345.
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Affiliation(s)
| | - Jessica Hicks
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tracy Jones
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - John T Isaacs
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kiara Bowers
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alyza Skist
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - Laura Sena
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | - David Sanin
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - Hanfei Qi
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Mark Markowski
- 1Johns Hopkins University School of Medicine, Baltimore, MD
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20
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Mitchell JT, Huff A, Davis-Marcisak E, Chen F, Armstrong TD, Kagohara LT, Leatherman J, Wang R, Yegnasubramanian S, Jaffee EM, Fertig EJ, Zaidi N. Abstract 5076: Combination PancVAX neo-epitope vaccine with anti-CTLA-4 and anti-PD-1 antibodies enhances infiltration of cytotoxic T cells and mitigates T cell exhaustion in a murine model of pancreatic ductal adenocarcinoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5076] [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
Pancreatic ductal adenocarcinoma (PDAC) is a deadly cancer with a low tumor mutational burden and therefore few neoantigen targets that can be recognized by cytotoxic T cells. Most PDACs are thus insensitive to either single or dual immune checkpoint inhibitor (ICI) therapy. Personalized neoantigen vaccines can expand the number and repertoire of anti-tumor T cells that infiltrate the tumor and mediate cytotoxicity. To model a personalized neoantigen vaccine treatment strategy in PDAC, we previously developed PancVAX, a peptide-based vaccine targeting 12 neoantigens expressed in the murine pancreatic cell line Panc02 (Kinkead et al, JCI Insight 2018). Although we observed increased T cell infiltration present in the tumor post-vaccination, these cells expressed high levels of exhaustion markers. We therefore hypothesized that sequential administration of anti-CTLA-4 and anti-PD-1 would enhance the pool of T cells primed by the neoantigen vaccine and maintain activation of antigen-experienced T cells, respectively, to yield optimal and durable neoantigen-specific anti-tumor immunity in PDAC. To address this, mice bearing subcutaneous Panc02 tumors were vaccinated with two rounds of the PancVAX neoantigen vaccine followed by anti-CTLA-4 and anti-PD-1 3 days later. Anti-PD-1 maintenance was given twice weekly beginning at the first vaccine dose. Twelve days after the last peptide vaccine dose, tumors were harvested and dissociated into single-cell suspensions for paired single-cell RNA-sequencing and TCR-sequencing. Mice that were untreated or given ICIs without PancVAX had the highest proportions of CD8+ T cells expressing exhaustion markers. PancVAX-treated mice had more intratumoral cycling CD8 T cells and effector CD8+ T cells with high cytotoxic gene expression. Among mice treated with PancVAX, tumors from mice treated with PancVAX + anti-PD1 or PancVAX + anti-PD1 + anti-CTLA-4 had the highest proportions of effector CD8+ T cells. Ongoing analyses include differential gene expression and pathway analysis between treatment conditions in the T cell compartment in mice treated with combination ICI and PancVAX. Additionally, we will assess changes in T cell clonality and diversity within the tumors when mice are treated with single or combination therapy. These results will define a transcriptional signature associated with the generation of a productive anti-tumor immune response when neoantigen vaccines and ICI are used in combination. This work demonstrates how the addition of ICIs to personalized neo-epitope vaccines for PDAC can further enhance the quality of vaccine-induced T cell effector function in an otherwise immunologically cold tumor type and supports their inclusion in neoantigen vaccination strategies for patients with PDAC.
Citation Format: Jacob T. Mitchell, Amanda Huff, Emily Davis-Marcisak, Fangluo Chen, Todd D. Armstrong, Luciane T. Kagohara, James Leatherman, Rulin Wang, Srinivasan Yegnasubramanian, Elizabeth M. Jaffee, Elana J. Fertig, Neeha Zaidi. Combination PancVAX neo-epitope vaccine with anti-CTLA-4 and anti-PD-1 antibodies enhances infiltration of cytotoxic T cells and mitigates T cell exhaustion in a murine model of pancreatic ductal adenocarcinoma. [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 5076.
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Affiliation(s)
| | - Amanda Huff
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Fangluo Chen
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | - Rulin Wang
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | - Neeha Zaidi
- 1Johns Hopkins University School of Medicine, Baltimore, MD
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21
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Botsis T, Murray JC, Ghanem P, Balan A, Kernagis A, Hardart K, He T, Spiker J, Kreimeyer K, Tao J, Baras AS, Yegnasubramanian S, Canzoniero J, Anagnostou V. Precision Oncology Core Data Model to Support Clinical Genomics Decision Making. JCO Clin Cancer Inform 2023; 7:e2200108. [PMID: 37040583 PMCID: PMC10281442 DOI: 10.1200/cci.22.00108] [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: 07/25/2022] [Revised: 10/26/2022] [Accepted: 01/20/2023] [Indexed: 04/13/2023] Open
Abstract
PURPOSE Precision oncology mandates developing standardized common data models (CDMs) to facilitate analyses and enable clinical decision making. Expert-opinion-based precision oncology initiatives are epitomized in Molecular Tumor Boards (MTBs), which process large volumes of clinical-genomic data to match genotypes with molecularly guided therapies. METHODS We used the Johns Hopkins University MTB as a use case and developed a precision oncology core data model (Precision-DM) to capture key clinical-genomic data elements. We leveraged existing CDMs, building upon the Minimal Common Oncology Data Elements model (mCODE). Our model was defined as a set of profiles with multiple data elements, focusing on next-generation sequencing and variant annotations. Most elements were mapped to terminologies or code sets and the Fast Healthcare Interoperability Resources (FHIR). We subsequently compared our Precision-DM with existing CDMs, including the National Cancer Institute's Genomic Data Commons (NCI GDC), mCODE, OSIRIS, the clinical Genome Data Model (cGDM), and the genomic CDM (gCDM). RESULTS Precision-DM contained 16 profiles and 355 data elements. 39% of the elements derived values from selected terminologies or code sets, and 61% were mapped to FHIR. Although we used most elements contained in mCODE, we significantly expanded the profiles to include genomic annotations, resulting in a partial overlap of 50.7% between our core model and mCODE. Limited overlap was noted between Precision-DM and OSIRIS (33.2%), NCI GDC (21.4%), cGDM (9.3%), and gCDM (7.9%). Precision-DM covered most of the mCODE elements (87.7%), with less coverage for OSIRIS (35.8%), NCI GDC (11%), cGDM (26%) and gCDM (33.3%). CONCLUSION Precision-DM supports clinical-genomic data standardization to support the MTB use case and may allow for harmonized data pulls across health care systems, academic institutions, and community medical centers.
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Affiliation(s)
- Taxiarchis Botsis
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Joseph C. Murray
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Paola Ghanem
- Department of Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Archana Balan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alexander Kernagis
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kent Hardart
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ting He
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jonathan Spiker
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kory Kreimeyer
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica Tao
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alexander S. Baras
- Department of Pathology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Srinivasan Yegnasubramanian
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jenna Canzoniero
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Valsamo Anagnostou
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
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Jackson C, Cherry C, Bom S, Dykema AG, Thompson E, Zheng M, Ji Z, Hou W, Li R, Zhang H, Choi J, Rodriguez F, Weingart J, Yegnasubramanian S, Lim M, Bettegowda C, Powell J, Eliesseff J, Ji H, Pardoll D. Distinct Myeloid Derived Suppressor Cell Populations Promote Tumor Aggression in Glioblastoma. bioRxiv 2023:2023.03.26.534192. [PMID: 37034584 PMCID: PMC10081225 DOI: 10.1101/2023.03.26.534192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The diversity of genetic programs and cellular plasticity of glioma-associated myeloid cells, and thus their contribution to tumor growth and immune evasion, is poorly understood. We performed single cell RNA-sequencing of immune and tumor cells from 33 glioma patients of varying tumor grades. We identified two populations characteristic of myeloid derived suppressor cells (MDSC), unique to glioblastoma (GBM) and absent in grades II and III tumors: i) an early progenitor population (E-MDSC) characterized by strong upregulation of multiple catabolic, anabolic, oxidative stress, and hypoxia pathways typically observed within tumor cells themselves, and ii) a monocytic MDSC (M-MDSC) population. The E-MDSCs geographically co-localize with a subset of highly metabolic glioma stem-like tumor cells with a mesenchymal program in the pseudopalisading region, a pathognomonic feature of GBMs associated with poor prognosis. Ligand-receptor interaction analysis revealed symbiotic cross-talk between the stemlike tumor cells and E-MDSCs in GBM, whereby glioma stem cells produce chemokines attracting E-MDSCs, which in turn produce growth and survival factors for the tumor cells. Our large-scale single-cell analysis elucidated unique MDSC populations as key facilitators of GBM progression and mediators of tumor immunosuppression, suggesting that targeting these specific myeloid compartments, including their metabolic programs, may be a promising therapeutic intervention in this deadly cancer. One-Sentence Summary Aggressive glioblastoma harbors two unique myeloid populations capable of promoting stem-like properties of tumor cells and suppressing T cell function in the tumor microenvironment.
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Skinner NE, Ogega CO, Frumento N, Clark KE, Paul H, Yegnasubramanian S, Schuebel K, Meyers J, Gupta A, Wheelan S, Cox AL, Crowe JE, Ray SC, Bailey JR. Convergent antibody responses are associated with broad neutralization of hepatitis C virus. Front Immunol 2023; 14:1135841. [PMID: 37033983 PMCID: PMC10080129 DOI: 10.3389/fimmu.2023.1135841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Early development of broadly neutralizing antibodies (bNAbs) targeting the hepatitis C virus (HCV) envelope glycoprotein E2 is associated with spontaneous clearance of infection, so induction of bNAbs is a major goal of HCV vaccine development. However, the molecular antibody features important for broad neutralization are not known. Methods To identify B cell repertoire features associated with broad neutralization, we performed RNA sequencing of the B cell receptors (BCRs) of HCV E2-reactive B cells of HCV-infected individuals with either high or low plasma neutralizing breadth. We then produced a monoclonal antibody (mAb) expressed by pairing the most abundant heavy and light chains from public clonotypes identified among clearance, high neutralization subjects. Results We found distinctive BCR features associated with broad neutralization of HCV, including long heavy chain complementarity determining region 3 (CDRH3) regions, specific VH gene usage, increased frequencies of somatic hypermutation, and particular VH gene mutations. Most intriguing, we identified many E2-reactive public BCR clonotypes (heavy and light chain clones with the same V and J-genes and identical CDR3 sequences) present only in subjects who produced highly neutralizing plasma. The majority of these public clonotypes were shared by two subjects who cleared infection. A mAb expressing the most abundant public heavy and light chains from these clearance, high neutralization subjects had features enriched in high neutralization clonotypes, such as increased somatic hypermutation frequency and usage of IGHV1-69, and was cross-neutralizing. Discussion Together, these results demonstrate distinct BCR repertoires associated with high plasma neutralizing capacity. Further characterization of the molecular features and function of these antibodies can inform HCV vaccine development.
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Affiliation(s)
- Nicole E. Skinner
- Center for Vaccines and Immunity, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Medicine, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Clinton O. Ogega
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Nicole Frumento
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kaitlyn E. Clark
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Harry Paul
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Kornel Schuebel
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jennifer Meyers
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Anuj Gupta
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sarah Wheelan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrea L. Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - James E. Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Stuart C. Ray
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Justin R. Bailey
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Chen J, Zheng Q, Hicks JL, Trabzonlu L, Ozbek B, Jones T, Vaghasia A, Larman TC, Wang R, Markowski MC, Denmeade SR, Pienta KJ, Hruban RH, Antonarakis ES, Gupta A, Dang CV, Yegnasubramanian S, De Marzo AM. MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression. bioRxiv 2023:2023.02.20.529259. [PMID: 36865273 PMCID: PMC9979994 DOI: 10.1101/2023.02.20.529259] [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: 02/23/2023]
Abstract
Increased mitochondrial function may render some cancers vulnerable to mitochondrial inhibitors. Since mitochondrial function is regulated partly by mitochondrial DNA copy number (mtDNAcn), accurate measurements of mtDNAcn could help reveal which cancers are driven by increased mitochondrial function and may be candidates for mitochondrial inhibition. However, prior studies have employed bulk macrodissections that fail to account for cell type-specific or tumor cell heterogeneity in mtDNAcn. These studies have often produced unclear results, particularly in prostate cancer. Herein, we developed a multiplex in situ method to spatially quantify cell type specific mtDNAcn. We show that mtDNAcn is increased in luminal cells of high-grade prostatic intraepithelial neoplasia (HGPIN), is increased in prostatic adenocarcinomas (PCa), and is further elevated in metastatic castration-resistant prostate cancer. Increased PCa mtDNAcn was validated by two orthogonal methods and is accompanied by increases in mtRNAs and enzymatic activity. Mechanistically, MYC inhibition in prostate cancer cells decreases mtDNA replication and expression of several mtDNA replication genes, and MYC activation in the mouse prostate leads to increased mtDNA levels in the neoplastic prostate cells. Our in situ approach also revealed elevated mtDNAcn in precancerous lesions of the pancreas and colon/rectum, demonstrating generalization across cancer types using clinical tissue samples.
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Affiliation(s)
- Jiayu Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Qizhi Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jessica L. Hicks
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Levent Trabzonlu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Busra Ozbek
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tracy Jones
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ajay Vaghasia
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tatianna C. Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rulin Wang
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark C. Markowski
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sam R. Denmeade
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenneth J. Pienta
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ralph H. Hruban
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Emmanuel S. Antonarakis
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anuj Gupta
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chi V Dang
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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25
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Graham MK, Chikarmane R, Wang R, Vaghasia A, Gupta A, Zheng Q, Wodu B, Pan X, Castagna N, Liu J, Meyers J, Skaist A, Wheelan S, Simons BW, Bieberich C, Nelson WG, DeWeese TL, De Marzo AM, Yegnasubramanian S. Single-cell atlas of epithelial and stromal cell heterogeneity by lobe and strain in the mouse prostate. Prostate 2023; 83:286-303. [PMID: 36373171 DOI: 10.1002/pros.24460] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Evaluating the complex interplay of cell types in the tissue microenvironment is critical to understanding the origin and progression of diseases in the prostate and potential opportunities for intervention. Mouse models are an essential tool to investigate the molecular and cell-type-specific contributions of prostate disease at an organismal level. While there are well-documented differences in the extent, timing, and nature of disease development in various genetically engineered and exposure-based mouse models in different mouse strains and prostate lobes within each mouse strain, the underlying molecular phenotypic differences in cell types across mouse strains and prostate lobes are incompletely understood. METHODS In this study, we used single-cell RNA-sequencing (scRNA-seq) methods to assess the single-cell transcriptomes of 6-month-old mouse prostates from two commonly used mouse strains, friend virus B/NIH jackson (FVB/NJ) (N = 2) and C57BL/6J (N = 3). For each mouse, the lobes of the prostate were dissected (anterior, dorsal, lateral, and ventral), and individual scRNA-seq libraries were generated. In situ and pathological analyses were used to explore the spatial and anatomical distributions of novel cell types and molecular markers defining these cell types. RESULTS Data dimensionality reduction and clustering analysis of scRNA-seq data revealed that basal and luminal cells possessed strain-specific transcriptomic differences, with luminal cells also displaying marked lobe-specific differences. Gene set enrichment analysis comparing luminal cells by strain showed enrichment of proto-Oncogene targets in FVB/NJ mice. Additionally, three rare populations of epithelial cells clustered independently of strain and lobe: one population of luminal cells expressing Foxi1 and components of the vacuolar ATPase proton pump (Atp6v0d2 and Atp6v1g3), another population expressing Psca and other stem cell-associated genes (Ly6a/Sca-1, Tacstd2/Trop-2), and a neuroendocrine population expressing Chga, Chgb, and Syp. In contrast, stromal cell clusters, including fibroblasts, smooth muscle cells, endothelial cells, pericytes, and immune cell types, were conserved across strain and lobe, clustering largely by cell type and not by strain or lobe. One notable exception to this was the identification of two distinct fibroblast populations that we term subglandular fibroblasts and interstitial fibroblasts based on their strikingly distinct spatial distribution in the mouse prostate. CONCLUSIONS Altogether, these data provide a practical reference of the transcriptional profiles of mouse prostate from two commonly used mouse strains and across all four prostate lobes.
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Affiliation(s)
- Mindy K Graham
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, Maryland, USA
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roshan Chikarmane
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rulin Wang
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ajay Vaghasia
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Anuj Gupta
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Qizhi Zheng
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bulouere Wodu
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Xin Pan
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nicole Castagna
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jianyong Liu
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jennifer Meyers
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Alyza Skaist
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah Wheelan
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Brian W Simons
- Center for Comparative Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Charles Bieberich
- Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, Maryland, USA
| | - William G Nelson
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Theodore L DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, Maryland, USA
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Angelo M De Marzo
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, Maryland, USA
- School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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LaVigne AW, DeWeese TL, Wright JL, Deville C, Yegnasubramanian S, Alcorn SR. Radiotherapy Deserts: Impact of Race, Poverty and the Rural-Urban Continuum on Density of Providers and Utilization of Radiotherapy in the United States. Int J Radiat Oncol Biol Phys 2023; 116:17-27. [PMID: 36736631 DOI: 10.1016/j.ijrobp.2023.01.046] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023]
Abstract
PURPOSE Prior efforts to characterize disparities in radiotherapy access and receipt have not comprehensively investigated interplay between race, socioeconomic status, and geography relative to oncologic outcomes. We sought to define these complex relationships at the US county level for prostate (PC) and invasive breast (BC) cancer in order to build a tool that facilitates identification of "radiotherapy deserts"-regions with mismatch between radiotherapy resources and oncologic need. METHODS We constructed an ecologic study model using national databases to evaluate 3141 US counties. Radiotherapy resources and utilization densities were operationalized as physician (PPR) and utilization (UPR) per person at risk: number of attending radiation oncologists and Medicare beneficiaries per 100,000 persons at risk, respectively. Oncologic need was defined by "hot zone" counties with ≥2 standard deviations (SD) above mean incidence and death rates. Uni- and multivariable logistic regressions examined links between PPR and UPR densities, epidemiologic variables, and hot zones for oncologic outcomes. Reported statistics are p<.05. RESULTS Mean (SD) PPR and UPR densities were 2.1 (5.9) and 192.6 (557.6) for PC and 1.9 (5.3) and 174.4 (501.0) for BC, respectively. Counties with high PPR and UPR densities were predominately Metro [odds ratio (OR) 2.9-4.4], generally with higher %Black Non-Hispanic population (OR 1.5-2.3). Incidence and death rate hot zones were largely Non-Metro (OR 0.3-0.6), generally with higher %Black Non-Hispanic constituents (OR 3.2-6.3). Lower PPR density was associated with death rate hot zones for both cancers (OR 0.8-0.9); UPR density was generally not linked to oncologic outcomes on multivariable analysis. CONCLUSIONS Mismatch between oncologic need with PPR and UPR disproportionately affects Non-Metro communities with higher %Black Non-Hispanic population. We developed an interactive web platform (bit.ly/densitymaps) to visualize "radiotherapy deserts" and drive targeted investigation of underlying barriers to care in areas of highest need, with the goal of reducing health inequities in this context.
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Affiliation(s)
- Anna W LaVigne
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Theodore L DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jean L Wright
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Curtiland Deville
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Sara R Alcorn
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD.
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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.
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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.
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28
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Karantanos T, Teodorescu P, Arvanitis M, Perkins B, Jain T, DeZern AE, Dalton WB, Christodoulou I, Paun BC, Varadhan R, Esteb C, Rajkhowa T, Bonifant C, Gondek LP, Levis MJ, Yegnasubramanian S, Ghiaur G, Jones RJ. CCRL2 affects the sensitivity of myelodysplastic syndrome and secondary acute myeloid leukemia cells to azacitidine. Haematologica 2022. [PMID: 36519323 DOI: 10.3324/haematol.2022.281444] [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] [Received: 05/24/2022] [Indexed: 12/23/2022] Open
Abstract
Better understanding of the biology of resistance to DNA methyltransferase (DNMT) inhibitors (DNMTi) is required to identify therapies that can improve their efficacy for patients with highrisk myelodysplastic syndrome (MDS). CCRL2 is an atypical chemokine receptor that is upregulated in CD34+ cells from MDS patients and induces MDS and secondary AML (sAML) cell proliferation. In this study, we evaluated any role CCRL2 may have in the regulation of pathways associated with poor response or resistance to DNMTi. We found that CCRL2 KD in TF-1 cells downregulates DNA methylation and PRC2 activity pathways and increases DNA methyltransferases (DNMT) suppression by azacitidine in MDS/sAML vell lines (MDS92, MDS-L and TF-1). Consistently, CCRL2 deletion increased the sensitivity of these cells to azacitidine in vitro and the efficacy of azacitidine in an MDS-L xenograft model. Consistently, CCRL2 overexpression in MDS-L and TF-1 cells decreased their sensitivity to azacitidine. Finally, CCRL2 levels were higher in CD34+ cells from MDS and MDS/myeloproliferative neoplasm patients with poor response to DNMTi. In conclusion, we demonstrate that CCRL2 modulates epigenetic regulatory pathways, particularly DNMT levels, and affects MDS/sAML azacitidine sensitivity. These results support CCRL2 targeting as having MDS/sAML therapeutic potential.
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Affiliation(s)
- Theodoros Karantanos
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore.
| | - Patric Teodorescu
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Marios Arvanitis
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore
| | - Brandy Perkins
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Tania Jain
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Amy E DeZern
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - W Brian Dalton
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Ilias Christodoulou
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Bogdan C Paun
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Ravi Varadhan
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Christopher Esteb
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Trivikram Rajkhowa
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Challice Bonifant
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Mark J Levis
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Gabriel Ghiaur
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Richard J Jones
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
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29
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Wang Y, Cottle WT, Wang H, Gavrilov M, Zou RS, Pham MT, Yegnasubramanian S, Bailey S, Ha T. Achieving single nucleotide sensitivity in direct hybridization genome imaging. Nat Commun 2022; 13:7776. [PMID: 36522352 PMCID: PMC9755149 DOI: 10.1038/s41467-022-35476-y] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Direct visualization of point mutations in situ can be informative for studying genetic diseases and nuclear biology. We describe a direct hybridization genome imaging method with single-nucleotide sensitivity, single guide genome oligopaint via local denaturation fluorescence in situ hybridization (sgGOLDFISH), which leverages the high cleavage specificity of eSpCas9(1.1) variant combined with a rationally designed guide RNA to load a superhelicase and reveal probe binding sites through local denaturation. The guide RNA carries an intentionally introduced mismatch so that while wild-type target DNA sequence can be efficiently cleaved, a mutant sequence with an additional mismatch (e.g., caused by a point mutation) cannot be cleaved. Because sgGOLDFISH relies on genomic DNA being cleaved by Cas9 to reveal probe binding sites, the probes will only label the wild-type sequence but not the mutant sequence. Therefore, sgGOLDFISH has the sensitivity to differentiate the wild-type and mutant sequences differing by only a single base pair. Using sgGOLDFISH, we identify base-editor-modified and unmodified progeroid fibroblasts from a heterogeneous population, validate the identification through progerin immunofluorescence, and demonstrate accurate sub-nuclear localization of point mutations.
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Affiliation(s)
- Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - W Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Haobo Wang
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Momcilo Gavrilov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Roger S Zou
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Minh-Tam Pham
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Scott Bailey
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA.
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30
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Pani F, Yasuda Y, Rousseau ST, Bermea KC, Roshanmehr S, Wang R, Yegnasubramanian S, Caturegli P, Adamo L. Preconditioning of the immune system modulates the response of papillary thyroid cancer to immune checkpoint inhibitors. J Immunother Cancer 2022; 10:jitc-2022-005538. [PMID: 36521928 PMCID: PMC9756278 DOI: 10.1136/jitc-2022-005538] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The response of solid tumors such as papillary thyroid cancer (PTC) to immune checkpoint inhibitors (ICIs) is highly variable. The biological basis of this variability remains unknown. METHODS To test the hypothesis that preconditioning of the immune system modulates the therapeutic effect of ICIs, we used a murine model where PTC and iodine exacerbated thyroiditis (IET) can be induced in a temporally predictable fashion. A total of 122 mice were divided into 3 experimental groups. In the first one, named concomitant IET and PTC (No.=40), IET, and PTC were induced at the same time; in the second one, named pre-existing IET (No.=44), IET was induced prior to the induction of PTC; in the third one, named no IET (No.=38), only PTC was induced. Following disease induction, mice of each group were treated with anti-PD-1 antibody, anti-lymphocyte activation gene 3 antibody (anti-Lag3), anti-T-cell immunoglobulin and mucin domain 3 antibody (anti-Tim3), or IgG control. Ten weeks after the initial ICI injection, mice were sacrificed to collect the thyroid gland for histological analysis, to quantify the incidence and burden of PTC, and to perform high-throughput single-cell RNA sequencing of infiltrating CD45+ cells. RESULTS In the concomitant IET and PTC group, ICI treatment reduced PTC incidence (p=0.002 comparing treatment with any ICI vs control), while it had no effect in the pre-existing IET and no IET groups. Single-cell sequencing of thyroidal CD45+ cells showed that the different ICIs tested had both specific and shared effects on all the components of the thyroidal immune cell infiltrate. The shared effect of the tested ICIs was dependent on the presence of pre-existing versus concomitant IET. In the context of concomitant IET, ICI treatment resulted in the modulation of a greater number of pathways related to both innate and adaptive immunity. CONCLUSIONS Response to ICIs depends on the status of the immune system of the treated individual. Modulation of the immune system should be explored as a tool to improve response to ICIs in patients with PTC or other forms of cancer.
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Affiliation(s)
- Fabiana Pani
- Division of Cardiology, Department of Internal Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,GRC No. 16, GRC Tumeurs Thyroïdiennes, Thyroid and Endocrine Tumors Department; Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - Yoshinori Yasuda
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, Nagoya, Japan,Division of Immunology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sylvie T Rousseau
- Division of Cardiology, Department of Internal Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kevin C Bermea
- Division of Cardiology, Department of Internal Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Solmaz Roshanmehr
- Division of Immunology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rulin Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patrizio Caturegli
- Division of Immunology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Luigi Adamo
- Division of Cardiology, Department of Internal Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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31
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Sena LA, Kumar R, Sanin DE, Thompson EA, Rosen DM, Dalrymple SL, Antony L, Yang Y, Gomes-Alexandre C, Hicks JL, Jones T, Bowers KA, Eskra JN, Meyers J, Gupta A, Skaist A, Yegnasubramanian S, Luo J, Brennen WN, Kachhap SK, Antonarakis ES, De Marzo AM, Isaacs JT, Markowski MC, Denmeade SR. Androgen receptor activity in prostate cancer dictates efficacy of bipolar androgen therapy through MYC. J Clin Invest 2022; 132:e162396. [PMID: 36194476 PMCID: PMC9711876 DOI: 10.1172/jci162396] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Testosterone is the canonical growth factor of prostate cancer but can paradoxically suppress its growth when present at supraphysiological levels. We have previously demonstrated that the cyclical administration of supraphysiological androgen (SPA), termed bipolar androgen therapy (BAT), can result in tumor regression and clinical benefit for patients with castration-resistant prostate cancer. However, predictors and mechanisms of response and resistance have been ill defined. Here, we show that growth inhibition of prostate cancer models by SPA required high androgen receptor (AR) activity and were driven in part by downregulation of MYC. Using matched sequential patient biopsies, we show that high pretreatment AR activity predicted downregulation of MYC, improved clinical response, and prolonged progression-free and overall survival for patients on BAT. BAT induced strong downregulation of AR in all patients, which is shown to be a primary mechanism of acquired resistance to SPA. Acquired resistance was overcome by alternating SPA with the AR inhibitor enzalutamide, which induced adaptive upregulation of AR and resensitized prostate cancer to SPA. This work identifies high AR activity as a predictive biomarker of response to BAT and supports a treatment paradigm for prostate cancer involving alternating between AR inhibition and activation.
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32
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Vinson DA, Stephens KE, O’Meally RN, Bhat S, Dancy BCR, Cole RN, Yegnasubramanian S, Taverna SD. De novo methylation of histone H3K23 by the methyltransferases EHMT1/GLP and EHMT2/G9a. Epigenetics Chromatin 2022; 15:36. [PMID: 36411491 PMCID: PMC9677696 DOI: 10.1186/s13072-022-00468-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/15/2022] [Indexed: 11/22/2022] Open
Abstract
Epigenetic modifications to histone proteins serve an important role in regulating permissive and repressive chromatin states, but despite the identification of many histone PTMs and their perceived role, the epigenetic writers responsible for generating these chromatin signatures are not fully characterized. Here, we report that the canonical histone H3K9 methyltransferases EHMT1/GLP and EHMT2/G9a are capable of catalyzing methylation of histone H3 lysine 23 (H3K23). Our data show that while both enzymes can mono- and di-methylate H3K23, only EHMT1/GLP can tri-methylate H3K23. We also show that pharmacologic inhibition or genetic ablation of EHMT1/GLP and/or EHMT2/G9a leads to decreased H3K23 methylation in mammalian cells. Taken together, this work identifies H3K23 as a new direct methylation target of EHMT1/GLP and EHMT2/G9a, and highlights the differential activity of these enzymes on H3K23 as a substrate.
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Affiliation(s)
- David A. Vinson
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Kimberly E. Stephens
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.241054.60000 0004 4687 1637Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
| | - Robert N. O’Meally
- grid.21107.350000 0001 2171 9311Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Shri Bhat
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Blair C. R. Dancy
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.507680.c0000 0001 2230 3166Walter Reed Army Institute of Research, Silver Spring, MD 20910-7500 USA
| | - Robert N. Cole
- grid.21107.350000 0001 2171 9311Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Sean D. Taverna
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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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.
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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
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Alexandre CG, Jones T, Hicks JL, Isaacs JT, Gupta A, Skaist A, Sena L, Meyers J, Antonarakis E, Markowski M, Denmeade S, Yegnasubramanian S, De Marzo AM. Abstract 653: Molecular pathology of metastatic prostatic adenocarcinoma treated with bipolar androgen therapy (BAT) reveals a correlation between MYC mRNA and protein. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-653] [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
Molecular analysis of tissue samples from metastatic cancer lesions can improve our understanding of drug response and resistance. Since prostate cancer cells initially require androgen signaling through the androgen receptor (AR) for proliferation, the treatment of metastatic prostate cancer involves surgical or chemical castration. While most patients respond initially, nearly all develop acquired resistance to combined androgen blockade using both first and second line agents. This resistance is often related to overexpression of AR, which is frequently driven by AR gene amplification. In some patients, this increased AR appears to render tumor cells sensitive to high dose androgens in a manner that paradoxically inhibits their growth. Bipolar Androgen Therapy (BAT) was introduced several years ago at our institution in which patients with castration resistant prostate cancer (CRPC) are treated intermittently with high dose testosterone. Prior clinical trials have shown that BAT can produce biochemical and objective responses, and may re-sensitize prostate cancer to subsequent second generation AR inhibitors. To define the mechanism(s) by which BAT results in tumor regression, we performed a clinical trial (NCT03554317) for patients with CRPC that included biopsies of soft tissue metastases before BAT and after 3 cycles of BAT (C4D1). Up to four tissue cores were taken per biopsy with two cores for formalin fixation and paraffin embedding (FFPE) and the others snap frozen. Histologically viable tumor cells were present for both the pretreatment and C4D1 time points for 24 of the 42 enrolled patients. The FFPE samples were stained for H&E and by IHC for AR, MYC and Ki67. MYC and Ki67 IHC stained slides were subjected to quantitative image analysis using HALO software (Indica Labs). Adequate frozen tumor tissue was available for laser capture microdissection and adequate amounts of RNA were obtained from 15 patients with paired pretreatment and C4D1 biopsies. RNAseq libraries were prepared using the NuGEN Ovation RNA-Seq System V2 and barcoded libraries were sequenced to an average depth of > 100 million reads per sample on an Illumina NovaSeq. Gene expression values were obtained with RSEM using Star aligner with GRCh38 (human). When comparing the C4D1 samples to the pretreatment samples, there were marked decreases in tumor MYC protein levels in approximately half of the treated patients, which was associated with decreased Ki67, decreased tumor volume, and prolonged progression-free survival on BAT. Using an image analysis computed H-SCORE for MYC, there was a strong correlation between MYC protein levels and MYC mRNA using RNAseq (r=0.81, p = 2.3 x 10-7). This indicates that MYC protein levels correlate with MYC mRNA and that reductions of MYC protein by BAT are likely related to reductions of MYC mRNA in clinical metastatic tissue samples.
Citation Format: Carolina Gomes Alexandre, Tracy Jones, Jessica L. Hicks, John T. Isaacs, Anuj Gupta, Alyza Skaist, Laura Sena, Jennifer Meyers, Emmanuel Antonarakis, Mark Markowski, Samuel Denmeade, Srinivasan Yegnasubramanian, Angelo Michael De Marzo. Molecular pathology of metastatic prostatic adenocarcinoma treated with bipolar androgen therapy (BAT) reveals a correlation between MYC mRNA and protein [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 653.
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Affiliation(s)
| | - Tracy Jones
- 1The Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - John T. Isaacs
- 1The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Anuj Gupta
- 1The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alyza Skaist
- 1The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Laura Sena
- 1The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jennifer Meyers
- 1The Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Mark Markowski
- 1The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Samuel Denmeade
- 1The Johns Hopkins University School of Medicine, Baltimore, MD
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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.
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Affiliation(s)
| | | | | | | | - Anuj Gupta
- 1Johns Hopkins School of Medicine, Baltimore, MD
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Chen J, Zheng Q, Hicks JL, Trabzonlu L, Kulac I, Meeker AK, Yegnasubramanian S, De Marzo AM. Abstract 3772: Increased mitochondrial gene expression in prostate cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3772] [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
Warburg postulated that aerobic glycolysis, which is commonly observed in cancer, results from crippled mitochondrial function. Yet, most cancers and other rapidly proliferating cells rely on a functioning mitochondrial TCA cycle to generate important biosynthetic intermediates required for cell growth, and on the electron transport chain for pyrimidine synthesis and to recycle electron acceptors. Thus, increases in a number of mitochondrial activities have been proposed to be required for robust proliferation in most cancers. Mitochondrial function is regulated in part through mitochondrial biogenesis, which is influenced by mitochondrial DNA copy number (mtDNAcn). We previously developed an in situ hybridization method to quantify mtDNAcn in specific cell compartments in relation to normal physiological functioning and disease processes. We reported marked cell type heterogeneity across normal tissues including relatively higher mtDNAcn in a number of stem/proliferative compartments in humans and mice (PMID: 32304697). More recently, we combined this in situ approach with immunohistochemistry and reported increased mtDNAcn along with widespread heterogeneity in prostate cancer (DOI: 10.1158/1538-7445.AM2021-2404). We also found increased mtDNAcn in high grade prostatic intraepithelial neoplasia, the main precursor to prostate cancer, as well as precursor lesions in the large intestine and pancreas. To interrogate the functional significance of this mtDNAcn alteration, we sought to determine whether increased and heterogeneous mtDNAcn levels are accompanied by corresponding changes in its gene expression (mtRNA). To establish an initial survey of the landscape of steady state mtRNA levels, we used the RNAscope HiPlex system for multiplex in situ hybridization for 4 different mtRNAs along with in situ hybridization for mtDNA and combined this with immunofluorescence. In normal prostatic epithelium, we observed that the overall mtRNA expression pattern correlated with mtDNAcn, with higher levels in the basal cell layer compared with the luminal cell layer. We also found that, similar to changes in mtDNAcn in invasive prostate cancer, the 4 mtRNAs were upregulated yet heterogeneous in cancer lesions. Among the invasive tumors, cribriform prostate cancer showed distinct mtDNA and mtRNAs expression patterns, with higher signals in the peripheral cells than central cells, suggesting underlying biological differences in this unique histologic pattern. This spatial pattern in cribriform lesions correlated with the pattern of MYC protein expression, which is known to regulate mitochondrial biogenesis. Overall, we present a novel approach that advances the ability to quantify mtDNAcn and mtRNAs simultaneously in specific cell types while preserving the tissue spatial context. These findings suggest that increased mitochondrial function accompanies prostate cancer development and progression.
Citation Format: Jiayu Chen, Qizhi Zheng, Jessica L. Hicks, Levent Trabzonlu, Ibrahim Kulac, Alan K. Meeker, Srinivasan Yegnasubramanian, Angelo M. De Marzo. Increased mitochondrial gene expression 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 3772.
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Affiliation(s)
- Jiayu Chen
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - Qizhi Zheng
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | - Ibrahim Kulac
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alan K. Meeker
- 1Johns Hopkins University School of Medicine, Baltimore, MD
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Gupta H, Inoue H, Nakai Y, Nakayama M, Nelson WG, De Marzo AM, Yegnasubramanian S. Abstract 3734: Progressive spreading of CpG methylation in the CpG island of Glutathione S-Transferase pi 1 (GSTP1) alleles across transitions from precursor to invasive prostate cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3734] [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
Glutathione S-transferase pi 1 (GSTP1) is expressed at low levels in normal prostate luminal cells and becomes induced in most proliferative inflammatory atrophy lesions (PIA). GSTP1 becomes silenced in prostatic intraepithelial neoplasia (PIN) and prostate adenocarcinoma (CaP) via CpG island promoter hypermethylation. However, the specific methylation patterns in CaP and its precursors have not been investigated. We used bisulfite genomic sequencing to examine methylation of 39 CpG sites in the GSTP1 promoter. Radical prostatectomy specimens were selected from 32 subjects that underwent treatment for CaP. Serial sections were subjected to laser capture microdissection for enrichment of epithelial cells from benign, PIA, PIN, and CaP regions. Isolated DNA was bisulfite converted. Sequences corresponding to the GSTP1 promoter CpG island were amplified with nested PCR, and PCR products were cloned. 10 independent clones were sequenced and analyzed with a Java program, DNAMethylMap, to determine the methylation pattern of 39 CpG sites of the GSTP1 promoter in each lesion. The extent of methylation on an individual allele was classified as negative (<10% CpGs), mild (10-25%), moderate (25-50%), or high (>50%). 212 clones from 24 normal epithelium regions, 327 clones from 37 PIA regions, 167 clones from 18 PIN regions, and 202 clones from 23 CaP regions were sequenced, totaling 34863 CpG sites. Normal and PIA lesions were mostly unmethylated with 0.52% and 1.3% of total CpG sites methylated, respectively. Methylated PIA lesions were adjacent to CaP or PIN regions significantly more often than unmethylated PIA lesions (χ2, p = 0.012). PIN and CaP lesions had greater methylation with 24% and 51% of total CpG sites methylated, respectively. PIN lesions generally showed partial methylation with 28.7% of alleles in PIN having mild/moderate methylation density compared to 5.5% in PIA and 11% in CaP. PIA and PIN lesions were enriched for methylation changes at 6 CpG sites that aligned with AP1 and SP1 binding sites. Among 16 PIN and CaP lesions with an overall intermediate level of methylation, 5 of the lesions had clones that clustered into either fully methylated or unmethylated. One patient with 3 CaP lesions displayed significant heterogeneity in methylation patterns: full, moderate, or no methylation across all clones in a given lesion. The results demonstrate that methylation density in the GSTP1 CpG island from PIN was intermediate between normal prostate epithelium/PIA and CaP lesions. The observed methylation in PIA and PIN was enriched at binding sites of key transcription factors, AP1 and SP1. The results are consistent with gradual spreading of DNA methylation centered at the transcription factor binding sites in the putative precursor lesions, with subsequent spreading of methylation across the entire CpG island in transition to CaP.
Citation Format: Harshath Gupta, Hitoshi Inoue, Yasutomo Nakai, Masashi Nakayama, William G. Nelson, Angelo M. De Marzo, Srinivasan Yegnasubramanian. Progressive spreading of CpG methylation in the CpG island of Glutathione S-Transferase pi 1 (GSTP1) alleles across transitions from precursor to invasive 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 3734.
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Affiliation(s)
- Harshath Gupta
- 1Johns Hopkins University School of Medicine, Baltimore, MD
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Nizialek E, Haffner M, Bhamidipati A, Yegnasubramanian S. The effect of PARP inhibition on androgen receptor localization and activity in castration resistant prostate cancer. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e17037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e17037 Background: The poly(ADP-ribose) polymerase inhibitors (PARPi) olaparib and rucaparib have been approved for the treatment of metastatic castration resistant prostate cancer (mCRPC) in the setting of homologous recombination deficiency (HRD). Additionally, PARPi have been shown to modulate androgen receptor (AR) signaling, with a recent report demonstrating mono-ADP-ribosylation of cysteine residues in AR by Parp7. Here, we further evaluated the effect of PARPi on AR activity and localization. Methods: The effect of PARPi on cell growth and survival of CRPC cell lines was evaluated in vitro and in vivo. AR ribosylation was assessed in CRPC cell lines by immunoprecipitation (IP) assays and proximity ligation assays (PLA). The subcellular localization of AR was determined by quantitative immunofluorescence microscopy in CRPC cell lines and xenograft models. Changes in AR activity with PARPi treatment were evaluated by a luciferase reporter assay and AR target gene expression in a PDX model. Finally, PARPi mediated alteration in the AR protein interactome was evaluated by liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. Results: The PARPi olaparib and talazoparib, and to a lesser extent veliparib, inhibited CRPC cell growth. Evidence of AR ribosylation was seen by IP and PLA. PARPi treatment of multiple in vitro and in vivo prostate cancer models resulted in a shift of AR subcellular localization, from predominantly nuclear to cytoplasmic compartments. In luciferase reporter assays, AR transactivation activity was decreased after PARPi treatment in a dose dependent manner. In vivo, in prostate cancer xenograft models, decreased AR target gene expression was seen upon PARPi treatment. LC-MS/MS proteomic studies revealed that PARP inhibition resulted in significant changes in the composition of AR interaction partners, in particular of proteins related to intracellular trafficking and nuclear transport. This suggests a potential link between altered AR complex assembly and the observed changes in AR subcellular localization in the context of PARPi treatment. Conclusions: We describe a novel sequela of PARPi therapy to alter AR localization and activity in CRPC. Single agent PARP inhibition can alter prostate cancer cell growth in vitro and in vivo. With PARPi treatment, AR localization is shifted to the cytoplasm, the AR interactome is altered, and AR transcriptional activity decreased. These findings implicate a collateral mechanism of PARPi in preventing prostate cancer cell growth/survival that may augment previously described mechanisms related to HDR and synthetic lethality. It is essential to understand the role of PARPi beyond synthetic lethality in the context of HRD in order to better define the spectrum of response to PARPi across patients, and for development of biology-informed combination therapies.
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Affiliation(s)
- Emily Nizialek
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
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Markowski MC, Taplin ME, Aggarwal RR, Sena L, Wang H, Lalji A, Meyers J, Skaist A, Gupta A, Gomes-Alexandre C, Jones T, Hicks J, Kachhap S, Yegnasubramanian S, De Marzo AM, Denmeade SR, Antonarakis ES. Overall survival (OS) and biomarker results from combat: A phase 2 study of bipolar androgen therapy (BAT) plus nivolumab for patients with metastatic castrate-resistant prostate cancer (mCRPC). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.5064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5064 Background: During BAT, intramuscular (IM) administration of testosterone (T) results in rapid cycling of serum T from supraphysiologic to near-castrate levels in men with mCRPC. In a retrospective study, clinical responses to immune checkpoint blockade (ICB) in mCRPC patients (pts) previously treated with BAT were observed. Here, we report the OS and biomarker results of a Phase 2 study in mCRPC pts treated with BAT in combination with nivolumab (COMBAT; NCT03554317). Methods: This was a multi-center, single arm, open label Phase 2 study in mCRPC pts who received T cypionate 400mg IM (BAT) every 28 days plus nivolumab 480mg IV every 28 days. Pts initially received BAT alone for a 12-week period, prior to the addition of nivolumab. Eligible pts were those with asymptomatic mCRPC who had soft tissue metastases amenable to biopsy, and who progressed on at least one prior novel AR targeted therapy (and up to one prior chemo for mCRPC). The primary endpoint was confirmed PSA50 response. OS and radiographic progression free survival (rPFS) were key secondary endpoints. All pts underwent baseline metastatic biopsies, and 24 had a second biopsy after 12 weeks of BAT. Semi-quantitative IHC (for AR, Ki67, MYC, PTEN, TP53, RB1) was performed on 24 paired biopsies, of which 15 pairs were also evaluable for RNA (whole transcriptome) sequencing. Results: 45 pts were enrolled. As previously reported, the PSA50 response was 40% (18/45, 95% CI: 26-56%, P=0.02 against the 25% null hypothesis), and median rPFS was 5.6 (95% CI: 4.4–6.0) months. After a median follow-up of 17.8 months, the median OS was 27.8 (95%% CI: 17.6–NR) months. In 24 pts with paired biopsies prior to administration of nivolumab, BAT significantly decreased median MYC (P=0.046) and Ki-67 (P=0.030) expression by IHC. 71% (17/24) of pts had any decrease in MYC following BAT, with 29% (7/24) having a >50% decrease. A >50% MYC protein decline was associated with longer rPFS (HR 0.33, 95%CI 0.14–0.78, P=0.005) and a nonsignificant association towards longer OS (HR 0.78, 95%CI 0.24–2.48, P=0.679). MYC protein and mRNA levels were tightly intercorrelated (r=0.65, P<0.001). Both rPFS and OS were numerically longer in pts with >50% declines in MYC mRNA levels (P>0.1 for both). Conclusions: BAT combined with nivolumab led to a median overall survival of >2 years in heavily pretreated mCRPC pts. BAT attenuated MYC expression, correlating with better outcomes. Clinical trial information: NCT03554317.
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Affiliation(s)
| | - Mary-Ellen Taplin
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Hao Wang
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | | | | | | | | | | | - Tracy Jones
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica Hicks
- Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | - Samuel R. Denmeade
- Johns Hopkins University Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
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Casciola-Rosen L, Thiemann DR, Andrade F, Trejo-Zambrano MI, Leonard EK, Spangler JB, Skinner NE, Bailey J, Yegnasubramanian S, Wang R, Vaghasia AM, Gupta A, Cox AL, Ray SC, Linville RM, Guo Z, Searson PC, Machamer CE, Desiderio S, Sauer LM, Laeyendecker O, Garibaldi BT, Gao L, Damarla M, Hassoun PM, Hooper JE, Mecoli CA, Christopher-Stine L, Gutierrez-Alamillo L, Yang Q, Hines D, Clarke WA, Rothman RE, Pekosz A, Fenstermacher KZ, Wang Z, Zeger SL, Rosen A. IgM anti-ACE2 autoantibodies in severe COVID-19 activate complement and perturb vascular endothelial function. JCI Insight 2022; 7:e158362. [PMID: 35349483 PMCID: PMC9090251 DOI: 10.1172/jci.insight.158362] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 01/11/2022] [Accepted: 03/24/2022] [Indexed: 12/15/2022] Open
Abstract
BackgroundSome clinical features of severe COVID-19 represent blood vessel damage induced by activation of host immune responses initiated by the coronavirus SARS-CoV-2. We hypothesized autoantibodies against angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 receptor expressed on vascular endothelium, are generated during COVID-19 and are of mechanistic importance.MethodsIn an opportunity sample of 118 COVID-19 inpatients, autoantibodies recognizing ACE2 were detected by ELISA. Binding properties of anti-ACE2 IgM were analyzed via biolayer interferometry. Effects of anti-ACE2 IgM on complement activation and endothelial function were demonstrated in a tissue-engineered pulmonary microvessel model.ResultsAnti-ACE2 IgM (not IgG) autoantibodies were associated with severe COVID-19 and found in 18/66 (27.2%) patients with severe disease compared with 2/52 (3.8%) of patients with moderate disease (OR 9.38, 95% CI 2.38-42.0; P = 0.0009). Anti-ACE2 IgM autoantibodies were rare (2/50) in non-COVID-19 ventilated patients with acute respiratory distress syndrome. Unexpectedly, ACE2-reactive IgM autoantibodies in COVID-19 did not undergo class-switching to IgG and had apparent KD values of 5.6-21.7 nM, indicating they are T cell independent. Anti-ACE2 IgMs activated complement and initiated complement-binding and functional changes in endothelial cells in microvessels, suggesting they contribute to the angiocentric pathology of COVID-19.ConclusionWe identify anti-ACE2 IgM as a mechanism-based biomarker strongly associated with severe clinical outcomes in SARS-CoV-2 infection, which has therapeutic implications.FUNDINGBill & Melinda Gates Foundation, Gates Philanthropy Partners, Donald B. and Dorothy L. Stabler Foundation, and Jerome L. Greene Foundation; NIH R01 AR073208, R01 AR069569, Institutional Research and Academic Career Development Award (5K12GM123914-03), National Heart, Lung, and Blood Institute R21HL145216, and Division of Intramural Research, National Institute of Allergy and Infectious Diseases; National Science Foundation Graduate Research Fellowship (DGE1746891).
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Affiliation(s)
| | | | | | | | - Elissa K. Leonard
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jamie B. Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Translational Tissue Engineering Center
| | | | - Justin Bailey
- Department of Medicine, Division of Infectious Diseases; and
| | | | - Rulin Wang
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ajay M. Vaghasia
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anuj Gupta
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrea L. Cox
- Department of Medicine, Division of Infectious Diseases; and
| | - Stuart C. Ray
- Department of Medicine, Division of Infectious Diseases; and
| | - Raleigh M. Linville
- Institute for NanoBioTechnology and
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Peter C. Searson
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for NanoBioTechnology and
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Stephen Desiderio
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lauren M. Sauer
- Adult Emergency Department, Johns Hopkins Hospital, Baltimore, Maryland, USA
- Johns Hopkins Biocontainment Unit, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Oliver Laeyendecker
- Department of Medicine, Division of Infectious Diseases; and
- Division of Intramural Medicine, National Institute of Allergy and Infectious Diseases, NIH, Baltimore, Maryland, USA
| | - Brian T. Garibaldi
- Johns Hopkins Biocontainment Unit, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Li Gao
- Department of Medicine, Division of Allergy and Clinical Immunology; and
| | - Mahendra Damarla
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Paul M. Hassoun
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Jody E. Hooper
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | - David Hines
- Department of Medicine, Division of Rheumatology
| | - William A. Clarke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard E. Rothman
- Adult Emergency Department, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Andrew Pekosz
- Department of Environmental Health and Engineering
- Department of Molecular Microbiology and Immunology, and
| | | | - Zitong Wang
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Scott L. Zeger
- Department of Medicine, Division of Rheumatology
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Antony Rosen
- Department of Medicine, Division of Rheumatology
- Department of Cell Biology and
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Ozbek B, Ertunc O, Erickson A, Vidal ID, Gomes-Alexandre C, Guner G, Hicks JL, Jones T, Taube JM, Sfanos KS, Yegnasubramanian S, De Marzo AM. Multiplex immunohistochemical phenotyping of T cells in primary prostate cancer. Prostate 2022; 82:706-722. [PMID: 35188986 DOI: 10.1002/pros.24315] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/03/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Most prostate cancers are "immune cold" and poorly responsive to immune checkpoint inhibitors. However, the mechanisms responsible for the lack of a robust antitumor adaptive immune response in the prostate are poorly understood, which hinders the development of novel immunotherapeutic approaches. AIMS Most inflammatory infiltrates in the prostate are centered around benign glands and stroma, which can confound the molecular characterization of the antitumor immune response. We sought to analytically validate a chromogenic-based multiplex immunohistochemistry (IHC) approach applicable to whole slide digital image analysis to quantify T cell subsets from the tumor microenvironment of primary prostatic adenocarcinomas. As an initial application, we tested the hypothesis that PTEN loss leads to an altered antitumor immune response by comparing matched regions of tumors within the same individual with and without PTEN loss. MATERIALS & METHODS Using the HALO Image Analysis Platform (Indica Labs), we trained a classifier to quantify the densities of eight T cell phenotypes separately in the tumor epithelial and stromal subcompartments. RESULTS The iterative chromogenic approach using 7 different antibodies on the same slide provides highly similar findings to results using individually stained slides with single antibodies. Our main findings in carcinomas (benign removed) include the following: i) CD4+ T cells are present at higher density than CD8+ T cells; ii) all T cell subsets are present at higher densities in the stromal compartment compared to the epithelial tumor compartment; iii) most CD4+ and CD8+ T cells are PD1+; iv) cancer foci with PTEN loss harbored increased numbers of T cells compared to regions without PTEN loss, in both stromal and epithelial compartments; and v) the increases in T cells in PTEN loss regions were associated with ERG gene fusion status. DISCUSSION This modular approach can apply to any IHC-validated antibody combination and sets the groundwork for more detailed spatial analyses. CONCLUSION Iterative chromogenic IHC can be used for whole slide analysis of prostate tissue samples and can complement transcriptomic results including those using single cell and spatial genomic approaches.
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Affiliation(s)
- Busra Ozbek
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Onur Ertunc
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Erickson
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Igor D Vidal
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carolina Gomes-Alexandre
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gunes Guner
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jessica L Hicks
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tracy Jones
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Janis M Taube
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, Maryland, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins University, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Karen S Sfanos
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Brady Urological Research Institute, Johns Hopkins, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Brady Urological Research Institute, Johns Hopkins, Baltimore, Maryland, USA
| | - Angelo M De Marzo
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Brady Urological Research Institute, Johns Hopkins, Baltimore, Maryland, USA
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Singh AK, Wang R, Lombardo KA, Praharaj M, Bullen CK, Um P, Davis S, Komm O, Illei PB, Ordonez AA, Bahr M, Huang J, Gupta A, Psoter KJ, Jain SK, Bivalacqua TJ, Yegnasubramanian S, Bishai WR. Dynamic single-cell RNA sequencing reveals BCG vaccination curtails SARS-CoV-2 induced disease severity and lung inflammation. bioRxiv 2022:2022.03.15.484018. [PMID: 35313583 PMCID: PMC8936112 DOI: 10.1101/2022.03.15.484018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
COVID-19 continues to exact a toll on human health despite the availability of several vaccines. Bacillus Calmette Guérin (BCG) has been shown to confer heterologous immune protection against viral infections including COVID-19 and has been proposed as vaccine against SARS-CoV-2 (SCV2). Here we tested intravenous BCG vaccination against COVID-19 using the golden Syrian hamster model together with immune profiling and single cell RNA sequencing (scRNAseq). We observed that BCG reduced both lung SCV2 viral load and bronchopneumonia. This was accompanied by an increase in lung alveolar macrophages, a reversal of SCV2-mediated T cell lymphopenia, and reduced lung granulocytes. Single cell transcriptome profiling showed that BCG uniquely recruits immunoglobulin-producing plasma cells to the lung suggesting accelerated antibody production. BCG vaccination also recruited elevated levels of Th1, Th17, Treg, CTLs, and Tmem cells, and differentially expressed gene (DEG) analysis showed a transcriptional shift away from exhaustion markers and towards antigen presentation and repair. Similarly, BCG enhanced lung recruitment of alveolar macrophages and reduced key interstitial macrophage subsets, with both cell-types also showing reduced IFN-associated gene expression. Our observations indicate that BCG vaccination protects against SCV2 immunopathology by promoting early lung immunoglobulin production and immunotolerizing transcriptional patterns among key myeloid and lymphoid populations.
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Affiliation(s)
- Alok K. Singh
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Rulin Wang
- Sydney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Kara A. Lombardo
- Johns Hopkins University, School of Medicine, Department of Urology, Baltimore, MD, USA
| | - Monali Praharaj
- Bloomberg~Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD, USA
| | - C. Korin Bullen
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Peter Um
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Stephanie Davis
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Oliver Komm
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Peter B. Illei
- Johns Hopkins University, School of Medicine, Department of Pathology, Baltimore, MD, USA
| | - Alvaro A. Ordonez
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore MD, USA
| | - Melissa Bahr
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore MD, USA
| | - Joy Huang
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Anuj Gupta
- Sydney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Kevin J. Psoter
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of General Pediatrics, Baltimore, MD, USA
| | - Sanjay K. Jain
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore MD, USA
| | - Trinity J. Bivalacqua
- Perelman School of Medicine at the University of Pennsylvania, Division of Urology, Department of Surgery, Philadelphia, PA, USA
| | | | - William R. Bishai
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
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Sidiropoulos DN, Rafie CI, Jang JK, Castanon S, Baugh AG, Gonzalez E, Christmas BJ, Narumi VH, Davis-Marcisak EF, Sharma G, Bigelow E, Vaghasia A, Gupta A, Skaist A, Considine M, Wheelan SJ, Ganesan SK, Yu M, Yegnasubramanian S, Stearns V, Connolly RM, Gaykalova DA, Kagohara LT, Jaffee EM, Fertig EJ, Roussos Torres ET. Entinostat decreases immune suppression to promote anti-tumor responses in a HER2+ breast tumor microenvironment. Cancer Immunol Res 2022; 10:656-669. [PMID: 35201318 PMCID: PMC9064912 DOI: 10.1158/2326-6066.cir-21-0170] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/19/2021] [Accepted: 02/18/2022] [Indexed: 11/16/2022]
Abstract
Therapeutic combinations to alter immunosuppressive, solid tumor microenvironments (TMEs), such as in breast cancer, are essential to improve responses to immune checkpoint inhibitors (ICIs). Entinostat, an oral histone deacetylase inhibitor (HDACi), has been shown to improve responses to ICIs in various tumor models with immunosuppressive TMEs. The precise and comprehensive alterations to the TME induced by entinostat remain unknown. Here, we employed single-cell RNA-sequencing on HER2-overexpressing breast tumors from mice treated with entinostat and ICIs in order to fully characterize changes across multiple cell types within the TME. This analysis demonstrates that treatment with entinostat induced a shift from a pro-tumor to an anti-tumor TME signature, characterized predominantly by changes in myeloid cells. We confirmed myeloid-derived suppressor cells (MDSCs) within entinostat-treated tumors associated with a less suppressive granulocytic (G)-MDSC phenotype and exhibited altered suppressive signaling that involved the NFkB and STAT3 pathways. In addition to MDSCs, tumor-associated macrophages were epigenetically reprogrammed from a pro-tumor M2-like phenotype toward an anti-tumor M1-like phenotype, which may be contributing to a more sensitized TME. Overall, our in-depth analysis suggests that entinostat-induced changes on multiple myeloid cell types reduce immunosuppression and increase anti-tumor responses, which, in turn, improve sensitivity to ICIs. Sensitization of the TME by entinostat could ultimately broaden the population of patients with breast cancer who could benefit from ICIs.
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Affiliation(s)
| | | | - Julie K Jang
- University of Southern California, Los Angeles, United States
| | | | - Aaron G Baugh
- University of Southern California, Los Angeles, United States
| | - Edgar Gonzalez
- University of Southern California, Los Angeles, United States
| | | | | | | | | | - Emma Bigelow
- Johns Hopkins University School of Medicine, United States
| | - Ajay Vaghasia
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Anuj Gupta
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutes, Baltimore, MD, United States
| | - Alyza Skaist
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutes, Baltimore, MD, United States
| | | | - Sarah J Wheelan
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Min Yu
- University of Southern California, Los Angeles, CA, United States
| | | | - Vered Stearns
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | | | | | | | - Elana J Fertig
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Nelson WG, Brawley OW, Isaacs WB, Platz EA, Yegnasubramanian S, Sfanos KS, Lotan TL, De Marzo AM. Health inequity drives disease biology to create disparities in prostate cancer outcomes. J Clin Invest 2022; 132:e155031. [PMID: 35104804 PMCID: PMC8803327 DOI: 10.1172/jci155031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Prostate cancer exerts a greater toll on African American men than on White men of European descent (hereafter referred to as European American men): the disparity in incidence and mortality is greater than that of any other common cancer. The disproportionate impact of prostate cancer on Black men has been attributed to the genetics of African ancestry, to diet and lifestyle risk factors, and to unequal access to quality health care. In this Review, all of these influences are considered in the context of the evolving understanding that chronic or recurrent inflammatory processes drive prostatic carcinogenesis. Studies of inherited susceptibility highlight the contributions of genes involved in prostate cell and tissue repair (BRCA1/2, ATM) and regeneration (HOXB13 and MYC). Social determinants of health appear to accentuate these genetic influences by fueling prostate inflammation and associated cell and genome damage. Molecular characterization of the prostate cancers that arise in Black versus White men further implicates this inflammatory microenvironment in disease behavior. Yet, when Black and White men with similar grade and stage of prostate cancer are treated equally, they exhibit equivalent outcomes. The central role of prostate inflammation in prostate cancer development and progression augments the impact of the social determinants of health on disease pathogenesis. And, when coupled with poorer access to high-quality treatment, these inequities result in a disparate burden of prostate cancer on African American men.
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Coulter JB, Song DY, DeWeese TL, Yegnasubramanian S. Mechanisms, Challenges, and Opportunities in Combined Radiation and Hormonal Therapies. Semin Radiat Oncol 2021; 32:76-81. [PMID: 34861998 DOI: 10.1016/j.semradonc.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Androgen receptor signaling blockade is perhaps the first example of targeted therapy in the treatment of cancer. Since the initial observations that prostate cancers depend on hormone signaling, hormonal therapies remain a cornerstone in the treatment of metastatic prostate cancer. Androgen deprivation therapy has been shown to improve outcomes involving treatment of prostate cancers with radiotherapy, though a mechanistic understanding into the optimal sequencing of androgen deprivation therapy and radiotherapy remains incomplete. In this review we highlight key clinical trials designed to study combinations of hormonal and radiotherapies and introduce recent discoveries into the complex biology of androgen receptor signaling and DNA damage and repair. These emerging mechanistic and translational studies may have profound implications on both our understanding of hormonal therapy and radiotherapy combinations and the development of novel treatment strategies for locally-advanced and metastatic castrate resistant prostate cancer.
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Affiliation(s)
- Jonathan B Coulter
- The James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD; Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD.
| | - Daniel Y Song
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Theodore L DeWeese
- The James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD; Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
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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.
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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
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Zhang J, Caushi J, Oliveira G, Zhang B, Ji Z, Naidoo J, Marrone K, Taube J, Hellmann M, Brahmer J, Merghoub T, Forde P, Yegnasubramanian S, Wu C, Ji H, Pardoll A, Smith K. 327 Development and validation of a neoantigen-specific T cell gene signature to identify antitumor T cells in lung cancer and melanoma. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.327] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundMutation-associated neoantigen (MANA)-specific T cells play a key role in tumor control and response to immune checkpoint inhibition (ICI).1 2 However, the majority of tumor-infiltrating lymphocytes (TIL) are not specific for the tumor.3 Herein, we developed and validated MANAscore, a bioinformatic scoring algorithm based on the transcriptional programs of MANA-specific T cells to isolate antitumor T cells from bystander T cells in lung cancer and melanoma.MethodsCombined single-cell (sc) RNA-seq/TCR-seq was performed on TIL obtained from 15 resectable non-small cell lung cancer (NSCLC) patients receiving neoadjuvant anti-PD-1 (NCT02259621). MANA-specific clonotypes were identified by coculturing autologous T cells with predicted MANA, and were validated by cloning the full TCR alpha and beta chain as previously described.1 Using the TCRβ CDR3 as a barcode, antigen-specific T cells were linked with their intratumoral sc expression profile. Using the first two patients enrolled in the clinical trial as a discovery cohort, MANAscore was developed to identify gene programs that best distinguish MANA-specific vs viral-specific T cells from NSCLC. Prediction performance was assessed in independent patients from the NSCLC and melanoma cohort.2 Seven MANAscore< sup >hi</sup > TCRs were cloned and queried for reactivity to peptide libraries of putative MANA derived from whole-exome sequencing of the respective tumor. Association of MANAscorehi clones with response to ICIs among all patients was assessed.ResultsA total of 890 MANA- and 542 viral-specific T cells were identified in sc TIL from six NSCLC patients. MANA- and viral-specific TIL presented with unique transcriptional profiles. Particularly, MANA-specific CD8 TIL expressed a partially activated cytolytic program with co-expression of multiple immune checkpoints and upregulated transcriptional regulators of T cell dysfunction. MANAscore showed high prediction accuracy and outperformed CD39 in identifying tumor-reactive T cells in independent NSCLC patients, as well as in an external validation cohort of melanoma patients (3936 MANA-specific T cells and 626 viral-specific T cells from 4 patients). Of seven MANAscore< sup >hi</sup > clones tested for reactivity, three were confirmed as MANA-specific. The pseudobulk expression profile of MANAscore< sup >hi</sup > clones showed a significant correlation with response to ICI, which is not observed in total CD8+ TIL.ConclusionsMANA-specific TIL demonstrated a distinct gene signature that enabled us to identify de novo antitumor TIL in NSCLC and melanoma. MANAscore may serve as a useful tool in facilitating mechanistic studies of ICI response and resistance.Trial RegistrationNCT01970358,NCT02259621ReferencesSimoni, Yannick, et al. “Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates.” Nature 557.7706 (2018):575–579.Caushi, Justina X, et al. “Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers.” Nature (2021):1–7.Oliveira, Giacomo, et al. “Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma.” Nature (2021):1–7.Ethics ApprovalThe melanoma clinical trial was approved by the Dana-Farber/Harvard Cancer Center Institutional Review Board (IRB) (NCT01970358). The NSCLC clinical trial was approved by the Institutional Review Boards (IRB) at Johns Hopkins University (JHU) and Memorial Sloan Kettering Cancer Center (NCT02259621)ConsentWritten informed consent was obtained from the patient for publication of this abstract and any accompanying images. A copy of the written consent is available for review by the Editor of this journal
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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.
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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
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LaVigne A, DeWeese T, Yegnasubramanian S, Wright J, Deville C, Alcorn S. Radiotherapy Deserts: Impact of Race, Poverty and the Rural-Urban Continuum on Density of Radiation Oncologists in the United States. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Mishra A, Zennami K, Velarde E, Thorek DLJ, Yegnasubramanian S, DeWeese TL, Lupold SE. Longitudinal measurement of subcutaneous and intratibial human prostate cancer xenograft growth and response to ionizing radiation by plasma Alu and LINE-1 ctDNA: A comparison to standard methods. Prostate 2021; 81:745-753. [PMID: 34032307 DOI: 10.1002/pros.24171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/28/2021] [Accepted: 05/07/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Current preclinical models of metastatic prostate cancer (PCa) require sophisticated technologies and/or genetically engineered cells for the noninvasive monitoring of tumors in remote sites, such as bone. Recent developments in circulating tumor DNA (ctDNA) analysis provide an alternative method for noninvasive tumor monitoring at a low cost. Here, we sought to evaluate human Alu and LINE-1 ctDNA for the longitudinal measurement of subcutaneous and intratibial human PCa xenograft growth and response to ionizing radiation (IR) through comparison with standard slide caliper and bioluminescence measurements. MATERIAL AND METHODS Intratibial and subcutaneous xenografts were established in male athymic nude mice using LNCaP cells that stably express firefly luciferase. A subset of tumors was treated with a single dose of IR (CT-guided focal IR, 6 Gy). Tumor measurements were simultaneously taken by slide caliper (subcutaneous only), in vivo bioluminescence imaging, and quantitative real-time PCR (qPCR) of human-specific Alu and LINE-1 ctDNA for several weeks. RESULTS Levels of ctDNA and bioluminescence increased concordantly with subcutaneous and intratibial tumor growth. A statistically significant correlation (Spearman) was observed between ctDNA and subcutaneous tumor volume (LINE-1, r = .94 and Alu, r = .95, p < .0001), ctDNA and bioluminescence (LINE-1, r = .66 and Alu, r = .60, p < .002), and bioluminescence and tumor volume (r = .66, p = .0003). Bioluminescence and ctDNA were also significantly correlated in intratibial tumors (LINE-1, r = .82 and Alu, r = .81, p < .0001). Following external beam IR, the tumor responses varied briefly by method of measurement, but followed a similar trend. Statistically significant correlations were maintained between ctDNA and slide caliper measurement in irradiated subcutaneous tumors (LINE-1, r = .64 and Alu, r = .44, p < .02), and ctDNA and bioluminescence in intratibial tumors (LINE-1, r = .55, p = .018). CONCLUSIONS Real-time qPCR of circulating human Alu and LINE-1 DNA provides an accurate measurement of subcutaneous and intratibial xenograft burden that is comparable with conventional bioluminescence imaging and slide caliper measurement. Transient differences in measurements were observed following tumor-targeted IR, but overall all measurements mirrored tumor growth and response.
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Affiliation(s)
- Alok Mishra
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenji Zennami
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Esteban Velarde
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel L J Thorek
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Radiology and Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Srinivasan Yegnasubramanian
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Theodore L DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shawn E Lupold
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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