1
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Graham MK, Wang R, Chikarmane R, Abel B, Vaghasia A, Gupta A, Zheng Q, Hicks J, Sysa-Shah P, Pan X, Castagna N, Liu J, Meyers J, Skaist A, Zhang Y, Rubenstein M, 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. Nat Commun 2024; 15:7414. [PMID: 39198404 PMCID: PMC11358296 DOI: 10.1038/s41467-024-51450-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 08/07/2024] [Indexed: 09/01/2024] Open
Abstract
How prostate cancer cells and their precursors mediate changes in the tumor microenvironment (TME) to drive prostate cancer progression is unclear, in part due to the inability to longitudinally study the disease evolution in human tissues. To overcome this limitation, we perform extensive single-cell RNA-sequencing (scRNA-seq) and molecular pathology of the comparative biology between human prostate cancer and key stages in the disease evolution of a genetically engineered mouse model (GEMM) of prostate cancer. Our studies of human tissues reveal that cancer cell-intrinsic activation of MYC signaling is a common denominator across the well-known molecular and pathological heterogeneity of human prostate cancer. Cell communication network and pathway analyses in GEMMs show that MYC oncogene-expressing neoplastic cells, directly and indirectly, reprogram the TME during carcinogenesis, leading to a convergence of cell state alterations in neighboring epithelial, immune, and fibroblast cell types that parallel key findings in human prostate cancer.
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Affiliation(s)
- Mindy K Graham
- 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
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Rulin Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Roshan Chikarmane
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Bulouere Abel
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Ajay Vaghasia
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Anuj Gupta
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Qizhi Zheng
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Jessica Hicks
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Polina Sysa-Shah
- The Brady Urological Institute and Department of Urology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Xin Pan
- Department of Neurology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Nicole Castagna
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Jianyong Liu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Jennifer Meyers
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Alyza Skaist
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Yan Zhang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Michael Rubenstein
- Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, MD, USA
| | - Kornel Schuebel
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Brian W Simons
- Center for Comparative Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Charles J Bieberich
- Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, MD, USA
| | - William G Nelson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- The Brady Urological Institute and Department of Urology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Shawn E Lupold
- 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
- The Brady Urological Institute and Department of Urology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Theodore L DeWeese
- 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
- The Brady Urological Institute and Department of Urology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Angelo M De Marzo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- The Brady Urological Institute and Department of Urology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Srinivasan Yegnasubramanian
- 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.
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
- inHealth Precision Medicine Program, Johns Hopkins Medicine, Baltimore, MD, USA.
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2
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Carey-Smith SL, Kotecha RS, Cheung LC, Malinge S. Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer. Int J Mol Sci 2024; 25:6815. [PMID: 38999925 PMCID: PMC11241182 DOI: 10.3390/ijms25136815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Copy number alterations (CNAs), resulting from the gain or loss of genetic material from as little as 50 base pairs or as big as entire chromosome(s), have been associated with many congenital diseases, de novo syndromes and cancer. It is established that CNAs disturb the dosage of genomic regions including enhancers/promoters, long non-coding RNA and gene(s) among others, ultimately leading to an altered balance of key cellular functions. In cancer, CNAs have been associated with almost all steps of the disease: predisposition, initiation, development, maintenance, response to treatment, resistance, and relapse. Therefore, understanding how specific CNAs contribute to tumourigenesis may provide prognostic insight and ultimately lead to the development of new therapeutic approaches to improve patient outcomes. In this review, we provide a snapshot of what is currently known about CNAs and cancer, incorporating topics regarding their detection, clinical impact, origin, and nature, and discuss the integration of innovative genetic engineering strategies, to highlight the potential for targeting CNAs using novel, dosage-sensitive and less toxic therapies for CNA-driven cancer.
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Affiliation(s)
- Shannon L. Carey-Smith
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Rishi S. Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Laurence C. Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Sébastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
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3
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Carceles-Cordon M, Orme JJ, Domingo-Domenech J, Rodriguez-Bravo V. The yin and yang of chromosomal instability in prostate cancer. Nat Rev Urol 2024; 21:357-372. [PMID: 38307951 PMCID: PMC11156566 DOI: 10.1038/s41585-023-00845-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2023] [Indexed: 02/04/2024]
Abstract
Metastatic prostate cancer remains an incurable lethal disease. Studies indicate that prostate cancer accumulates genomic changes during disease progression and displays the highest levels of chromosomal instability (CIN) across all types of metastatic tumours. CIN, which refers to ongoing chromosomal DNA gain or loss during mitosis, and derived aneuploidy, are known to be associated with increased tumour heterogeneity, metastasis and therapy resistance in many tumour types. Paradoxically, high CIN levels are also proposed to be detrimental to tumour cell survival, suggesting that cancer cells must develop adaptive mechanisms to ensure their survival. In the context of prostate cancer, studies indicate that CIN has a key role in disease progression and might also offer a therapeutic vulnerability that can be pharmacologically targeted. Thus, a comprehensive evaluation of the causes and consequences of CIN in prostate cancer, its contribution to aggressive advanced disease and a better understanding of the acquired CIN tolerance mechanisms can translate into new tumour classifications, biomarker development and therapeutic strategies.
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Affiliation(s)
| | - Jacob J Orme
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Josep Domingo-Domenech
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
| | - Veronica Rodriguez-Bravo
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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4
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O'Malley DE, Raspin K, Melton PE, Burdon KP, Dickinson JL, FitzGerald LM. Acquired copy number variation in prostate tumours: a review of common somatic copy number alterations, how they are formed and their clinical utility. Br J Cancer 2024; 130:347-357. [PMID: 37945750 PMCID: PMC10844642 DOI: 10.1038/s41416-023-02485-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
Prostate cancer is one of the most commonly diagnosed cancers in men and unfortunately, disease will progress in up to a third of patients despite primary treatment. Currently, there is a significant lack of prognostic tests that accurately predict disease course; however, the acquisition of somatic chromosomal variation in the form of DNA copy number variants may help understand disease progression. Notably, studies have found that a higher burden of somatic copy number alterations (SCNA) correlates with more aggressive disease, recurrence after surgery and metastasis. Here we will review the literature surrounding SCNA formation, including the roles of key tumour suppressors and oncogenes (PTEN, BRCA2, NKX3.1, ERG and AR), and their potential to inform diagnostic and prognostic clinical testing to improve predictive value. Ultimately, SCNAs, or inherited germline alterations that predispose to SCNAs, could have significant clinical utility in diagnostic and prognostic tests, in addition to guiding therapeutic selection.
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Affiliation(s)
- Dannielle E O'Malley
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillip E Melton
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- School of Population and Global Health, The University of Western Australia, Crawley, WA, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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5
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Wei D, Liu Y, Yuan Y, Li Y, Zhao F, Qin X. Molecular map of cGAS-STING pathway-related genes in bladder cancer: the perspective toward immune microenvironment and prognosis. Aging (Albany NY) 2024; 16:1516-1535. [PMID: 38240703 PMCID: PMC10866408 DOI: 10.18632/aging.205442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/06/2023] [Indexed: 02/06/2024]
Abstract
BACKGROUND The cGAS-STING pathway emerges as a pivotal innate immune pathway with the potential to profoundly influence all facets of tumor initiation and progression. The prognostic significance and immunological role of cGAS-STING pathway-related genes (CRGs) in individuals diagnosed with bladder cancer (BLCA) have not yet been fully elucidated. METHODS Performed unsupervised cluster analysis to identify distinct clusters. Utilizing LASSO and multivariate Cox regression analysis to construct a prognostic risk model. The IMvigor210, GSE13507 and GSE78220 cohorts were utilized to explore the potential value of risk score in immune therapy response and survival prediction. RESULTS A risk model was developed utilizing four CRGs in order to forecast the overall survival (OS) of BLCA patients. The risk score to be a standalone risk factor, which was further corroborated by the external validation set obtained from the GEO database (GSE13507). We established an integrated nomogram that combined risk scoring and clinical information, exhibiting commendable clinical practicality in predicting the overall survival period of BLCA patients. It is noteworthy that risk score could differentiate tumor microenvironments among different risk groups and individuals who were more responsive to immunotherapy in IMvigor210 and GSE13507 cohorts. In vitro experiments, we noted an up-regulation of IRF3 and IKBKB upon the activation of the cGAS-STING pathway. Conversely, the activation of the cGAS-STING pathway resulted in a down-regulation of POLR3G and CTNNB1. CONCLUSIONS CRG risk model shows promise as a potential stratification approach for bladder cancer patients.
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Affiliation(s)
- Dong Wei
- Department of Urology, Hebei General Hospital, Shijiazhuang 050000, China
| | - Ying Liu
- Department of Neurology, Xingtai Third Hospital, Xingtai 054000, China
| | - Ying Yuan
- Department of Neurology, Xingtai Third Hospital, Xingtai 054000, China
| | - Yishuai Li
- Department of Thoracic Surgery, Hebei Chest Hospital, Shijiazhuang 050000, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Xuebo Qin
- Department of Thoracic Surgery, Hebei Chest Hospital, Shijiazhuang 050000, China
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050000, China
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6
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Salachan PV, Ulhøi BP, Borre M, Sørensen KD. Association between copy number alterations estimated using low-pass whole genome sequencing of formalin-fixed paraffin-embedded prostate tumor tissue and cancer-specific clinical parameters. Sci Rep 2023; 13:22445. [PMID: 38105358 PMCID: PMC10725894 DOI: 10.1038/s41598-023-49811-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
Copy number alterations (CNAs) are frequently observed in early-stage prostate cancer and are associated with disease recurrence and tumor aggressiveness. Cost-effective assessment of CNAs could enhance clinical utility of CNAs. Here, we combined the cost-effectiveness of low-pass (low coverage) whole genome sequencing (LPWGS) and the routine availability of formalin-fixed paraffin-embedded (FFPE) tumor tissue for assessing CNAs in a cohort of 187 men with early-stage localised prostate cancer. We detected well known CNAs in 8p, 8q, 13q and 16q and recurrent gains of the oncogene MYC and losses of the tumor suppressor genes NKX3-1, PTEN and RB1, indicating assay reliability. The estimated burden of CNAs was significantly associated with Gleason score, pathological T stage, surgical margin status and biochemical recurrence. Further, genomic losses or gains in specific chromosomal arms were significantly associated with worse BCR-free survival. Copy number signatures extracted from the LPWGS data showed potential for risk stratifying patients, where signatures S1 and S2 showed significant association to worse BCR-free survival compared to S3. Our study provides clinical validation of the associations between CNAs and tumor aggressiveness in an independent and representative RP cohort, while demonstrating the feasibility of performing LPWGS of FFPE tumor tissue for cost-effective assessment of CNAs.
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Affiliation(s)
- Paul Vinu Salachan
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus N, Denmark
| | | | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus N, Denmark
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus N, Denmark.
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7
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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8
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Raspin K, Marthick JR, Donovan S, Blizzard L, Malley RC, Jung CH, Banks A, Redwig F, Skala M, Dickinson JL, FitzGerald LM. Identification of a novel recurrent EEF2 gene amplification in familial prostate tumors. Genes Chromosomes Cancer 2023; 62:247-255. [PMID: 36520140 DOI: 10.1002/gcc.23117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Recurrent tumor copy number variations (CNVs) in prostate cancer (PrCa) have predominantly been discovered in sporadic tumor cohorts. Here, we examined familial prostate tumors for novel CNVs as prior studies suggest these harbor distinct CNVs. Array comparative genomic hybridization of 12 tumors from an Australian PrCa family, PcTas9, highlighted multiple recurrent CNVs, including amplification of EEF2 (19p13.3) in 100% of tumors. The EEF2 CNV was examined in a further 26 familial and seven sporadic tumors from the Australian cohort and in 494 tumors unselected for family history from The Cancer Genome Atlas (TCGA). EEF2 overexpression was observed in seven PcTas9 tumors, in addition to seven other predominantly familial tumors (ntotal = 34%). EEF2 amplification was only observed in 1.4% of TCGA tumors, however 7.5% harbored an EEF2 deletion. Analysis of genes co-expressed with EEF2 revealed significant upregulation of two genes, ZNF74 and ADSL, and downregulation of PLSCR1 in both EEF2 amplified familial tumors and EEF2 deleted TCGA tumors. Furthermore, in TCGA tumors, EEF2 amplification and deletion were significantly associated with a higher Gleason score. In summary, we identified a novel PrCa CNV that was predominantly amplified in familial tumors and deleted in unselected tumors. Our results provide further evidence that familial tumors harbor distinct CNVs, potentially due to an inherited predisposition, but also suggest that regardless of how EEF2 is dysregulated, a similar set of genes involved in key cancer pathways are impacted. Given the current lack of gene-based biomarkers and clinical targets in PrCa, further investigation of EEF2 is warranted.
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Affiliation(s)
- Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Shaun Donovan
- Diagnostic Services, Sonic Healthcare, Hobart, Tasmania, Australia
| | - Leigh Blizzard
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Roslyn C Malley
- Diagnostic Services, Sonic Healthcare, Hobart, Tasmania, Australia.,Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia
| | - Annette Banks
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Frank Redwig
- Department of Urology, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Marketa Skala
- WP Holman Clinic, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
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9
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Alfahed A, Ebili HO, Waggiallah HA. Chromosome-specific segment size alterations are determinants of prognosis in prostate cancer. Saudi J Biol Sci 2023; 30:103629. [PMID: 37091119 PMCID: PMC10119956 DOI: 10.1016/j.sjbs.2023.103629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/01/2023] [Accepted: 03/17/2023] [Indexed: 04/25/2023] Open
Abstract
Currently, risk stratification is the most difficult problem in prostate cancer (PCa) management. Gleason grading cannot adequately predict cancer progression. This study aimed to identify chromosome-specific segment size alterations that could aid risk stratification and predict metastasis using a retrospective cohort-study strategy. A binary logistic regression model was generated using 16 chromosome-specific segments with size alterations (deletions and amplifications) that showed associations with disease stage (primary versus metastatic). The regression model was trained with the MSKCC PIK3R1 PCa cohort (n = 1417), and validated with the TCGA Firehose Legacy (n = 500), MSKCC Prostate Oncogenome Project (n = 218), and the SU2C/PCF Dream Team (n = 150) PCa cohorts. Furthermore, the capacity of the model to predict metastasis between primary tumours with metastasis (n = 54) and primary tumours without metastasis (n = 54) was tested. The accuracy, sensitivity, and specificity of the model at disease stage stratification ranged from 69.02% to 88.55%, 72.8% to 86.00% and 66.30% to 89.50%, respectively. The model also showed good performance at metastasis prediction with accuracy, sensitivity, and specificity of 57.41%, 62.96% and 51.85%, respectively. The study conclusion was that chromosome-specific segment size alterations can aid risk stratification and metastasis prediction. The significance of the study findings is that in combinations with clinical, biochemical, and histopathological variables, chromosome-specific alterations could improve current risk stratification and prediction models for PCa.
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Affiliation(s)
- Abdulaziz Alfahed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudia Arabia
- Corresponding author.
| | - Henry Okuchukwu Ebili
- Morbid Anatomy and Histopathology Department, Olabisi Onabanjo University, Ago-Iwoye, Nigeria
| | - Hisham Ali Waggiallah
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudia Arabia
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10
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Alfahed A, Ebili HO, Almoammar NE, Alasiri G, AlKhamees OA, Aldali JA, Al Othaim A, Hakami ZH, Abdulwahed AM, Waggiallah HA. Prognostic Values of Gene Copy Number Alterations in Prostate Cancer. Genes (Basel) 2023; 14:genes14050956. [PMID: 37239316 DOI: 10.3390/genes14050956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Whilst risk prediction for individual prostate cancer (PCa) cases is of a high priority, the current risk stratification indices for PCa management have severe limitations. This study aimed to identify gene copy number alterations (CNAs) with prognostic values and to determine if any combination of gene CNAs could have risk stratification potentials. Clinical and genomic data of 500 PCa cases from the Cancer Genome Atlas stable were retrieved from the Genomic Data Commons and cBioPortal databases. The CNA statuses of a total of 52 genetic markers, including 21 novel markers and 31 previously identified potential prognostic markers, were tested for prognostic significance. The CNA statuses of a total of 51/52 genetic markers were significantly associated with advanced disease at an odds ratio threshold of ≥1.5 or ≤0.667. Moreover, a Kaplan-Meier test identified 27/52 marker CNAs which correlated with disease progression. A Cox Regression analysis showed that the amplification of MIR602 and deletions of MIR602, ZNF267, MROH1, PARP8, and HCN1 correlated with a progression-free survival independent of the disease stage and Gleason prognostic group grade. Furthermore, a binary logistic regression analysis identified twenty-two panels of markers with risk stratification potentials. The best model of 7/52 genetic CNAs, which included the SPOP alteration, SPP1 alteration, CCND1 amplification, PTEN deletion, CDKN1B deletion, PARP8 deletion, and NKX3.1 deletion, stratified the PCa cases into a localised and advanced disease with an accuracy of 70.0%, sensitivity of 85.4%, specificity of 44.9%, positive predictive value of 71.67%, and negative predictive value of 65.35%. This study validated prognostic gene level CNAs identified in previous studies, as well as identified new genetic markers with CNAs that could potentially impact risk stratification in PCa.
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Affiliation(s)
- Abdulaziz Alfahed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Henry Okuchukwu Ebili
- Department of Morbid Anatomy and Histopathology, Olabisi Onabanjo University, Ago-Iwoye P.M.B. 2002, Nigeria
| | - Nasser Eissa Almoammar
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Glowi Alasiri
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud University, Riyadh 13317, Saudi Arabia
| | - Osama A AlKhamees
- Department of Pharmacology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia
| | - Jehad A Aldali
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia
| | - Ayoub Al Othaim
- Department of Medical Laboratories, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia
| | - Zaki H Hakami
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 82817, Saudi Arabia
| | - Abdulhadi M Abdulwahed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Hisham Ali Waggiallah
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
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11
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Dhital B, Santasusagna S, Kirthika P, Xu M, Li P, Carceles-Cordon M, Soni RK, Li Z, Hendrickson RC, Schiewer MJ, Kelly WK, Sternberg CN, Luo J, Lujambio A, Cordon-Cardo C, Alvarez-Fernandez M, Malumbres M, Huang H, Ertel A, Domingo-Domenech J, Rodriguez-Bravo V. Harnessing transcriptionally driven chromosomal instability adaptation to target therapy-refractory lethal prostate cancer. Cell Rep Med 2023; 4:100937. [PMID: 36787737 PMCID: PMC9975292 DOI: 10.1016/j.xcrm.2023.100937] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/27/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023]
Abstract
Metastatic prostate cancer (PCa) inevitably acquires resistance to standard therapy preceding lethality. Here, we unveil a chromosomal instability (CIN) tolerance mechanism as a therapeutic vulnerability of therapy-refractory lethal PCa. Through genomic and transcriptomic analysis of patient datasets, we find that castration and chemotherapy-resistant tumors display the highest CIN and mitotic kinase levels. Functional genomics screening coupled with quantitative phosphoproteomics identify MASTL kinase as a survival vulnerability specific of chemotherapy-resistant PCa cells. Mechanistically, MASTL upregulation is driven by transcriptional rewiring mechanisms involving the non-canonical transcription factors androgen receptor splice variant 7 and E2F7 in a circuitry that restrains deleterious CIN and prevents cell death selectively in metastatic therapy-resistant PCa cells. Notably, MASTL pharmacological inhibition re-sensitizes tumors to standard therapy and improves survival of pre-clinical models. These results uncover a targetable mechanism promoting high CIN adaptation and survival of lethal PCa.
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Affiliation(s)
- Brittiny Dhital
- Biochemistry and Molecular Biology Department, Mayo Clinic, Rochester, MN 55905, USA; Urology Department, Mayo Clinic, Rochester, MN 55905, USA; Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | - Sandra Santasusagna
- Biochemistry and Molecular Biology Department, Mayo Clinic, Rochester, MN 55905, USA; Urology Department, Mayo Clinic, Rochester, MN 55905, USA
| | - Perumalraja Kirthika
- Biochemistry and Molecular Biology Department, Mayo Clinic, Rochester, MN 55905, USA; Urology Department, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael Xu
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | - Peiyao Li
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | | | - Rajesh K Soni
- Microchemistry and Proteomics Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zhuoning Li
- Microchemistry and Proteomics Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronald C Hendrickson
- Microchemistry and Proteomics Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew J Schiewer
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | - William K Kelly
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | - Cora N Sternberg
- Englander Institute for Precision Medicine, Weill Cornell Department of Medicine, Meyer Cancer Center, New York-Presbyterian Hospital, New York, NY 10021, USA
| | - Jun Luo
- Urology Department, Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Amaia Lujambio
- Oncological Sciences Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Cordon-Cardo
- Pathology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Monica Alvarez-Fernandez
- Head & Neck Cancer Department, Institute de Investigación Sanitaria Principado de Asturias (ISPA), Institute Universitario de Oncología Principado de Asturias (IUOPA), 33011 Oviedo, Spain
| | - Marcos Malumbres
- Cell Division & Cancer Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; Cancer Cell Cycle group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Haojie Huang
- Biochemistry and Molecular Biology Department, Mayo Clinic, Rochester, MN 55905, USA; Urology Department, Mayo Clinic, Rochester, MN 55905, USA
| | - Adam Ertel
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | - Josep Domingo-Domenech
- Biochemistry and Molecular Biology Department, Mayo Clinic, Rochester, MN 55905, USA; Urology Department, Mayo Clinic, Rochester, MN 55905, USA.
| | - Veronica Rodriguez-Bravo
- Biochemistry and Molecular Biology Department, Mayo Clinic, Rochester, MN 55905, USA; Urology Department, Mayo Clinic, Rochester, MN 55905, USA.
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12
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Nørgaard M, Bjerre MT, Fredsøe J, Vang S, Jensen JB, De Laere B, Grönberg H, Borre M, Lindberg J, Sørensen KD. Prognostic Value of Low-Pass Whole Genome Sequencing of Circulating Tumor DNA in Metastatic Castration-Resistant Prostate Cancer. Clin Chem 2023; 69:386-398. [PMID: 36762756 DOI: 10.1093/clinchem/hvac224] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/08/2022] [Indexed: 02/11/2023]
Abstract
BACKGROUND Multiple treatments are available for metastatic castration-resistant prostate cancer (mCRPC), including androgen receptor signaling inhibitors (ARSI) enzalutamide and abiraterone, but therapy resistance remains a major clinical obstacle. We examined the clinical utility of low-pass whole-genome sequencing (LPWGS) of circulating tumor DNA (ctDNA) for prognostication in mCRPC. METHODS A total of 200 plasma samples from 143 mCRPC patients collected at the start of first-line ARSI treatment (baseline) and at treatment termination (n = 57, matched) were analyzed by LPWGS (median: 0.50X) to access ctDNA% and copy number alteration (CNA) patterns. The best confirmed prostate specific antigen (PSA) response (≥50% decline [PSA50]), PSA progression-free survival (PFS), and overall survival (OS) were used as endpoints. For external validation, we used plasma LPWGS data from an independent cohort of 70 mCRPC patients receiving first-line ARSI. RESULTS Baseline ctDNA% ranged from ≤3.0% to 73% (median: 6.6%) and CNA burden from 0% to 82% (median: 13.1%) in the discovery cohort. High ctDNA% and high CNA burden at baseline was associated with poor PSA50 response (P = 0.0123/0.0081), poor PFS (P < 0.0001), and poor OS (P < 0.0001). ctDNA% and CNA burden was higher at PSA progression than at baseline in 32.7% and 42.3% of the patients. High ctDNA% and high CNA burden at baseline was also associated with poor PFS and OS (P ≤ 0.0272) in the validation cohort. CONCLUSIONS LPWGS of ctDNA provides clinically relevant information about the tumor genome in mCRPC patients. Using LPWGS data, we show that high ctDNA% and CNA burden at baseline is associated with short PFS and OS in 2 independent cohorts.
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Affiliation(s)
- Maibritt Nørgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marianne T Bjerre
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark.,Department of Urology, Regional Hospital West Jutland, Holstebro, Denmark
| | - Jacob Fredsøe
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jørgen B Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Regional Hospital West Jutland, Holstebro, Denmark
| | - Bram De Laere
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden.,Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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13
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Vidotto T, Imada EL, Faisal F, Murali S, Mendes AA, Kaur H, Zheng S, Xu J, Schaeffer EM, Isaacs WB, Sfanos KS, Marchionni L, Lotan TL. Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer. JCI Insight 2023; 8:e162409. [PMID: 36752203 PMCID: PMC9977441 DOI: 10.1172/jci.insight.162409] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/27/2022] [Indexed: 02/09/2023] Open
Abstract
The genomic and immune landscapes of prostate cancer differ by self-identified race. However, few studies have examined the genome-wide copy number landscape and immune content of matched cohorts with genetic ancestry data and clinical outcomes. Here, we assessed prostate cancer somatic copy number alterations (sCNA) and tumor immune content of a grade-matched, surgically treated cohort of 145 self-identified Black (BL) and 145 self-identified White (WH) patients with genetic ancestry estimation. A generalized linear model adjusted with age, preoperative prostate-specific antigen (PSA), and Gleason Grade Group and filtered for germline copy number variations (gCNV) identified 143 loci where copy number varied significantly by percent African ancestry, clustering on chromosomes 6p, 10q, 11p, 12p, and 17p. Multivariable Cox regression models adjusted for age, preoperative PSA levels, and Gleason Grade Group revealed that chromosome 8q gains (including MYC) were significantly associated with biochemical recurrence and metastasis, independent of genetic ancestry. Finally, Treg density in BL and WH patients was significantly correlated with percent genome altered, and these findings were validated in the TCGA cohort. Taken together, our findings identify specific sCNA linked to genetic ancestry and outcome in primary prostate cancer and demonstrate that Treg infiltration varies by global sCNA burden in primary disease.
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Affiliation(s)
- Thiago Vidotto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eddie L. Imada
- Department of Pathology, Weill-Cornell School of Medicine, New York, New York, USA
| | - Farzana Faisal
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sanjana Murali
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adrianna A. Mendes
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harsimar Kaur
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Siqun Zheng
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Edward M. Schaeffer
- Department of Urology, Northwestern University School of Medicine, Chicago, Illinois, USA
| | | | - Karen S. Sfanos
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Luigi Marchionni
- Department of Pathology, Weill-Cornell School of Medicine, New York, New York, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology and
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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Chen X, Lin L, Chen G, Yan H, Li Z, Xiao M, He X, Zhang F, Zhang Y. High Levels of DEAH-Box Helicases Relate to Poor Prognosis and Reduction of DHX9 Improves Radiosensitivity of Hepatocellular Carcinoma. Front Oncol 2022; 12:900671. [PMID: 35814441 PMCID: PMC9256992 DOI: 10.3389/fonc.2022.900671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundLiver hepatocellular carcinoma (LIHC), one of the most common primary malignancies, exhibits high levels of molecular and clinical heterogeneity. Increasing evidence has confirmed the important roles of some RNA helicase families in tumor development, but the function of the DEAH-box RNA helicase family in LIHC therapeutic strategies has not yet been clarified.MethodsThe LIHC dataset was downloaded from The Cancer Genome Atlas (TCGA). Consensus clustering was applied to group the patients. Least absolute shrinkage and selection operator Cox regression and univariate and multivariate Cox regression were used to develop and validate a prognostic risk model. The Tumor Immune Estimation Resource and Tumor Immune Single Cell Hub databases were used to explore the role of DEAH-box RNA helicases in LIHC immunotherapy. In vitro experiments were performed to investigate the role of DHX9 in LIHC radiosensitivity.ResultsTwelve survival-related DEAH-box RNA helicases were identified. High helicase expression levels were associated with a poor prognosis and clinical features. A prognostic model comprising six DEAH-box RNA helicases (DHX8, DHX9, DHX34, DHX35, DHX38, and DHX57) was constructed. The risk score of this model was found to be an independent prognostic indicator, and LIHC patients with different prognosis were distinguished by the model in the training and test cohorts. DNA damage repair pathways were also enriched in patients with high-risk scores. The six DEAH-box RNA helicases in the risk model were substantially related to innate immune cell infiltration and immune inhibitors. In vitro experiments showed that DHX9 knockdown improved radiosensitivity by increasing DNA damage.ConclusionThe DEAH-box RNA helicase signature can be used as a reliable prognostic biomarker for LIHC. In addition, DHX9 may be a definitive indicator and therapeutic target in radiotherapy and immunotherapy for LIHC.
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Affiliation(s)
- Xi Chen
- Department of Minimally Invasive Interventional Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Letao Lin
- Department of Minimally Invasive Interventional Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Guanyu Chen
- Department of Minimally Invasive Interventional Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Huzheng Yan
- Department of Interventional Radiology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhenyu Li
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Meigui Xiao
- Department of Minimally Invasive Interventional Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xu He
- Interventional Medical Center, Zhuhai People’s Hospital, Zhuhai, China
| | - Fujun Zhang
- Department of Minimally Invasive Interventional Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- *Correspondence: Fujun Zhang, ; Yanling Zhang,
| | - Yanling Zhang
- Department of Minimally Invasive Interventional Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- *Correspondence: Fujun Zhang, ; Yanling Zhang,
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15
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Liang Y, Rong E, Qian J, Ma C, Hu J. Transcriptome subtyping of metastatic Castration Resistance Prostate Cancer (mCRPC) for the precision therapeutics: an in silico analysis. Prostate Cancer Prostatic Dis 2022; 25:327-335. [DOI: 10.1038/s41391-022-00495-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/21/2021] [Accepted: 01/12/2022] [Indexed: 11/09/2022]
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16
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Cheaito K, Bahmad HF, Hadadeh O, Msheik H, Monzer A, Ballout F, Dagher C, Telvizian T, Saheb N, Tawil A, El-Sabban M, El-Hajj A, Mukherji D, Al-Sayegh M, Abou-Kheir W. Establishment and characterization of prostate organoids from treatment-naïve patients with prostate cancer. Oncol Lett 2022; 23:6. [PMID: 34820005 PMCID: PMC8607232 DOI: 10.3892/ol.2021.13124] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
Three-dimensional (3D) organoid culture systems are emerging as potential reliable tools to investigate basic developmental processes of human disease, especially cancer. The present study used established and modified culture conditions to report successful generation and characterization of patient-derived organoids from fresh primary tissue specimens of patients with treatment-naïve prostate cancer (PCa). Fresh tissue specimens were collected, digested enzymatically and the resulting cell suspensions were plated in a 3D environment using Matrigel as an extracellular matrix. Previously established 12-factor medium for organoid culturing was modified to create a minimal 5-factor medium. Organoids and corresponding tissue specimens were characterized using transcriptomic analysis, immunofluorescent analysis, and immunohistochemistry. Furthermore, patient-derived organoids were used to assess the drug response. Treatment-naïve patient-derived PCa organoids were obtained from fresh radical prostatectomy specimens. These PCa organoids mimicked the heterogeneity of corresponding parental tumor tissue. Histopathological analysis demonstrated similar tissue architecture and cellular morphology, as well as consistent immunohistochemical marker expression. Also, the results confirmed the potential of organoids as an in vitro model to assess potential personalized treatment responses as there was a differential drug response between different patient samples. In conclusion, the present study investigated patient-derived organoids from a cohort of treatment-naïve patients. Derived organoids mimicked the histological features and prostate lineage profiles of their corresponding parental tissue and may present a potential model to predict patient-specific treatment response in a pre-clinical setting.
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Affiliation(s)
- Katia Cheaito
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Hisham F. Bahmad
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
- Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Ola Hadadeh
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Hiba Msheik
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Alissar Monzer
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Farah Ballout
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Christelle Dagher
- Department of Internal Medicine, Division of Hematology/Oncology, Faculty of Medicine, American University of Beirut Medical Center, Beirut 1107-2020, Lebanon
| | - Talar Telvizian
- Department of Internal Medicine, Division of Hematology/Oncology, Faculty of Medicine, American University of Beirut Medical Center, Beirut 1107-2020, Lebanon
| | - Nour Saheb
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut 1107-2020, Lebanon
| | - Ayman Tawil
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut 1107-2020, Lebanon
| | - Marwan El-Sabban
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Albert El-Hajj
- Department of Surgery, Division of Urology, American University of Beirut Medical Center, Beirut 1107-2020, Lebanon
| | - Deborah Mukherji
- Department of Internal Medicine, Division of Hematology/Oncology, Faculty of Medicine, American University of Beirut Medical Center, Beirut 1107-2020, Lebanon
| | - Mohamed Al-Sayegh
- Biology Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
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17
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Genomic Features and Clinical Implications of Intraductal Carcinoma of the Prostate. Int J Mol Sci 2021; 22:ijms222313125. [PMID: 34884926 PMCID: PMC8658449 DOI: 10.3390/ijms222313125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 01/29/2023] Open
Abstract
Intraductal carcinoma of the prostate (IDC-P) is a rare and unique form of aggressive prostate carcinoma, which is characterized by an expansile proliferation of malignant prostatic epithelial cells within prostatic ducts or acini and the preservation of basal cell layers around the involved glands. The vast majority of IDC-P tumors result from adjacent high-grade invasive cancer via the retrograde spreading of tumor cells into normal prostatic ducts or acini. A subset of IDC-P tumors is rarely derived from the de novo intraductal proliferation of premalignant cells. The presence of IDC-P in biopsy or surgical specimens is significantly associated with aggressive pathologic features, such as high Gleason grade, large tumor volume, and advanced tumor stage, and with poor clinical courses, including earlier biochemical recurrence, distant metastasis, and worse survival outcomes. These architectural and behavioral features of IDC-P may be driven by specific molecular properties. Notably, IDC-P possesses distinct genomic profiles, including higher rates of TMPRSS2–ERG gene fusions and PTEN loss, increased percentage of genomic instability, and higher prevalence of germline BRCA2 mutations. Considering that IDC-P tumors are usually resistant to conventional therapies for prostate cancer, further studies should be performed to develop optimal therapeutic strategies based on distinct genomic features, such as treatment with immune checkpoint blockades or poly (adenosine diphosphate–ribose) polymerase inhibitors for patients harboring increased genomic instability or BRCA2 mutations, as well as genetic counseling with genetic testing. Patient-derived xenografts and tumor organoid models can be the promising in vitro platforms for investigating the molecular features of IDC-P tumor.
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18
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Ansari-Pour N, Zheng Y, Yoshimatsu TF, Sanni A, Ajani M, Reynier JB, Tapinos A, Pitt JJ, Dentro S, Woodard A, Rajagopal PS, Fitzgerald D, Gruber AJ, Odetunde A, Popoola A, Falusi AG, Babalola CP, Ogundiran T, Ibrahim N, Barretina J, Van Loo P, Chen M, White KP, Ojengbede O, Obafunwa J, Huo D, Wedge DC, Olopade OI. Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes. Nat Commun 2021; 12:6946. [PMID: 34836952 PMCID: PMC8626467 DOI: 10.1038/s41467-021-27079-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 11/02/2021] [Indexed: 02/08/2023] Open
Abstract
Black women across the African diaspora experience more aggressive breast cancer with higher mortality rates than white women of European ancestry. Although inter-ethnic germline variation is known, differential somatic evolution has not been investigated in detail. Analysis of deep whole genomes of 97 breast cancers, with RNA-seq in a subset, from women in Nigeria in comparison with The Cancer Genome Atlas (n = 76) reveal a higher rate of genomic instability and increased intra-tumoral heterogeneity as well as a unique genomic subtype defined by early clonal GATA3 mutations with a 10.5-year younger age at diagnosis. We also find non-coding mutations in bona fide drivers (ZNF217 and SYPL1) and a previously unreported INDEL signature strongly associated with African ancestry proportion, underscoring the need to expand inclusion of diverse populations in biomedical research. Finally, we demonstrate that characterizing tumors for homologous recombination deficiency has significant clinical relevance in stratifying patients for potentially life-saving therapies. Breast cancer heterogeneity and tumour evolutionary trajectories remain largely unknown among women of African ancestry. Here, the authors perform whole genome and transcriptome sequencing of Nigerian breast cancer patients and identify unique evolutionary phenomena.
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Affiliation(s)
- Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK.,MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Jean-Baptiste Reynier
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Avraam Tapinos
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Stefan Dentro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Anna Woodard
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Department of Computer Science, The University of Chicago, Chicago, IL, 60637, USA
| | - Padma Sheila Rajagopal
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Andreas J Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK.,Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Chinedum Peace Babalola
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Temidayo Ogundiran
- Department of Surgery, University College Hospital, Ibadan, Oyo, Nigeria
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Jordi Barretina
- Girona Biomedical Research Institute (IDIBGI), Hospital Universitari de Girona Dr Josep Trueta, Girona, Spain
| | | | - Mengjie Chen
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.,Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Dezheng Huo
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK. .,Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK.
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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19
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System Analysis of ROS-Related Genes in the Prognosis, Immune Infiltration, and Drug Sensitivity in Hepatocellular Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6485871. [PMID: 34795841 PMCID: PMC8593590 DOI: 10.1155/2021/6485871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive malignant tumor with a poor prognosis. Reactive oxygen species (ROS) play an important role in tumors; however, the role of ROS-related genes is still unclear in HCC. Therefore, we analyzed the role of ROS-related genes in HCC via bioinformatics methods. Firstly, a prognosis model was constructed using LASSO Cox regression and multivariate analyses. We also investigated the potential function of the ROS-related genes and the correlation with immune infiltration, tumor stemness, and drug sensitivity. ICGC database was used for validation. Secondly, we further analyzed the role of 11 ROS-related genes in HCC. As a member of ROS gene family, the role of STK25 has remained unclear in HCC. We explored the biological function of STK25 using in vitro experiments. The present study was the first to construct a ROS-related prognostic model in HCC. The correlation of ROS-related genes with immune infiltration, tumor stemness, and drug sensitivity was dissected. Furthermore, we demonstrated that STK25 knockdown could increase the proliferation, migration, and invasion capacity of HCC cells.
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20
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Lu Z, Chen H, Li S, Gong J, Li J, Zou J, Wu L, Yu J, Han W, Sun H, Jiao X, Zhang X, Peng Z, Lu M, Wang Z, Zhang H, Shen L. Tumor copy-number alterations predict response to immune-checkpoint-blockade in gastrointestinal cancer. J Immunother Cancer 2021; 8:jitc-2019-000374. [PMID: 32792358 PMCID: PMC7430454 DOI: 10.1136/jitc-2019-000374] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2020] [Indexed: 12/14/2022] Open
Abstract
Background Despite the great achievements made in immune-checkpoint-blockade (ICB) in cancer therapy, there are no effective predictive biomarkers in gastrointestinal (GI) cancer. Methods This study included 93 metastatic GI patients treated with ICBs. The first cohort comprising 73 GI cancer patients were randomly assigned into discovery (n=44) and validation (n=29) cohorts. Comprehensive genomic profiling was performed on all samples to determine tumor mutational burden (TMB) and copy-number alterations (CNAs). A subset of samples was collected for RNA immune oncology (IO) panel sequencing, microsatellite instability (MSI)/mismatch repair and program death ligand 1 (PD-L1) expression evaluation. In addition, 20 gastric cancer (GC) patients were recruited as the second validation cohort. Results In the first cohort of 73 GI cancer patients, a lower burden of CNA was observed in patients with durable clinical benefit (DCB). In both the discovery (n=44) and validation (n=29) subsets, lower burden of CNA was associated with an improved clinical benefit and better overall survival (OS). Efficacy also correlated with a higher TMB. Of note, a combinatorial biomarker of TMB and CNA may better stratify DCB patients from ICB treatment, which was further confirmed in the second validation cohort of 20 GC patients. Finally, patients with lower burden of CNA revealed increased immune signatures in our cohort and The Cancer Genome Atlas data sets as well. Conclusions Our results suggest that the burden of CNA may have superior predictive value compared with other signatures, including PD-L1, MSI and TMB. The joint biomarker of CNA burden and TMB may better stratify DCB patients, thereby providing a rational choice for GI patients treated with ICBs.
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Affiliation(s)
- Zhihao Lu
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Huan Chen
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Shuang Li
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jifang Gong
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jian Li
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jianling Zou
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Lihong Wu
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Jianing Yu
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Wenbo Han
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Huaibo Sun
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Xi Jiao
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaotian Zhang
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhi Peng
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Ming Lu
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhenghang Wang
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
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21
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Mukha A, Kahya U, Linge A, Chen O, Löck S, Lukiyanchuk V, Richter S, Alves TC, Peitzsch M, Telychko V, Skvortsov S, Negro G, Aschenbrenner B, Skvortsova II, Mirtschink P, Lohaus F, Hölscher T, Neubauer H, Rivandi M, Labitzky V, Lange T, Franken A, Behrens B, Stoecklein NH, Toma M, Sommer U, Zschaeck S, Rehm M, Eisenhofer G, Schwager C, Abdollahi A, Groeben C, Kunz-Schughart LA, Baretton GB, Baumann M, Krause M, Peitzsch C, Dubrovska A. GLS-driven glutamine catabolism contributes to prostate cancer radiosensitivity by regulating the redox state, stemness and ATG5-mediated autophagy. Theranostics 2021; 11:7844-7868. [PMID: 34335968 PMCID: PMC8315064 DOI: 10.7150/thno.58655] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Radiotherapy is one of the curative treatment options for localized prostate cancer (PCa). The curative potential of radiotherapy is mediated by irradiation-induced oxidative stress and DNA damage in tumor cells. However, PCa radiocurability can be impeded by tumor resistance mechanisms and normal tissue toxicity. Metabolic reprogramming is one of the major hallmarks of tumor progression and therapy resistance. Specific metabolic features of PCa might serve as therapeutic targets for tumor radiosensitization and as biomarkers for identifying the patients most likely to respond to radiotherapy. The study aimed to characterize a potential role of glutaminase (GLS)-driven glutamine catabolism as a prognostic biomarker and a therapeutic target for PCa radiosensitization. Methods: We analyzed primary cell cultures and radioresistant (RR) derivatives of the conventional PCa cell lines by gene expression and metabolic assays to identify the molecular traits associated with radiation resistance. Relative radiosensitivity of the cell lines and primary cell cultures were analyzed by 2-D and 3-D clonogenic analyses. Targeting of glutamine (Gln) metabolism was achieved by Gln starvation, gene knockdown, and chemical inhibition. Activation of the DNA damage response (DDR) and autophagy was assessed by gene expression, western blotting, and fluorescence microscopy. Reactive oxygen species (ROS) and the ratio of reduced glutathione (GSH) to oxidized glutathione (GSSG) were analyzed by fluorescence and luminescence probes, respectively. Cancer stem cell (CSC) properties were investigated by sphere-forming assay, CSC marker analysis, and in vivo limiting dilution assays. Single circulating tumor cells (CTCs) isolated from the blood of PCa patients were analyzed by array comparative genome hybridization. Expression levels of the GLS1 and MYC gene in tumor tissues and amino acid concentrations in blood plasma were correlated to a progression-free survival in PCa patients. Results: Here, we found that radioresistant PCa cells and prostate CSCs have a high glutamine demand. GLS-driven catabolism of glutamine serves not only for energy production but also for the maintenance of the redox state. Consequently, glutamine depletion or inhibition of critical regulators of glutamine utilization, such as GLS and the transcription factor MYC results in PCa radiosensitization. On the contrary, we found that a combination of glutamine metabolism inhibitors with irradiation does not cause toxic effects on nonmalignant prostate cells. Glutamine catabolism contributes to the maintenance of CSCs through regulation of the alpha-ketoglutarate (α-KG)-dependent chromatin-modifying dioxygenase. The lack of glutamine results in the inhibition of CSCs with a high aldehyde dehydrogenase (ALDH) activity, decreases the frequency of the CSC populations in vivo and reduces tumor formation in xenograft mouse models. Moreover, this study shows that activation of the ATG5-mediated autophagy in response to a lack of glutamine is a tumor survival strategy to withstand radiation-mediated cell damage. In combination with autophagy inhibition, the blockade of glutamine metabolism might be a promising strategy for PCa radiosensitization. High blood levels of glutamine in PCa patients significantly correlate with a shorter prostate-specific antigen (PSA) doubling time. Furthermore, high expression of critical regulators of glutamine metabolism, GLS1 and MYC, is significantly associated with a decreased progression-free survival in PCa patients treated with radiotherapy. Conclusions: Our findings demonstrate that GLS-driven glutaminolysis is a prognostic biomarker and therapeutic target for PCa radiosensitization.
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Affiliation(s)
- Anna Mukha
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) Dresden, Germany
| | - Uğur Kahya
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) Dresden, Germany
| | - Annett Linge
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Oleg Chen
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- Department of Cell Signaling, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine
| | - Steffen Löck
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Vasyl Lukiyanchuk
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) Dresden, Germany
| | - Susan Richter
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Tiago C Alves
- Department for Clinical Pathobiochemistry, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Mirko Peitzsch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Vladyslav Telychko
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
| | - Sergej Skvortsov
- Department of Therapeutic Radiology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
- EXTRO-Lab, Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Giulia Negro
- Department of Therapeutic Radiology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
- EXTRO-Lab, Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Bertram Aschenbrenner
- Department of Therapeutic Radiology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
- EXTRO-Lab, Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Ira-Ida Skvortsova
- Department of Therapeutic Radiology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
- EXTRO-Lab, Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Peter Mirtschink
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Fabian Lohaus
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Tobias Hölscher
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Hans Neubauer
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Düsseldorf, Germany
| | - Mahdi Rivandi
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Düsseldorf, Germany
| | - Vera Labitzky
- Institute of Anatomy and Experimental Morphology, Center for Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Germany
| | - Tobias Lange
- Institute of Anatomy and Experimental Morphology, Center for Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Germany
| | - André Franken
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Düsseldorf, Germany
| | - Bianca Behrens
- General, Visceral and Paediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Nikolas H Stoecklein
- General, Visceral and Paediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Marieta Toma
- Institute of Pathology, University of Bonn, Bonn, Germany
- Institute of Pathology, Universitätsklinikum Carl Gustav Carus Dresden, Dresden, Germany
| | - Ulrich Sommer
- Institute of Pathology, Universitätsklinikum Carl Gustav Carus Dresden, Dresden, Germany
| | - Sebastian Zschaeck
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Maximilian Rehm
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Graeme Eisenhofer
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Christian Schwager
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK) Core Center, Clinical Cooperation Units (CCU) Translational Radiation Oncology and Radiation Oncology, Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), German Cancer Research Center (DKFZ) and Heidelberg University Hospital (UKHD), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty (HDMF), Heidelberg University, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK) Core Center, Clinical Cooperation Units (CCU) Translational Radiation Oncology and Radiation Oncology, Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), German Cancer Research Center (DKFZ) and Heidelberg University Hospital (UKHD), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty (HDMF), Heidelberg University, Heidelberg, Germany
| | - Christer Groeben
- Department of Urology, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Leoni A Kunz-Schughart
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Gustavo B Baretton
- Institute of Pathology, Universitätsklinikum Carl Gustav Carus Dresden, Dresden, Germany
| | - Michael Baumann
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Mechthild Krause
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Claudia Peitzsch
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Anna Dubrovska
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Germany
- Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
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22
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Porter LH, Bakshi A, Pook D, Clark A, Clouston D, Kourambas J, Goode DL, Risbridger GP, Taylor RA, Lawrence MG. Androgen receptor enhancer amplification in matched patient-derived xenografts of primary and castrate-resistant prostate cancer. J Pathol 2021; 254:121-134. [PMID: 33620092 DOI: 10.1002/path.5652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 12/30/2022]
Abstract
Amplifications of the androgen receptor (AR) occur in up to 80% of men with castration-resistant prostate cancer (CRPC). Recent studies highlighted that these amplifications not only span the AR gene but usually encompass a distal enhancer. This represents a newly recognised, non-coding mechanism of resistance to AR-directed therapies, including enzalutamide. To study disease progression before and after AR amplification, we used tumour samples from a castrate-sensitive primary tumour and castrate-resistant metastasis of the same patient. For subsequent functional and genomic studies, we established serially transplantable patient-derived xenografts (PDXs). Whole genome sequencing showed that alterations associated with poor prognosis, such as TP53 and PTEN loss, existed before androgen deprivation therapy, followed by co-amplification of the AR gene and enhancer after the development of metastatic CRPC. The PDX of the primary tumour, without the AR amplification, was sensitive to AR-directed treatments, including castration, enzalutamide, and apalutamide. The PDX of the metastasis, with the AR amplification, had higher AR and AR-V7 expression in castrate conditions, and was resistant to castration, apalutamide, and enzalutamide in vivo. Treatment with a BET inhibitor outperformed the AR-directed therapies for the metastasis, resulting in tumour regression for some, but not all, grafts. Therefore, this study provides novel matched PDXs to test potential treatments that target the overabundance of AR in tumours with AR enhancer amplifications. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura H Porter
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Andrew Bakshi
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David Pook
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Medical Oncology, Monash Health, Clayton, VIC, Australia
| | - Ashlee Clark
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | | | - John Kourambas
- Department of Medicine, Monash Health, Casey Hospital, Berwick, VIC, Australia
| | -
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Melbourne Urological Research Alliance (MURAL), Biomedicine Discovery Institute Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - David L Goode
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Gail P Risbridger
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Renea A Taylor
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.,Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, VIC, Australia
| | - Mitchell G Lawrence
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
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23
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Brezina S, Feigl M, Gumpenberger T, Staudinger R, Baierl A, Gsur A. Genome-wide association study of germline copy number variations reveals an association with prostate cancer aggressiveness. Mutagenesis 2021; 35:283-290. [PMID: 32255470 DOI: 10.1093/mutage/geaa010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/16/2020] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer is a major health burden, being the second most commonly diagnosed malignancy in men worldwide. Overtreatment represents a major problem in prostate cancer therapy, leading to significant long-term quality-of-life effects for patients and a broad socio-ecological burden. Biomarkers that could facilitate risk stratification of prostate cancer aggressiveness at the time of diagnosis may help to guide clinical treatment decisions and reduce overtreatment. Previous research on genetic variations in prostate cancer has shown that germline copy number variations as well as somatic copy number alterations are commonly present in cancer patients, altering a greater portion of the cancer genome than any other type of genetic variation. To investigate the effect of germline copy number variations on cancer aggressiveness we have compared genome-wide screening data from genomic DNA isolated from the blood of 120 patients with aggressive prostate cancer, 231 patients with non-aggressive prostate cancer and 87 controls with benign prostatic hyperplasia from the Prostate Cancer Study of Austria biobank using the Affymetrix SNP 6.0 array. We could show that patients with an aggressive form of prostate cancer had a higher frequency of copy number variations [mean count of copy number segments (CNS) = 12.9, median count of CNS = 9] compared to patients with non-aggressive prostate cancer (mean count of CNS = 10.4, median count of CNS = 8) or control patients diagnosed with benign prostatic hyperplasia (mean count of CNS = 9.3, median count of CNS = 8). In general, we observed that copy number gain is a rarer event, compared to copy number loss within all three patient groups. Furthermore, we could show a significant effect of copy number losses located on chromosomes 8, 9 and 10 on prostate cancer aggressiveness (P = 0.040, P = 0.037 and P = 0.005, respectively). Applying a cross-validation analysis yielded an area under the curve of 0.63. Our study reports promising findings suggesting that copy number losses might play an important role in the establishment of novel biomarkers to predict prostate cancer aggressiveness at the time of diagnosis. Such markers could be used to facilitate risk stratification to reduce overtreatment of prostate cancer patients.
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Affiliation(s)
- Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Moritz Feigl
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Institute for Hydrology and Water Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tanja Gumpenberger
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Ricarda Staudinger
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Andreas Baierl
- Department of Statistics and Operations Research, University of Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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24
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van Leenders GJLH, Verhoef EI, Hollemans E. Prostate cancer growth patterns beyond the Gleason score: entering a new era of comprehensive tumour grading. Histopathology 2020; 77:850-861. [PMID: 32683729 PMCID: PMC7756302 DOI: 10.1111/his.14214] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/18/2022]
Abstract
The Gleason grading system is one of the most important factors in clinical decision‐making for prostate cancer patients, and is entirely based on the classification of tumour growth patterns. In recent years it has become clear that some individual growth patterns themselves have independent prognostic value, and could be used for better personalised risk stratification. In this review we summarise recent literature on the clinicopathological value and molecular characteristics of individual prostate cancer growth patterns, and show how these, most particularly cribriform architecture, could alter treatment decisions for prostate cancer patients.
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Affiliation(s)
| | - Esther I Verhoef
- Department of Pathology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - Eva Hollemans
- Department of Pathology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
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25
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Simpson BS, Camacho N, Luxton HJ, Pye H, Finn R, Heavey S, Pitt J, Moore CM, Whitaker HC. Genetic alterations in the 3q26.31-32 locus confer an aggressive prostate cancer phenotype. Commun Biol 2020; 3:440. [PMID: 32796921 PMCID: PMC7429505 DOI: 10.1038/s42003-020-01175-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Large-scale genetic aberrations that underpin prostate cancer development and progression, such as copy-number alterations (CNAs), have been described but the consequences of specific changes in many identified loci is limited. Germline SNPs in the 3q26.31 locus are associated with aggressive prostate cancer, and is the location of NAALADL2, a gene overexpressed in aggressive disease. The closest gene to NAALADL2 is TBL1XR1, which is implicated in tumour development and progression. Using publicly-available cancer genomic data we report that NAALADL2 and TBL1XR1 gains/amplifications are more prevalent in aggressive sub-types of prostate cancer when compared to primary cohorts. In primary disease, gains/amplifications occurred in 15.99% (95% CI: 13.02–18.95) and 14.96% (95% CI: 12.08–17.84%) for NAALADL2 and TBL1XR1 respectively, increasing in frequency in higher Gleason grade and stage tumours. Gains/amplifications result in transcriptional changes and the development of a pro-proliferative and aggressive phenotype. These results support a pivotal role for copy-number gains in this genetic region. Benjamin Simpson et al. use publicly available cancer genomic data to investigate copy number changes at the 3q26.31–32 locus, which has been associated with aggressive prostate cancer based on single-nucleotide polymorphisms. They find that gains of NAALADL2 and TBL1XR1 in this locus are associated with more aggressive subtypes of prostate cancer and the transcription of pro-proliferative signalling processes.
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Affiliation(s)
- Benjamin S Simpson
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Niedzica Camacho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hayley J Luxton
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Hayley Pye
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Ron Finn
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Susan Heavey
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK
| | - Jason Pitt
- Cancer Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Hayley C Whitaker
- Molecular Diagnostics and Therapeutics Group, Research Department of Targeted Intervention, Division of Surgery & Interventional Science, University College London, London, UK.
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26
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Jonnalagadda B, Arockiasamy S, Krishnamoorthy S. Cellular growth factors as prospective therapeutic targets for combination therapy in androgen independent prostate cancer (AIPC). Life Sci 2020; 259:118208. [PMID: 32763294 DOI: 10.1016/j.lfs.2020.118208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/27/2020] [Accepted: 08/02/2020] [Indexed: 12/21/2022]
Abstract
Cancer is the second leading cause of death worldwide, with prostate cancer, the second most commonly diagnosed cancer among men. Prostate cancer develops in the peripheral zone of the prostate gland, and the initial progression largely depends on androgens, the male reproductive hormone that regulates the growth and development of the prostate gland and testis. The currently available treatments for androgen dependent prostate cancer are, however, effective for a limited period, where the patients show disease relapse, and develop androgen-independent prostate cancer (AIPC). Studies have shown various intricate cellular processes such as, deregulation in multiple biochemical and signaling pathways, intra-tumoral androgen synthesis; AR over-expression and mutations and AR activation via alternative growth pathways are involved in progression of AIPC. The currently approved treatment strategies target a single cellular protein or pathway, where the cells slowly develop resistance and adapt to proliferate via other cellular pathways over a period of time. Therefore, an increased research aims to understand the efficacy of combination therapy, which targets multiple interlinked pathways responsible for acquisition of resistance and survival. The combination therapy is also shown to enhance efficacy as well as reduce toxicity of the drugs. Thus, the present review focuses on the signaling pathways involved in the progression of AIPC, comprising a heterogeneous population of cells and the advantages of combination therapy. Several clinical and pre-clinical studies on a variety of combination treatments have shown beneficial outcomes, yet further research is needed to understand the potential of combination therapy and its diverse strategies.
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Affiliation(s)
- Bhavana Jonnalagadda
- Department of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Sumathy Arockiasamy
- Department of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.
| | - Sriram Krishnamoorthy
- Department of Urology, Sri Ramachandra Medical Centre, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
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27
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A copy number gain on 18q present in primary prostate tumors is associated with metastatic outcome. Urol Oncol 2020; 38:932.e1-932.e7. [PMID: 32665124 DOI: 10.1016/j.urolonc.2020.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Most prostate cancers (CaPs) grow slowly and remain indolent, yet some become aggressive and metastasize. Clinical decision-making requires prognostic markers that can be utilized at the time of diagnosis to identify aggressive tumors. Previous studies have shown a correlation between genomic alterations on the long arm of chromosome 18 (18q) and metastatic CaP. OBJECTIVE The goal of this study was to comprehensively profile copy number alterations found on 18q in prostate tumors with varying outcomes to identify putative biomarkers associated with more aggressive disease METHODS: A custom comparative genomic hybridization array was created composed of high-density tiling of 18q sequences. Primary prostate tumor tissues were gathered from men who underwent radical prostatectomy and were categorized based on the patient's long-term clinical outcome as either metastatic disease (MET) or no evidence of disease (NED). DNA was isolated from formalin-fixed, paraffin-embedded prostatectomy tumor tissues, and analyzed for copy number variations (CNVs). Protein levels of genes found within the region of CNVs were analyzed using immunohistochemistry. RESULTS Thirty-Four primary prostate tumors were analyzed: 17 NEDs and 17 METs. Two significant regions of copy number gains were found on 18q associated with outcome. One gain located at 18q11.2 was found exclusively in NED outcome tumors while another gain, located at 18q21.31, was found exclusively in MET outcome tumors (P -value< 0.0076). Immunohistochemistry analysis of protein levels showed more protein associated with copy number gain in the MET samples vs. those without the gain as indicated by H-scores of 184.7 and 121.0 respectively. CONCLUSIONS The latter of these CNVs represent a putative biomarker for aggressive disease and highlights a putative metastasis promoting gene. Further study of known connections to CaP suggests that the paracaspase MALT1 is the most likely target of the copy number gain and represents a potential therapeutic target. Future studies would be of interest to determine MALT1's role in aggressive CaP and the ability of this CNV region to differentiate CaP that will eventually metastasize.
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28
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Vidotto T, Melo CM, Castelli E, Koti M, Dos Reis RB, Squire JA. Emerging role of PTEN loss in evasion of the immune response to tumours. Br J Cancer 2020; 122:1732-1743. [PMID: 32327707 PMCID: PMC7283470 DOI: 10.1038/s41416-020-0834-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 02/10/2020] [Accepted: 03/18/2020] [Indexed: 12/31/2022] Open
Abstract
Mutations in PTEN activate the phosphoinositide 3-kinase (PI3K) signalling network, leading to many of the characteristic phenotypic changes of cancer. However, the primary effects of this gene on oncogenesis through control of the PI3K-AKT-mammalian target of rapamycin (mTOR) pathway might not be the only avenue by which PTEN affects tumour progression. PTEN has been shown to regulate the antiviral interferon network and thus alter how cancer cells communicate with and are targeted by immune cells. An active, T cell-infiltrated microenvironment is critical for immunotherapy success, which is also influenced by mutations in DNA damage repair pathways and the overall mutational burden of the tumour. As PTEN has a role in the maintenance of genomic integrity, it is likely that a loss of PTEN affects the immune response at two different levels and might therefore be instrumental in mediating failed responses to immunotherapy. In this review, we summarise findings that demonstrate how the loss of PTEN function elicits specific changes in the immune response in several types of cancer. We also discuss ongoing clinical trials that illustrate the potential utility of PTEN as a predictive biomarker for immune checkpoint blockade therapies.
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Affiliation(s)
- Thiago Vidotto
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Camila Morais Melo
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Erick Castelli
- Department of Pathology, Medicine School of Botucatu, Paulista State University, Botucatu, Brazil
| | - Madhuri Koti
- Cancer Biology and Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | | | - Jeremy A Squire
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.
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29
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Zhang ZH, Luan ZY, Han F, Chen HQ, Liu WB, Liu JY, Cao J. Diagnostic and prognostic value of the BEX family in lung adenocarcinoma. Oncol Lett 2019; 18:5523-5533. [PMID: 31612060 PMCID: PMC6781490 DOI: 10.3892/ol.2019.10905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/23/2019] [Indexed: 02/07/2023] Open
Abstract
Previous studies have demonstrated that members of the brain-expressed X-linked (BEX) family participate in a wide range of biological functions in normal and tumor tissues. However, their role and clinical significance in lung adenocarcinoma (LUAD) remains unclear. The present study investigated The Cancer Genome Atlas data and revealed that the BEX family was downregulated in LUAD tissues compared with adjacent non-cancerous tissues. Additionally, analysis of LUAD cohorts from the Oncomine database revealed similar results. Furthermore, the expression of BEX members was significantly decreased in several LUAD cell lines compared with normal lung epithelial cells in vitro. The aforementioned data mining and in vitro results suggested that the BEX family may be involved in the development of LUAD. Furthermore, receiver operating characteristic curve analysis revealed that BEX members exhibited high sensitivity and specificity for the diagnosis of patients with LUAD. The low expression levels of BEX1, BEX4 and BEX5 were associated with certain pathologic features, particularly in advanced LUAD. Survival analysis demonstrated that BEX members, particularly BEX4, were involved in the prognosis of patients with LUAD at early and late clinical stages. The results obtained in the current study suggested that BEX members may serve as potential tumor biomarkers for the diagnosis and prognosis of patients with LUAD.
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Affiliation(s)
- Zhong-Hao Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Zhi-Yu Luan
- Department of Medical Affairs, Chinese PLA No. 964 Hospital, Changchun, Jilin 130062, P.R. China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Hong-Qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
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30
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Testa U, Castelli G, Pelosi E. Cellular and Molecular Mechanisms Underlying Prostate Cancer Development: Therapeutic Implications. MEDICINES (BASEL, SWITZERLAND) 2019; 6:E82. [PMID: 31366128 PMCID: PMC6789661 DOI: 10.3390/medicines6030082] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/19/2019] [Accepted: 07/25/2019] [Indexed: 12/15/2022]
Abstract
Prostate cancer is the most frequent nonskin cancer and second most common cause of cancer-related deaths in man. Prostate cancer is a clinically heterogeneous disease with many patients exhibiting an aggressive disease with progression, metastasis, and other patients showing an indolent disease with low tendency to progression. Three stages of development of human prostate tumors have been identified: intraepithelial neoplasia, adenocarcinoma androgen-dependent, and adenocarcinoma androgen-independent or castration-resistant. Advances in molecular technologies have provided a very rapid progress in our understanding of the genomic events responsible for the initial development and progression of prostate cancer. These studies have shown that prostate cancer genome displays a relatively low mutation rate compared with other cancers and few chromosomal loss or gains. The ensemble of these molecular studies has led to suggest the existence of two main molecular groups of prostate cancers: one characterized by the presence of ERG rearrangements (~50% of prostate cancers harbor recurrent gene fusions involving ETS transcription factors, fusing the 5' untranslated region of the androgen-regulated gene TMPRSS2 to nearly the coding sequence of the ETS family transcription factor ERG) and features of chemoplexy (complex gene rearrangements developing from a coordinated and simultaneous molecular event), and a second one characterized by the absence of ERG rearrangements and by the frequent mutations in the E3 ubiquitin ligase adapter SPOP and/or deletion of CDH1, a chromatin remodeling factor, and interchromosomal rearrangements and SPOP mutations are early events during prostate cancer development. During disease progression, genomic and epigenomic abnormalities accrued and converged on prostate cancer pathways, leading to a highly heterogeneous transcriptomic landscape, characterized by a hyperactive androgen receptor signaling axis.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Vaile Regina Elena 299, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Vaile Regina Elena 299, 00161 Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Vaile Regina Elena 299, 00161 Rome, Italy
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31
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Mulvaney EP, O'Sullivan ÁG, Eivers SB, Reid HM, Kinsella BT. Differential expression of the TPα and TPβ isoforms of the human T Prostanoid receptor during chronic inflammation of the prostate: Role for FOXP1 in the transcriptional regulation of TPβ during monocyte-macrophage differentiation. Exp Mol Pathol 2019; 110:104277. [PMID: 31271729 DOI: 10.1016/j.yexmp.2019.104277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/21/2019] [Accepted: 06/22/2019] [Indexed: 11/16/2022]
Abstract
Inflammation is linked to prostate cancer (PCa) and to other diseases of the prostate. The prostanoid thromboxane (TX)A2 is a pro-inflammatory mediator implicated in several prostatic diseases, including PCa. TXA2 signals through the TPα and TPβ isoforms of the T Prostanoid receptor (TP) which exhibit several functional differences and transcriptionally regulated by distinct promoters Prm1 and Prm3, respectively, within the TBXA2R gene. This study examined the expression of TPα and TPβ in inflammatory infiltrates within human prostate tissue. Strikingly, TPβ expression was detected in 94% of infiltrates, including in B- and T-lymphocytes and macrophages. In contrast, TPα was more variably expressed and, where present, expression was mainly confined to macrophages. To gain molecular insight into these findings, expression of TPα and TPβ was evaluated as a function of monocyte-to-macrophage differentiation in THP-1 cells. Expression of both TPα and TPβ was upregulated following phorbol-12-myristate-13-acetate (PMA)-induced differentiation of monocytic THP-1 to their macrophage lineage. Furthermore, FOXP1, an essential transcriptional regulator down-regulated during monocyte-to-macrophage differentiation, was identified as a key trans-acting factor regulating TPβ expression through Prm3 in THP-1 cells. Knockdown of FOXP1 increased TPβ, but not TPα, expression in THP-1 cells, while genetic reporter and chromatin immunoprecipitation (ChIP) analyses established that FOXP1 exerts its repressive effect on TPβ through binding to four cis-elements within Prm3. Collectively, FOXP1 functions as a transcriptional repressor of TPβ in monocytes. This repression is lifted in differentiated macrophages, allowing for upregulation of TPβ expression and possibly accounting for the prominent expression of TPβ in prostate tissue-resident macrophages.
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Affiliation(s)
- Eamon P Mulvaney
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; ATXA Therapeutics Limited, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Áine G O'Sullivan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sarah B Eivers
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Helen M Reid
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; ATXA Therapeutics Limited, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - B Therese Kinsella
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; ATXA Therapeutics Limited, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
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32
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Bhagirath D, Yang TL, Tabatabai ZL, Shahryari V, Majid S, Dahiya R, Tanaka Y, Saini S. Role of a novel race-related tumor suppressor microRNA located in frequently deleted chromosomal locus 8p21 in prostate cancer progression. Carcinogenesis 2019; 40:633-642. [PMID: 30874288 PMCID: PMC7331454 DOI: 10.1093/carcin/bgz058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/07/2019] [Accepted: 03/12/2019] [Indexed: 12/14/2022] Open
Abstract
The prostate cancer (PCa) genome is characterized by deletions of chromosome 8p21-22 region that increase significantly with tumor grade and are associated with poor prognosis. We proposed and validated a novel, paradigm-shifting hypothesis that this region is associated with a set of microRNA genes-miR-3622, miR-3622b, miR-383-that are lost in PCa and play important mechanistic roles in PCa progression and metastasis. Extending our hypothesis, in this study, we evaluated the role of a microRNA gene located in chromosome 8p-miR-4288-by employing clinical samples and cell lines. Our data suggests that (i) miR-4288 is widely downregulated in primary prostate tumors and cell lines; (ii) miR-4288 expression is lost in metastatic castration-resistant PCa; (ii) miR-4288 downregulation is race-related PCa alteration that is prevalent in Caucasian patients and not in African Americans; (iii) in Caucasians, miR-4288 was found to be associated with increasing tumor grade and high serum prostate-specific antigen, suggesting that miR-4288 downregulation/loss may be associated with tumor progression specifically in Caucasians; (iv) miR-4288 possess significant potential as a molecular biomarker to predict aggressiveness/metastasis; and (v) miR-4288 is anti-proliferative, is anti-invasive and inhibits epithelial-to-mesenchymal transition; and (vi) miR-4288 directly represses expression of metastasis/invasion-associated genes MMP16 and ROCK1. Thus, the present study demonstrates a tumor suppressor role for a novel miRNA located with a frequently lost region in PCa, strengthening our hypothesis that this locus is causally related to PCa disease progression via loss of microRNA genes. Our study suggests that miR-4288 may be a novel biomarker and therapeutic target, particularly in Caucasians.
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Affiliation(s)
- Divya Bhagirath
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California, San Francisco, CA, USA
| | - Thao Ly Yang
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California, San Francisco, CA, USA
| | - Z Laura Tabatabai
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California, San Francisco, CA, USA
| | - Varahram Shahryari
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California, San Francisco, CA, USA
| | - Shahana Majid
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California, San Francisco, CA, USA
| | - Rajvir Dahiya
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California, San Francisco, CA, USA
| | - Yuichiro Tanaka
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California, San Francisco, CA, USA
| | - Sharanjot Saini
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California, San Francisco, CA, USA
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33
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Comprehensive Genomic Profiling of Androgen-Receptor-Negative Canine Prostate Cancer. Int J Mol Sci 2019; 20:ijms20071555. [PMID: 30925701 PMCID: PMC6480132 DOI: 10.3390/ijms20071555] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/10/2019] [Accepted: 03/11/2019] [Indexed: 12/16/2022] Open
Abstract
Canine carcinomas have been considered natural models for human diseases; however, the genomic profile of canine prostate cancers (PCs) has not been explored. In this study, 14 PC androgen-receptor-negative cases, 4 proliferative inflammatory atrophies (PIA), and 5 normal prostate tissues were investigated by array-based comparative genomic hybridization (aCGH). Copy number alterations (CNAs) were assessed using the Canine Genome CGH Microarray 4 × 44K (Agilent Technologies). Genes covered by recurrent CNAs were submitted to enrichment and cross-validation analysis. In addition, the expression levels of TP53, MDM2 and ZBTB4 were evaluated in an independent set of cases by qPCR. PC cases presented genomic complexity, while PIA samples had a small number of CNAs. Recurrent losses covering well-known tumor suppressor genes, such as ATM, BRCA1, CDH1, MEN1 and TP53, were found in PC. The in silico functional analysis showed several cancer-related genes associated with canonical pathways and interaction networks previously described in human PC. The MDM2, TP53, and ZBTB4 copy number alterations were translated into altered expression levels. A cross-validation analysis using The Cancer Genome Atlas (TCGA) database for human PC uncovered similarities between canine and human PCs. Androgen-receptor-negative canine PC is a complex disease characterized by high genomic instability, showing a set of genes with similar alterations to human cancer.
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34
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Elfandy H, Armenia J, Pederzoli F, Pullman E, Pertega-Gomes N, Schultz N, Viswanathan K, Vosoughi A, Blattner M, Stopsack KH, Zadra G, Penney KL, Mosquera JM, Tyekucheva S, Mucci LA, Barbieri C, Loda M. Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate. Mol Cancer Res 2019; 17:446-456. [PMID: 30333152 PMCID: PMC6359952 DOI: 10.1158/1541-7786.mcr-18-0440] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/24/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022]
Abstract
Among prostate cancers containing Gleason pattern 4, cribriform morphology is associated with unfavorable clinicopathologic factors, but its genetic features and association with long-term outcomes are incompletely understood. In this study, genetic, transcriptional, and epigenetic features of invasive cribriform carcinoma (ICC) tumors were compared with non-cribriform Gleason 4 (NC4) in The Cancer Genome Atlas (TCGA) cohort. ICC (n = 164) had distinctive molecular features when compared with NC4 (n = 102). These include: (i) increased somatic copy number variations (SCNV), specifically deletions at 6q, 8p and 10q, which encompassed PTEN and MAP3K7 losses and gains at 3q; (ii) increased SPOP mut and ATMmut ; (iii) enrichment for mTORC1 and MYC pathways by gene expression; and (iv) increased methylation of selected genes. In addition, when compared with the metastatic prostate cancer, ICC clustered more closely to metastatic prostate cancer than NC4. Validation in clinical cohorts and genomically annotated murine models confirmed the association with SPOPmut (n = 38) and PTENloss (n = 818). The association of ICC with lethal disease was evaluated in the Health Professionals Follow-up Study (HPFS) and Physicians' Health Study (PHS) prospective prostate cancer cohorts (median follow-up, 13.4 years; n = 818). Patients with ICC were more likely to develop lethal cancer [HR, 1.62; 95% confidence interval (CI), 1.05-2.49], independent from Gleason score (GS). IMPLICATIONS: ICC has a distinct molecular phenotype that resembles metastatic prostate cancer and is associated with progression to lethal disease.
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Affiliation(s)
- Habiba Elfandy
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Joshua Armenia
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Eli Pullman
- George Washington University, Washington, D.C
| | - Nelma Pertega-Gomes
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Aram Vosoughi
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Mirjam Blattner
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
- Department of Urology, Weill Cornell Medicine, New York, New York
| | - Konrad H Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Giorgia Zadra
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Juan Miguel Mosquera
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Svitlana Tyekucheva
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, Massachusetts
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Christopher Barbieri
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
- Department of Urology, Weill Cornell Medicine, New York, New York
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- The Broad Institute, Cambridge, Massachusetts
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35
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Verhoef EI, van Cappellen WA, Slotman JA, Kremers GJ, Ewing-Graham PC, Houtsmuller AB, van Royen ME, van Leenders GJLH. Three-dimensional analysis reveals two major architectural subgroups of prostate cancer growth patterns. Mod Pathol 2019; 32:1032-1041. [PMID: 30737469 PMCID: PMC6760644 DOI: 10.1038/s41379-019-0221-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/15/2022]
Abstract
The Gleason score is one of the most important parameters for therapeutic decision-making in prostate cancer patients. Gleason growth patterns are defined by their histological features on 4- to 5-µm cross sections, and little is known about their three-dimensional architecture. Our objective was to characterize the three-dimensional architecture of prostate cancer growth patterns. Intact tissue punches (n = 46) of representative Gleason growth patterns from radical prostatectomy specimens were fluorescently stained with antibodies targeting Keratin 8/18 and Keratin 5 for the detection of luminal and basal epithelial cells, respectively. Punches were optically cleared in benzyl alcohol-benzyl benzoate and imaged using a confocal laser scanning microscope up to a depth of 500 µm. Gleason pattern 3, poorly formed pattern 4, and cords pattern 5 all formed a continuum of interconnecting tubules in which the diameter of the structures and the lumen size decreased with higher grades. In fused pattern 4, the interconnections between the tubules were markedly closer together. In these patterns, all tumor cells were in direct contact with the surrounding stroma. In contrast, cribriform Gleason pattern 4 and solid pattern 5 demonstrated a three-dimensional continuum of contiguous tumor cells, in which the vast majority of cells had no contact with the surrounding stroma. Transitions between cribriform pattern 4 and solid pattern 5 were seen. There was a decrease in the number and size of intercellular lumens from cribriform to solid growth pattern. Glomeruloid pattern 4 formed an intermediate structure consisting of a tubular network with intraluminal epithelial protrusions close to the tubule splitting points. In conclusion, three-dimensional microscopy revealed two major architectural subgroups of prostate cancer growth patterns: (1) a tubular interconnecting network including Gleason pattern 3, poorly formed and fused Gleason pattern 4, and cords Gleason pattern 5, and (2) serpentine contiguous epithelial proliferations including cribriform Gleason pattern 4 and solid Gleason pattern 5.
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Affiliation(s)
- Esther I. Verhoef
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wiggert A. van Cappellen
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan A. Slotman
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gert-Jan Kremers
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Patricia C. Ewing-Graham
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Adriaan B. Houtsmuller
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin E. van Royen
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Geert J. L. H. van Leenders
- 000000040459992Xgrid.5645.2Department of Pathology, University Medical Center Rotterdam, Rotterdam, The Netherlands
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36
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Kesch C, Radtke JP, Wintsche A, Wiesenfarth M, Luttje M, Gasch C, Dieffenbacher S, Pecqueux C, Teber D, Hatiboglu G, Nyarangi-Dix J, Simpfendörfer T, Schönberg G, Dimitrakopoulou-Strauss A, Freitag M, Duensing A, Grüllich C, Jäger D, Götz M, Grabe N, Schweiger MR, Pahernik S, Perner S, Herpel E, Roth W, Wieczorek K, Maier-Hein K, Debus J, Haberkorn U, Giesel F, Galle J, Hadaschik B, Schlemmer HP, Hohenfellner M, Bonekamp D, Sültmann H, Duensing S. Correlation between genomic index lesions and mpMRI and 68Ga-PSMA-PET/CT imaging features in primary prostate cancer. Sci Rep 2018; 8:16708. [PMID: 30420756 PMCID: PMC6232089 DOI: 10.1038/s41598-018-35058-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/30/2018] [Indexed: 02/01/2023] Open
Abstract
Magnetic resonance imaging (MRI) and prostate specific membrane antigen (PSMA)- positron emission tomography (PET)/computed tomography (CT)-imaging of prostate cancer (PCa) are emerging techniques to assess the presence of significant disease and tumor progression. It is not known, however, whether and to what extent lesions detected by these imaging techniques correlate with genomic features of PCa. The aim of this study was therefore to define a genomic index lesion based on chromosomal copy number alterations (CNAs) as marker for tumor aggressiveness in prostate biopsies in direct correlation to multiparametric (mp) MRI and 68Ga-PSMA-PET/CT imaging features. CNA profiles of 46 biopsies from five consecutive patients with clinically high-risk PCa were obtained from radiologically suspicious and unsuspicious areas. All patients underwent mpMRI, MRI/TRUS-fusion biopsy, 68Ga-PSMA-PET/CT and a radical prostatectomy. CNAs were directly correlated to imaging features and radiogenomic analyses were performed. Highly significant CNAs (≥10 Mbp) were found in 22 of 46 biopsies. Chromosome 8p, 13q and 5q losses were the most common findings. There was an strong correspondence between the radiologic and the genomic index lesions. The radiogenomic analyses suggest the feasibility of developing radiologic signatures that can distinguish between genomically more or less aggressive lesions. In conclusion, imaging features of mpMRI and 68Ga-PSMA-PET/CT can guide to the genomically most aggressive lesion of a PCa. Radiogenomics may help to better differentiate between indolent and aggressive PCa in the future.
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Affiliation(s)
- Claudia Kesch
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Jan-Philipp Radtke
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Axel Wintsche
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107, Leipzig, Germany
| | - Manuel Wiesenfarth
- Division of Biostatistics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Mariska Luttje
- Imaging Division, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX Utrecht, The Netherlands
| | - Claudia Gasch
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Svenja Dieffenbacher
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Carine Pecqueux
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Dogu Teber
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Gencay Hatiboglu
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Joanne Nyarangi-Dix
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Tobias Simpfendörfer
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Gita Schönberg
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - Antonia Dimitrakopoulou-Strauss
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Martin Freitag
- Department of Radiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Anette Duensing
- Cancer Therapeutics Program and Department of Pathology, Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Carsten Grüllich
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany
| | - Michael Götz
- Division of Medical Image Computing, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Niels Grabe
- Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University of Heidelberg, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany
| | - Michal-Ruth Schweiger
- Functional Epigenomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, D-50931, Cologne, Germany
| | - Sascha Pahernik
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany.,Department of Urology, University Hospital Nuremberg, Nuremberg, Germany
| | - Sven Perner
- Pathology of the University Hospital Schleswig-Holstein, Campus Lübeck and the Research Center Borstel, Leibniz Lung Center, Ratzeburger Allee 160, D-23538 Lübeck and Parkallee 1-40, D-23845, Borstel, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, D-69120, Heidelberg, Germany
| | - Wilfried Roth
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, D-69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Mainz, Mainz, Germany
| | - Kathrin Wieczorek
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, D-69120, Heidelberg, Germany.,Pathology Rosenheim, Rosenheim, Germany
| | - Klaus Maier-Hein
- Division of Medical Image Computing, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Jürgen Debus
- Department of Radiation Oncology, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120, Heidelberg, Germany
| | - Uwe Haberkorn
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.,Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120, Heidelberg, Germany
| | - Frederik Giesel
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.,Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120, Heidelberg, Germany
| | - Jörg Galle
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107, Leipzig, Germany
| | - Boris Hadaschik
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany.,Department of Urology, University Hospital Essen, Essen, Germany
| | - Heinz-Peter Schlemmer
- Department of Radiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Markus Hohenfellner
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany
| | - David Bonekamp
- Department of Radiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Holger Sültmann
- Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany.
| | - Stefan Duensing
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany. .,Molecular Urooncology, University Hospital Heidelberg, Im Neuenheimer Feld 517, D-69120, Heidelberg, Germany.
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37
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Nava Rodrigues D, Casiraghi N, Romanel A, Crespo M, Miranda S, Rescigno P, Figueiredo I, Riisnaes R, Carreira S, Sumanasuriya S, Gasperini P, Sharp A, Mateo J, Makay A, McNair C, Schiewer M, Knudsen K, Boysen G, Demichelis F, de Bono JS. RB1 Heterogeneity in Advanced Metastatic Castration-Resistant Prostate Cancer. Clin Cancer Res 2018; 25:687-697. [PMID: 30257982 DOI: 10.1158/1078-0432.ccr-18-2068] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/09/2018] [Accepted: 09/18/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Metastatic castration-resistant prostate cancer (mCRPC) is a lethal but clinically heterogeneous disease, with patients having variable benefit from endocrine and cytotoxic treatments. Intrapatient genomic heterogeneity could be a contributing factor to this clinical heterogeneity. Here, we used whole-genome sequencing (WGS) to investigate genomic heterogeneity in 21 previously treated CRPC metastases from 10 patients to investigate intrapatient molecular heterogeneity (IPMH).Experimental Design: WGS was performed on topographically separate metastases from patients with advanced metastatic prostate cancer. IPMH of the RB1 gene was identified and further evaluated by FISH and IHC assays. RESULTS WGS identified limited IPMH for putative driver events. However, heterogeneous genomic aberrations of RB1 were detected. We confirmed the presence of these RB1 somatic copy-number aberrations, initially identified by WGS, with FISH, and identified novel structural variants involving RB1 in 6 samples from 3 of these 10 patients (30%; 3/10). WGS uncovered a novel deleterious RB1 structural lesion constituted of an intragenic tandem duplication involving multiple exons and associating with protein loss. Using RB1 IHC in a large series of mCRPC biopsies, we identified heterogeneous expression in approximately 28% of mCRPCs. CONCLUSIONS mCRPCs have a high prevalence of RB1 genomic aberrations, with structural variants, including rearrangements, being common. Intrapatient genomic and expression heterogeneity favors RB1 aberrations as late, subclonal events that increase in prevalence due to treatment-selective pressures.
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Affiliation(s)
- Daniel Nava Rodrigues
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- The Institute of Cancer Research, London, United Kingdom
| | - Nicola Casiraghi
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Functional and Computational Oncology, Trento, Italy
| | - Alessandro Romanel
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Bioinformatics and Computational Genomics, Trento, Italy
| | - Mateus Crespo
- The Institute of Cancer Research, London, United Kingdom
| | - Susana Miranda
- The Institute of Cancer Research, London, United Kingdom
| | - Pasquale Rescigno
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- The Institute of Cancer Research, London, United Kingdom
| | | | - Ruth Riisnaes
- The Institute of Cancer Research, London, United Kingdom
| | | | - Semini Sumanasuriya
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- The Institute of Cancer Research, London, United Kingdom
| | - Paola Gasperini
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Functional and Computational Oncology, Trento, Italy
| | - Adam Sharp
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- The Institute of Cancer Research, London, United Kingdom
| | - Joaquin Mateo
- Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Alan Makay
- The Institute of Cancer Research, London, United Kingdom
| | - Christopher McNair
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York
| | - Matthew Schiewer
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York
| | - Karen Knudsen
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York
| | - Gunther Boysen
- The Institute of Cancer Research, London, United Kingdom
| | - Francesca Demichelis
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Functional and Computational Oncology, Trento, Italy.
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York
| | - Johann S de Bono
- The Royal Marsden NHS Foundation Trust, London, United Kingdom.
- The Institute of Cancer Research, London, United Kingdom
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38
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Hieronymus H, Murali R, Tin A, Yadav K, Abida W, Moller H, Berney D, Scher H, Carver B, Scardino P, Schultz N, Taylor B, Vickers A, Cuzick J, Sawyers CL. Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death. eLife 2018; 7:e37294. [PMID: 30178746 PMCID: PMC6145837 DOI: 10.7554/elife.37294] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/13/2018] [Indexed: 12/14/2022] Open
Abstract
The level of copy number alteration (CNA), termed CNA burden, in the tumor genome is associated with recurrence of primary prostate cancer. Whether CNA burden is associated with prostate cancer survival or outcomes in other cancers is unknown. We analyzed the CNA landscape of conservatively treated prostate cancer in a biopsy and transurethral resection cohort, reflecting an increasingly common treatment approach. We find that CNA burden is prognostic for cancer-specific death, independent of standard clinical prognosticators. More broadly, we find CNA burden is significantly associated with disease-free and overall survival in primary breast, endometrial, renal clear cell, thyroid, and colorectal cancer in TCGA cohorts. To assess clinical applicability, we validated these findings in an independent pan-cancer cohort of patients whose tumors were sequenced using a clinically-certified next generation sequencing assay (MSK-IMPACT), where prognostic value varied based on cancer type. This prognostic association was affected by incorporating tumor purity in some cohorts. Overall, CNA burden of primary and metastatic tumors is a prognostic factor, potentially modulated by sample purity and measurable by current clinical sequencing.
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Affiliation(s)
- Haley Hieronymus
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Rajmohan Murali
- Department of PathologyMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Amy Tin
- Department of Epidemiology and BiostatisticsMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Kamlesh Yadav
- Department of UrologyIcahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Wassim Abida
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkUnited States
- Genitourinary Oncology Service, Department of MedicineMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Henrik Moller
- Department of Cancer Epidemiology, Population and Global HealthKing's College LondonLondonUnited Kingdom
| | - Daniel Berney
- Department of Molecular OncologyBarts Cancer Institute, Queen Mary University of LondonLondonUnited Kingdom
| | - Howard Scher
- Genitourinary Oncology Service, Department of MedicineMemorial Sloan Kettering Cancer CenterNew YorkUnited States
- Department of MedicineWeill Cornell Medical CollegeNew YorkUnited States
| | - Brett Carver
- Department of UrologyMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Peter Scardino
- Department of UrologyMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular OncologyMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Barry Taylor
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkUnited States
- Department of Epidemiology and BiostatisticsMemorial Sloan Kettering Cancer CenterNew YorkUnited States
- Marie-Josée and Henry R. Kravis Center for Molecular OncologyMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Andrew Vickers
- Department of Epidemiology and BiostatisticsMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Jack Cuzick
- Centre for Cancer Prevention, Wolfson Institute of Preventive MedicineQueen Mary University of LondonLondonUnited Kingdom
| | - Charles L Sawyers
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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39
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Markowski MC, Hubbard GK, Hicks JL, Zheng Q, King A, Esopi D, Rege A, Yegnasubramanian S, Bieberich CJ, De Marzo AM. Characterization of novel cell lines derived from a MYC-driven murine model of lethal metastatic adenocarcinoma of the prostate. Prostate 2018; 78:992-1000. [PMID: 29851094 PMCID: PMC9844589 DOI: 10.1002/pros.23657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/07/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Loss or mutation of PTEN alleles at 10q23 in combination with 8q24 amplification (encompassing MYC) are common findings in aggressive, human prostate cancer. Our group recently developed a transgenic murine model of prostate cancer involving prostate-specific Pten deletion and forced expression of MYC under the control of the Hoxb13 promoter. MYC overexpression cooperated with Pten loss to recapitulate lethal, human prostate cancer. METHOD We now report on the generation of two mouse prostate cancer cell lines, BMPC1 and BMPC2, derived from a lymph node, and liver metastasis, respectively. RESULTS Both cell lines demonstrate a phenotype consistent with adenocarcinoma and grew under standard tissue culture conditions. Androgen receptor (AR) protein expression is minimal (BMPC1) or absent (BMPC2) consistent with AR loss observed in the BMPC mouse model of invasive adenocarcinoma. Growth in media containing charcoal-stripped serum resulted in an increase in AR mRNA in BMPC1 cells with no effect on protein expression, unless androgens were added, in which case AR protein was stabilized, and showed nuclear localization. AR expression in BMPC2 cells was not effected by growth media or treatment with androgens. Treatment with an anti-androgen/castration or androgen supplemented media did not affect in vitro or in vivo growth of either cell line, irrespective of nuclear AR detection. DISCUSSION These cell lines are a novel model of androgen-insensitive prostatic adenocarcinoma driven by MYC over-expression and Pten loss.
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Affiliation(s)
- Mark C. Markowski
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Gretchen K. Hubbard
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jessica L. Hicks
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qizhi Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexia King
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David Esopi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Apurv Rege
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland
| | | | - Charles J. Bieberich
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland
| | - Angelo M. De Marzo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins University School, Baltimore, Maryland
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40
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Kluth M, Scherzai S, Büschek F, Fraune C, Möller K, Höflmayer D, Minner S, Göbel C, Möller-Koop C, Hinsch A, Neubauer E, Tsourlakis MC, Sauter G, Heinzer H, Graefen M, Wilczak W, Luebke AM, Burandt E, Steurer S, Schlomm T, Simon R. 13q deletion is linked to an adverse phenotype and poor prognosis in prostate cancer. Genes Chromosomes Cancer 2018; 57:504-512. [PMID: 29923647 DOI: 10.1002/gcc.22645] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/13/2023] Open
Abstract
Deletions of chromosome arm 13q belong to the most frequent molecular alterations in prostate cancer. To better understand the role of 13q deletion in prostate cancer we took advantage of our large prostate cancer tissue microarray comprising more than 12 000 cancer samples with full pathological and clinical follow-up data. Fluorescence in situ hybridization with probes for ENOX1 (13q14.11) and the retinoblastoma gene (RB1, 13q14.2) was employed. A 13q deletion was found in 21% of 7375 analyzable cancers. Deletions were always heterozygous and associated with high Gleason grade (P < .0001), advanced tumor stage (P < .0001), high preoperative prostate-specific antigen (PSA) levels (P = .0125), lymph node metastasis (P = .0377), positive resection margin (P = .0064), and early biochemical recurrence (P < .0001). 13q deletions were marginally more frequent in prostate cancers with negative ERG status (22.9%) than in ERG-positive tumors (18.7%; P < .0001). Loss of 13q predicted patient prognosis independently from established prognostic parameters that are available at the time of biopsy (P = .0004), including preoperative PSA level, clinical tumor stage, and biopsy Gleason grade. In summary, the results of our study identify 13q deletion as a frequent event in prostate cancer, which is linked to an adverse phenotype and poor prognosis in this disease.
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Affiliation(s)
- Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Sekander Scherzai
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Franziska Büschek
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Christoph Fraune
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Katharina Möller
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Doris Höflmayer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Cosima Göbel
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | | | - Andrea Hinsch
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Emily Neubauer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | | | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Hans Heinzer
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Andreas M Luebke
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany.,Department of Urology, Section for Prostate Cancer Research, University Medical Center Hamburg-Eppendorf, Germany.,Department of Urology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
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41
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Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet 2018; 50:682-692. [PMID: 29662167 PMCID: PMC6372064 DOI: 10.1038/s41588-018-0086-z] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 02/22/2018] [Indexed: 12/18/2022]
Abstract
Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.
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Affiliation(s)
- David C Wedge
- Oxford Big Data Institute, University of Oxford, Oxford, UK.
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thomas Mitchell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Dan J Woodcock
- Oxford Big Data Institute, University of Oxford, Oxford, UK
| | | | - Mohammed Ghori
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jorge Zamora
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Hayley Whitaker
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | | | | | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Early Detection Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stefan Dentro
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Clare Verrill
- Oxford NIHR Biomedical Research Centre, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan M Berney
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nening Dennis
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Sue Merson
- The Institute of Cancer Research, London, UK
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - William Howat
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam Lambert
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jonathan Kay
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Katalin Karaszi
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Hayley Luxton
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Niedzica Camacho
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- The Institute of Cancer Research, London, UK
| | - Luke Marsden
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Lucy Matthews
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Valeria Bo
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Daniel Leongamornlert
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- The Institute of Cancer Research, London, UK
| | - Stuart McLaren
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anthony Ng
- The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yongwei Yu
- Second Military Medical University, Shanghai, China
| | | | | | - Sarah Thomas
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Elizabeth Bancroft
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Cyril Fisher
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Naomi Livni
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Nicol
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Simon Tavaré
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Pelvender Gill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Vincent Khoo
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Pardeep Kumar
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Declan Cahill
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Alan Thompson
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Erik Mayer
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Edward Rowe
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Tim Dudderidge
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Vincent Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Nimish C Shah
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | | | | | | | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | | | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Andrew G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
- School of Mathematics and Statistics/School of Medicine, University of St. Andrews, Fife, UK
| | - G Steven Bova
- Johns Hopkins School of Medicine, Baltimore, MD, USA
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Daniel S Brewer
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Colin S Cooper
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK.
- Royal Marsden NHS Foundation Trust, London and Sutton, UK.
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42
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Kluth M, Graunke M, Möller-Koop C, Hube-Magg C, Minner S, Michl U, Graefen M, Huland H, Pompe R, Jacobsen F, Hinsch A, Wittmer C, Lebok P, Steurer S, Büscheck F, Clauditz T, Wilczak W, Sauter G, Schlomm T, Simon R. Deletion of 18q is a strong and independent prognostic feature in prostate cancer. Oncotarget 2018; 7:86339-86349. [PMID: 27861151 PMCID: PMC5349918 DOI: 10.18632/oncotarget.13404] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/02/2016] [Indexed: 11/25/2022] Open
Abstract
Deletion of 18q recurrently occurs in prostate cancer. To evaluate its clinical relevance, dual labeling fluorescence in-situ hybridization (FISH) using probes for 18q21 and centromere 18 was performed on a prostate cancer tissue microarray (TMA). An 18q deletion was found in 517 of 6,881 successfully analyzed cancers (7.5%). 18q deletion was linked to unfavorable tumor phenotype. An 18q deletion was seen in 6.4% of 4,360 pT2, 8.0% of 1,559 pT3a and 11.8% of 930 pT3b-pT4 cancers (P < 0.0001). Deletions of 18q were detected in 6.9% of 1,636 Gleason ≤ 3 + 3, 6.8% of 3,804 Gleason 3 + 4, 10.1% of 1,058 Gleason 4+3, and 9.9% of 344 Gleason ≥ 4 + 4 tumors (P = 0.0013). Deletions of 18q were slightly more frequent in ERG-fusion negative (8.2%) than in ERG-fusion positive cancers (6.4%, P = 0.0063). 18q deletions were also linked to biochemical recurrence (BCR, P < 0.0001). This was independent from established pre- and postoperative prognostic factors (P ≤ 0.0004). In summary, the results of our study identify 18q deletion as an independent prognostic parameter in prostate cancer. As it is easy to measure, 18q deletion may be a suitable component for multiparametric molecular prostate cancer prognosis tests.
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Affiliation(s)
- Martina Kluth
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Maximilian Graunke
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Christina Möller-Koop
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Sarah Minner
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Uwe Michl
- Martini-Clinic, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Raisa Pompe
- Martini-Clinic, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Frank Jacobsen
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Andrea Hinsch
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Corinna Wittmer
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Patrick Lebok
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Stefan Steurer
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Franziska Büscheck
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Till Clauditz
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Waldemar Wilczak
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Guido Sauter
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany.,Department of Urology, Section for prostate cancer research, University Medical Center Hamburg-Eppendorf, Germany
| | - Ronald Simon
- Institute of Pathology, Prostate Cancer Center at University Medical Center Hamburg-Eppendorf, Germany
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43
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Deletion of 8p is an independent prognostic parameter in prostate cancer. Oncotarget 2018; 8:379-392. [PMID: 27880722 PMCID: PMC5352127 DOI: 10.18632/oncotarget.13425] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 11/12/2016] [Indexed: 11/25/2022] Open
Abstract
Deletion of chromosome 8p is the second most frequent genomic alteration in prostate cancer. To better understand its clinical significance, 8p deletion was analyzed by fluorescence in-situ hybridization on a prostate cancer tissue microarray. 8p deletion was found in 2,581 of 7,017 cancers (36.8%), and was linked to unfavorable tumor phenotype. 8p deletion increased from 29.5% in 4,456 pT2 and 47.8% in 1,598 pT3a to 53.0% in 931 pT3b-pT4 cancers (P < 0,0001). Deletions of 8p were detected in 25.5% of 1,653 Gleason ≤ 3 + 3, 36.6% of 3,880 Gleason 3 + 4, 50.2% of 1,090 Gleason 4 + 3, and 51.1% of 354 Gleason ≥ 4 + 4 tumors (P < 0,0001). 8p deletions were strongly linked to biochemical recurrence (P < 0.0001) independently from established pre- and postoperative prognostic factors (P = 0.0100). However, analysis of morphologically defined subgroups revealed, that 8p deletion lacked prognostic significance in subgroups with very good (Gleason ≤ 3 + 3, 3 + 4 with ≤ 5% Gleason 4) or very poor prognosis (pT3b, Gleason ≥ 8, pN1). 8p deletions were markedly more frequent in cancers with (53.5%) than without PTEN deletions (36.4%; P < 0,0001) and were slightly more frequent in ERG-positive (40.9%) than in ERG-negative cancers (34.7%, P < 0.0001) due to the association with the ERG-associated PTEN deletion. Cancers with 8p/PTEN co-deletions had a strikingly worse prognosis than cancers with deletion of PTEN or 8p alone (P ≤ 0.0003). In summary, 8p deletion is an independent prognostic parameter in prostate cancer that may act synergistically with PTEN deletions. Even statistically independent prognostic biomarkers like 8p may have limited clinical impact in morphologically well defined high or low risk cancers.
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44
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Novel tumor suppressor microRNA at frequently deleted chromosomal region 8p21 regulates epidermal growth factor receptor in prostate cancer. Oncotarget 2018; 7:70388-70403. [PMID: 27611943 PMCID: PMC5342560 DOI: 10.18632/oncotarget.11865] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/13/2016] [Indexed: 12/22/2022] Open
Abstract
Genomic loss of chromosome (chr) 8p21 region, containing prostate-specific NKX3.1 gene, is a frequent alteration of the prostate cancer (PCa) oncogenome. We propose a novel, paradigm shifting hypothesis that this frequently deleted locus is also associated with a cluster of microRNA genes- miR-3622a/b- that are lost in PCa and play an important mechanistic role in progression and metastasis. In this study, we demonstrate the role of miR-3622b in prostate cancer. Expression analyses in a cohort of PCa clinical specimens and cell lines show that miR-3622b expression is frequently lost in prostate cancer. Low miR-3622b expression was found to be associated with tumor progression and poor biochemical recurrence-free survival. Further, our analyses suggest that miR-3622b expression is a promising prostate cancer diagnostic biomarker that exhibits 100% specificity and 66% sensitivity. Restoration of miR-3622b expression in PCa cell lines led to reduced cellular viability, proliferation, invasiveness, migration and increased apoptosis. miR-3622b overexpression in vivo induced regression of established prostate tumor xenografts pointing to its therapeutic potential. Further, we found that miR-3622b directly represses Epidermal Growth Factor Receptor (EGFR). In conclusion, our study suggests that miR-3622b plays a tumor suppressive role and is frequently downregulated in prostate cancer, leading to EGFR upregulation. Importantly, miR-3622b has associated diagnostic, prognostic and therapeutic potential. Considering the association of chr8p21 loss with poor prognosis, our findings are highly significant and support a novel concept that associates a long standing observation of frequent loss of a chromosomal region with a novel miRNA in prostate cancer.
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45
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Nowinski S, Santaolalla A, O'Leary B, Loda M, Mirchandani A, Emberton M, Van Hemelrijck M, Grigoriadis A. Systematic identification of functionally relevant risk alleles to stratify aggressive versus indolent prostate cancer. Oncotarget 2018; 9:12812-12824. [PMID: 29560112 PMCID: PMC5849176 DOI: 10.18632/oncotarget.24400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
Novel approaches for classification, including molecular features, are needed to direct therapy for men with low-grade prostate cancer (PCa), especially men on active surveillance. Risk alleles identified from genome-wide association studies (GWAS) could improve prognostication. Those risk alleles that coincided with genes and somatic copy number aberrations associated with progression of PCa were selected as the most relevant for prognostication. In a systematic literature review, a total of 698 studies were collated. Fifty-three unique SNPs residing in 29 genomic regions, including 8q24, 10q11 and 19q13, were associated with PCa progression. Functional studies implicated 21 of these single nucleotide polymorphisms (SNPs) as modulating the expression of genes in the androgen receptor pathway and several other oncogenes. In particular, 8q24, encompassing MYC, harbours a high density of SNPs conferring unfavourable pathological characteristics in low-grade PCa, while a copy number gain of MYC in low-grade PCa was associated with prostate-specific antigen recurrence after radical prostatectomy. By combining GWAS data with gene expression and structural rearrangements, risk alleles were identified that could provide a new basis for developing a prognostication tool to guide therapy for men with early prostate cancer.
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Affiliation(s)
- Salpie Nowinski
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Aida Santaolalla
- Translational Oncology & Urology Research, King's College London, London, UK
| | - Ben O'Leary
- Breast Cancer NOW Centre, The Institute of Cancer Research, The Royal Marsden Hospital, London, UK
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ayesha Mirchandani
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Mark Emberton
- Division of Surgery and Interventional Science, University College London, London, UK
| | | | - Anita Grigoriadis
- Cancer Bioinformatics, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
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46
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Pettersson A, Gerke T, Penney KL, Lis RT, Stack EC, Pértega-Gomes N, Zadra G, Tyekucheva S, Giovannucci EL, Mucci LA, Loda M. MYC Overexpression at the Protein and mRNA Level and Cancer Outcomes among Men Treated with Radical Prostatectomy for Prostate Cancer. Cancer Epidemiol Biomarkers Prev 2018; 27:201-207. [PMID: 29141848 PMCID: PMC5831163 DOI: 10.1158/1055-9965.epi-17-0637] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 12/16/2022] Open
Abstract
Background: The proto-oncogene MYC is implicated in prostate cancer progression. Whether MYC tumor expression at the protein or mRNA level is associated with poorer prognosis has not been well studied.Methods: We conducted a cohort study including 634 men from the Physicians' Health Study and Health Professionals Follow-up Study treated with radical prostatectomy for prostate cancer in 1983-2004 and followed up for a median of 13.7 years. MYC protein expression was evaluated using IHC, and we used Cox regression to calculate HRs and 95% confidence intervals (CIs) of its association with lethal prostate cancer (distant metastases/prostate cancer-related death). We assessed the association between MYC mRNA expression and lethal prostate cancer in a case-control study, including 113 lethal cases and 291 indolent controls.Results: MYC nuclear protein expression was present in 97% of tumors. MYC protein expression was positively correlated with tumor proliferation rate (r = 0.37; P < 0.001) and negatively correlated with apoptotic count (r = -0.17; P < 0.001). There were no significant associations between MYC protein expression and stage, grade, or PSA level at diagnosis. The multivariable HR for lethal prostate cancer among men in the top versus bottom quartile of MYC protein expression was 1.09 (95% CI, 0.50-2.35). There was no significant association between MYC mRNA expression and lethal prostate cancer.Conclusions: Neither MYC protein overexpression nor MYC mRNA overexpression are strong prognostic markers in men treated with radical prostatectomy for prostate cancer.Impact: This is the largest study to examine the prognostic role of MYC protein and mRNA expression in prostate cancer. Cancer Epidemiol Biomarkers Prev; 27(2); 201-7. ©2017 AACR.
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Affiliation(s)
- Andreas Pettersson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Travis Gerke
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Rosina T Lis
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edward C Stack
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Nelma Pértega-Gomes
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Giorgia Zadra
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Svitlana Tyekucheva
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Departments of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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47
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Abstract
The management of newly diagnosed prostate cancer is challenging because of its heterogeneity in histology, genetics and clinical outcome. The clinical outcome of patients with Gleason score 7 prostate cancer varies greatly. Improving risk assessment in this group is of particular interest, as Gleason score 7 prostate cancer on biopsy is an important clinical threshold for active treatment. Architecturally, four Gleason grade 4 growth patterns are recognized: ill-formed, fused, glomeruloid and cribriform. The aim of this review is to describe the role of cribriform growth in prostate cancer with respect to diagnosis, prognosis and molecular pathology. Secondly, we will discuss clinical applications for cribriform prostate cancer and give recommendations for future research.
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Affiliation(s)
- Charlotte F Kweldam
- Department of Pathology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Geert J van Leenders
- Department of Pathology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
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48
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Vidotto T, Tiezzi DG, Squire JA. Distinct subtypes of genomic PTEN deletion size influence the landscape of aneuploidy and outcome in prostate cancer. Mol Cytogenet 2018; 11:1. [PMID: 29308088 PMCID: PMC5753467 DOI: 10.1186/s13039-017-0348-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Abstract
Background Inactivation of the PTEN tumor suppressor gene by deletion occurs in 20-30% of prostate cancer tumors and loss strongly correlates with a worse outcome. PTEN loss of function not only leads to activation of the PI3K/AKT pathway, but is also thought to affect genome stability and increase levels of tumor aneuploidy. We performed an in silico integrative genomic and transcriptomic analysis of 491 TCGA prostate cancer tumors. These data were used to map the genomic sizes of PTEN gene deletions and to characterize levels of instability and patterns of aneuploidy acquisition. Results PTEN homozygous deletions had a significant increase in aneuploidy compared to PTEN tumors without an apparent deletion, and hemizygous deletions showed an intermediate aneuploidy profile. A supervised clustering of somatic copy number alterations (SCNA) demonstrated that the size of PTEN deletions was not random, but comprised five distinct subtypes: (1) "Small Interstitial" (70 bp-789Kb); (2) "Large Interstitial" (1-7 MB); (3) "Large Proximal" (3-65 MB); (4) "Large Terminal" (8-64 MB), and (5) "Extensive" (71-132 MB). Many of the deleted fragments in each subtype were flanked by low copy repetitive (LCR) sequences. SCNAs such as gain at 3q21.1-3q29 and deletions at 8p, RB1, TP53 and TMPRSS2-ERG were variably present in all subtypes. Other SCNAs appeared to be recurrent in some deletion subtypes, but absent from others. To determine how the aneuploidy influenced global levels of gene expression, we performed a comparative transcriptome analysis. One deletion subtype (Large Interstitial) was characterized by gene expression changes associated with angiogenesis and cell adhesion, structure, and metabolism. Logistic regression demonstrated that this deletion subtype was associated with a high Gleason score (HR = 2.386; 95% C.I. 1.245-4.572), extraprostatic extension (HR = 2.423, 95% C.I. 1.157-5.075), and metastasis (HR = 7.135; 95% C.I. 1.540-33.044). Univariate and multivariate Cox Regression showed that presence of this deletion subtype was also strongly predictive of disease recurrence. Conclusions Our findings indicate that genomic deletions of PTEN fall into five different size distributions, with breakpoints that often occur close LCR regions, and that each subtype is associated with a characteristic aneuploidy signature. The Large Interstitial deletion had a distinct gene expression signature that was related to cancer progression and was also predictive of a worse prognosis.
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Affiliation(s)
- Thiago Vidotto
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Daniel Guimarães Tiezzi
- Deparment of Gynecology and Obstetrics, Clinical Hospital of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Jeremy A Squire
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, 3900 Bandeirantes Avenue, Monte Alegre, Ribeirão Preto, São Paulo 14040-900 Brazil.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
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49
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Böttcher R, Kweldam CF, Livingstone J, Lalonde E, Yamaguchi TN, Huang V, Yousif F, Fraser M, Bristow RG, van der Kwast T, Boutros PC, Jenster G, van Leenders GJLH. Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations. BMC Cancer 2018; 18:8. [PMID: 29295717 PMCID: PMC5751811 DOI: 10.1186/s12885-017-3976-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 12/21/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Invasive cribriform and intraductal carcinoma (CR/IDC) is associated with adverse outcome of prostate cancer patients. The aim of this study was to determine the molecular aberrations associated with CR/IDC in primary prostate cancer, focusing on genomic instability and somatic copy number alterations (CNA). METHODS Whole-slide images of The Cancer Genome Atlas Project (TCGA, N = 260) and the Canadian Prostate Cancer Genome Network (CPC-GENE, N = 199) radical prostatectomy datasets were reviewed for Gleason score (GS) and presence of CR/IDC. Genomic instability was assessed by calculating the percentage of genome altered (PGA). Somatic copy number alterations (CNA) were determined using Fisher-Boschloo tests and logistic regression. Primary analysis were performed on TCGA (N = 260) as discovery and CPC-GENE (N = 199) as validation set. RESULTS CR/IDC growth was present in 80/260 (31%) TCGA and 76/199 (38%) CPC-GENE cases. Patients with CR/IDC and ≥ GS 7 had significantly higher PGA than men without this pattern in both TCGA (2.2 fold; p = 0.0003) and CPC-GENE (1.7 fold; p = 0.004) cohorts. CR/IDC growth was associated with deletions of 8p, 16q, 10q23, 13q22, 17p13, 21q22, and amplification of 8q24. CNAs comprised a total of 1299 gene deletions and 369 amplifications in the TCGA dataset, of which 474 and 328 events were independently validated, respectively. Several of the affected genes were known to be associated with aggressive prostate cancer such as loss of PTEN, CDH1, BCAR1 and gain of MYC. Point mutations in TP53, SPOP and FOXA1were also associated with CR/IDC, but occurred less frequently than CNAs. CONCLUSIONS CR/IDC growth is associated with increased genomic instability clustering to genetic regions involved in aggressive prostate cancer. Therefore, CR/IDC is a pathologic substrate for progressive molecular tumour derangement.
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Affiliation(s)
- René Böttcher
- Department of Urology, Erasmus MC, Rotterdam, the Netherlands
| | - Charlotte F. Kweldam
- Department of Pathology, Erasmus University Medical Center, Josephine Nefkens Institute building, Be-222, P.O. Box 2040, Rotterdam, 3000 CA The Netherlands
| | - Julie Livingstone
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Emilie Lalonde
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Takafumi N. Yamaguchi
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Vincent Huang
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Fouad Yousif
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
| | - Michael Fraser
- Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada
| | - Robert G. Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
- Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON Canada
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, ON Canada
| | - Paul C. Boutros
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON Canada
| | - Guido Jenster
- Department of Urology, Erasmus MC, Rotterdam, the Netherlands
| | - Geert J. L. H. van Leenders
- Department of Pathology, Erasmus University Medical Center, Josephine Nefkens Institute building, Be-222, P.O. Box 2040, Rotterdam, 3000 CA The Netherlands
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50
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Kluth M, Jung S, Habib O, Eshagzaiy M, Heinl A, Amschler N, Masser S, Mader M, Runte F, Barow P, Frogh S, Omari J, Möller-Koop C, Hube-Magg C, Weischenfeldt J, Korbel J, Steurer S, Krech T, Huland H, Graefen M, Minner S, Sauter G, Schlomm T, Simon R. Deletion lengthening at chromosomes 6q and 16q targets multiple tumor suppressor genes and is associated with an increasingly poor prognosis in prostate cancer. Oncotarget 2017; 8:108923-108935. [PMID: 29312579 PMCID: PMC5752492 DOI: 10.18632/oncotarget.22408] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/16/2017] [Indexed: 12/21/2022] Open
Abstract
Prostate cancer is characterized by recurrent deletions that can considerably vary in size. We hypothesized that large deletions develop from small deletions and that this “deletion lengthening” might have a “per se” carcinogenic role through a combinatorial effect of multiple down regulated genes. In vitro knockdown of 37 genes located inside the 6q12-q22 deletion region identified 4 genes with additive tumor suppressive effects, further supporting a role of the deletion size for cancer aggressiveness. Employing fluorescence in-situ hybridization analysis on prostate cancer tissue microarrays, we determined the deletion size at 6q and 16q in more than 3,000 tumors. 16q and 6q deletion length was strongly linked to poor clinical outcome and this effect was even stronger if the length of both deletions was combined. To study deletion lengthening in cancer progression we eventually analyzed the entire cancers from 317 patients for 6q and 16q deletion length heterogeneity and found that the deletion expanded within 50-60% of 6q and 16q deleted cancers. Taken together, these data suggest continuous “deletion lengthening” as a key mechanism for prostate cancer progression leading to parallel down regulation of genes with tumor suppressive properties, some of which act cooperatively.
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Affiliation(s)
- Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Jung
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Omar Habib
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mina Eshagzaiy
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Heinl
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Amschler
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sawinee Masser
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Mader
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frederic Runte
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philipp Barow
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sohall Frogh
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jazan Omari
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christina Möller-Koop
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joachim Weischenfeldt
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jan Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Krech
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Urology, Section for Translational Prostate Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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