1
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Liu S, Obert C, Yu YP, Zhao J, Ren BG, Liu JJ, Wiseman K, Krajacich BJ, Wang W, Metcalfe K, Smith M, Ben-Yehezkel T, Luo JH. Utility analyses of AVITI sequencing chemistry. BMC Genomics 2024; 25:778. [PMID: 39127634 DOI: 10.1186/s12864-024-10686-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. RESULTS Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences' AVITI and Illumina's NextSeq 550 chemistries. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina's NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed an average 89.7% lower experimentally determined error rate when using the AVITI chemistry, compared to the NextSeq 550. For short-read RNA quantification, AVITI platform had an average of 32.5% lower error rate than that for NextSeq 550. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms' respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. CONCLUSION These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, USA.
| | - Caroline Obert
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Junhua Zhao
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Bao-Guo Ren
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Jia-Jun Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Kelly Wiseman
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Benjamin J Krajacich
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Wenjia Wang
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, USA
| | - Kyle Metcalfe
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Mat Smith
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Tuval Ben-Yehezkel
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, USA.
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2
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Kader M, Yu YP, Liu S, Luo JH. Immuno-targeting the ectopic phosphorylation sites of PDGFRA generated by MAN2A1-FER fusion in HCC. Hepatol Commun 2024; 8:e0511. [PMID: 39082961 DOI: 10.1097/hc9.0000000000000511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/30/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND HCC is one of the most lethal cancers for humans. Mannosidase alpha class 2A member 1 (MAN2A1)-FER is one of the most frequent oncogenic fusion genes in HCC. In this report, we showed that MAN2A1-FER ectopically phosphorylated the extracellular domains of PDGFRA, MET, AXL, and N-cadherin. The ectopic phosphorylation of these transmembrane proteins led to the activation of their kinase activities and initiated the activation cascades of their downstream signaling molecules. METHODS A panel of mouse monoclonal antibodies was developed to recognize the ectopic phosphorylation sites of PDGFRA. RESULTS AND CONCLUSIONS The analyses showed that these antibodies bound to the specific phosphotyrosine epitopes in the extracellular domain of PDGFRA with high affinity and specificity. The treatment of MAN2A1-FER-positive cancer HUH7 with one of the antibodies called 2-3B-G8 led to the deactivation of cell growth signaling pathways and cell growth arrest while having minimal impact on HUH7ko cells where MAN2A1-FER expression was disrupted. The treatment of 2-3B-G8 antibody also led to a large number of cell deaths of MAN2A1-FER-positive cancer cells such as HUH7, HEPG2, SNU449, etc., while the same treatment had no impact on HUH7ko cells. When severe combined immunodeficiency mice xenografted with HEPG2 or HUH7 were treated with monomethyl auristatin E-conjugated 2-3B-G8 antibody, it slowed the progression of tumor growth, eliminated the metastasis, and reduced the mortality, in comparison with the controls. Targeting the cancer-specific ectopic phosphorylation sites of PDGFRA induced by MAN2A1-FER may hold promise as an effective treatment for liver cancer.
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Affiliation(s)
- Muhamuda Kader
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- High Throughput Genome Center, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- High Throughput Genome Center, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- High Throughput Genome Center, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Yu YP, Liu S, Geller D, Luo JH. Serum Fusion Transcripts to Assess the Risk of Hepatocellular Carcinoma and the Impact of Cancer Treatment through Machine Learning. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:1262-1271. [PMID: 38537933 PMCID: PMC11220925 DOI: 10.1016/j.ajpath.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/05/2024] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the most fatal malignancies. Early diagnosis of HCC is crucial in reducing the risk for mortality. This study analyzed a panel of nine fusion transcripts in serum samples from 61 patients with HCC and 75 patients with non-HCC conditions, using TaqMan real-time quantitative RT-PCR. Seven of the nine fusions frequently detected in patients with HCC included: MAN2A1-FER (100%), SLC45A2-AMACR (62.3%), ZMPSTE24-ZMYM4 (62.3%), PTEN-NOLC1 (57.4%), CCNH-C5orf30 (55.7%), STAMBPL1-FAS (26.2%), and PCMTD1-SNTG1 (16.4%). Machine-learning models were constructed based on serum fusion-gene levels to predict HCC in the training cohort, using the leave-one-out cross-validation approach. One machine-learning model, called the four fusion genes logistic regression model (MAN2A1-FER≤40, CCNH-C5orf30≤38, SLC45A2-AMACR≤41, and PTEN-NOLC1≤40), produced accuracies of 91.5% and 83.3% in the training and testing cohorts, respectively. When serum α-fetal protein level was incorporated into the machine-learning model, a two fusion gene (MAN2A1-FER≤40, CCNH-C5orf30≤38) + α-fetal protein logistic regression model was found to generate an accuracy of 94.8% in the training cohort. The same model resulted in 95% accuracy in both the testing and combined cohorts. Cancer treatment was associated with reduced levels of most of the serum fusion transcripts. Serum fusion-gene machine-learning models may serve as important tools in screening for HCC and in monitoring the impact of HCC treatment.
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Affiliation(s)
- Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David Geller
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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4
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Liu S, Obert C, Yu YP, Zhao J, Ren BG, Liu JJ, Wiseman K, Krajacich BJ, Wang W, Metcalfe K, Smith M, Ben-Yehezkel T, Luo JH. Utility Analyses of AVITI Sequencing Chemistry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590136. [PMID: 38712138 PMCID: PMC11071311 DOI: 10.1101/2024.04.18.590136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Background DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Results Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences' AVITI and Illumina's NextSeq 550 chemistries. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina's NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed an average 89.7% lower experimentally determined error rate when using the AVITI chemistry, compared to the NextSeq 550. For short-read RNA quantification, AVITI platform had an average of 32.5% lower error rate than that for NextSeq 550. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms' respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. Conclusion These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, United States
| | - Caroline Obert
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, United States
| | - Junhua Zhao
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Bao-Guo Ren
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
| | - Jia-Jun Liu
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, United States
| | - Kelly Wiseman
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Benjamin J Krajacich
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Wenjia Wang
- Department of Biostatistics, University of Pittsburgh School of Public Health, United States
| | - Kyle Metcalfe
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Mat Smith
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Tuval Ben-Yehezkel
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, United States
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5
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Logotheti S, Papadaki E, Zolota V, Logothetis C, Vrahatis AG, Soundararajan R, Tzelepi V. Lineage Plasticity and Stemness Phenotypes in Prostate Cancer: Harnessing the Power of Integrated "Omics" Approaches to Explore Measurable Metrics. Cancers (Basel) 2023; 15:4357. [PMID: 37686633 PMCID: PMC10486655 DOI: 10.3390/cancers15174357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Prostate cancer (PCa), the most frequent and second most lethal cancer type in men in developed countries, is a highly heterogeneous disease. PCa heterogeneity, therapy resistance, stemness, and lethal progression have been attributed to lineage plasticity, which refers to the ability of neoplastic cells to undergo phenotypic changes under microenvironmental pressures by switching between developmental cell states. What remains to be elucidated is how to identify measurements of lineage plasticity, how to implement them to inform preclinical and clinical research, and, further, how to classify patients and inform therapeutic strategies in the clinic. Recent research has highlighted the crucial role of next-generation sequencing technologies in identifying potential biomarkers associated with lineage plasticity. Here, we review the genomic, transcriptomic, and epigenetic events that have been described in PCa and highlight those with significance for lineage plasticity. We further focus on their relevance in PCa research and their benefits in PCa patient classification. Finally, we explore ways in which bioinformatic analyses can be used to determine lineage plasticity based on large omics analyses and algorithms that can shed light on upstream and downstream events. Most importantly, an integrated multiomics approach may soon allow for the identification of a lineage plasticity signature, which would revolutionize the molecular classification of PCa patients.
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Affiliation(s)
- Souzana Logotheti
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Eugenia Papadaki
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
- Department of Informatics, Ionian University, 49100 Corfu, Greece;
| | - Vasiliki Zolota
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | | | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vasiliki Tzelepi
- Department of Pathology, University of Patras, 26504 Patras, Greece; (S.L.); (E.P.); (V.Z.)
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6
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Guo H, Vuille JA, Wittner BS, Lachtara EM, Hou Y, Lin M, Zhao T, Raman AT, Russell HC, Reeves BA, Pleskow HM, Wu CL, Gnirke A, Meissner A, Efstathiou JA, Lee RJ, Toner M, Aryee MJ, Lawrence MS, Miyamoto DT, Maheswaran S, Haber DA. DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs. Cell 2023; 186:2765-2782.e28. [PMID: 37327786 PMCID: PMC10436379 DOI: 10.1016/j.cell.2023.05.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/09/2023] [Accepted: 05/17/2023] [Indexed: 06/18/2023]
Abstract
Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution genome-wide single-cell DNA methylation sequencing, we identify 40 core domains that are uniformly hypomethylated from the earliest detectable stages of prostate malignancy through metastatic circulating tumor cells (CTCs). Nested among these repressive domains are smaller loci with preserved methylation that escape silencing and are enriched for cell proliferation genes. Transcriptionally silenced genes within the core hypomethylated domains are enriched for immune-related genes; prominent among these is a single gene cluster harboring all five CD1 genes that present lipid antigens to NKT cells and four IFI16-related interferon-inducible genes implicated in innate immunity. The re-expression of CD1 or IFI16 murine orthologs in immuno-competent mice abrogates tumorigenesis, accompanied by the activation of anti-tumor immunity. Thus, early epigenetic changes may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for CTCs.
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Affiliation(s)
- Hongshan Guo
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Joanna A Vuille
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Emily M Lachtara
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yu Hou
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maoxuan Lin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ting Zhao
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ayush T Raman
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hunter C Russell
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Brittany A Reeves
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Haley M Pleskow
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Chin-Lee Wu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Jason A Efstathiou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Richard J Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mehmet Toner
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Engineering in Medicine and Shriners Hospital for Children, Harvard Medical School, Boston, MA 02114, USA
| | - Martin J Aryee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David T Miyamoto
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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7
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Shin HJ, Hua JT, Li H. Recent advances in understanding DNA methylation of prostate cancer. Front Oncol 2023; 13:1182727. [PMID: 37234978 PMCID: PMC10206257 DOI: 10.3389/fonc.2023.1182727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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8
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Gallon J, Rodriguez-Calero A, Benjak A, Akhoundova D, Maletti S, Amstutz U, Hewer E, Genitsch V, Fleischmann A, Rushing EJ, Grobholz R, Fischer I, Jochum W, Cathomas G, Osunkoya AO, Bubendorf L, Moch H, Thalmann G, Feng FY, Gillessen S, Ng CK, Rubin MA, Piscuoglio S. DNA Methylation Landscapes of Prostate Cancer Brain Metastasis Are Shaped by Early Driver Genetic Alterations. Cancer Res 2023; 83:1203-1213. [PMID: 36749655 PMCID: PMC10102845 DOI: 10.1158/0008-5472.can-22-2236] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/05/2022] [Accepted: 02/01/2023] [Indexed: 02/08/2023]
Abstract
Metastases from primary prostate cancers to rare locations, such as the brain, are becoming more common due to longer life expectancy resulting from improved treatments. Epigenetic dysregulation is a feature of primary prostate cancer, and distinct DNA methylation profiles have been shown to be associated with the mutually exclusive SPOP-mutant or TMPRSS2-ERG fusion genetic backgrounds. Using a cohort of prostate cancer brain metastases (PCBM) from 42 patients, with matched primary tumors for 17 patients, we carried out a DNA methylation analysis to examine the epigenetic distinction between primary prostate cancer and PCBM, the association between epigenetic alterations and mutational background, and particular epigenetic alterations that may be associated with PCBM. Multiregion sampling of PCBM revealed epigenetic stability within metastases. Aberrant methylation in PCBM was associated with mutational background and PRC2 complex activity, an effect that is particularly pronounced in SPOP-mutant PCBM. While PCBM displayed a CpG island hypermethylator phenotype, hypomethylation at the promoters of genes involved in neuroactive ligand-receptor interaction and cell adhesion molecules such as GABRB3, CLDN8, and CLDN4 was also observed, suggesting that cells from primary tumors may require specific reprogramming to form brain metastasis. This study revealed the DNA methylation landscapes of PCBM and the potential mechanisms and effects of PCBM-associated aberrant DNA methylation. SIGNIFICANCE DNA methylation analysis reveals the molecular characteristics of PCBM and may serve as a starting point for efforts to identify and target susceptibilities of these rare metastases.
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Affiliation(s)
- John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Antonio Rodriguez-Calero
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Andrej Benjak
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Dilara Akhoundova
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Sina Maletti
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Ursula Amstutz
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ekkehard Hewer
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Vera Genitsch
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Achim Fleischmann
- Institute of Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology, Cantonal Hospital Thurgau, Münsterlingen, Switzerland
| | | | - Rainer Grobholz
- Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Ingeborg Fischer
- Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Wolfram Jochum
- Institute of Pathology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Gieri Cathomas
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Adeboye O. Osunkoya
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - George Thalmann
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Felix Y. Feng
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, California
| | - Silke Gillessen
- Faculty of Biomedical Sciences, USI, Lugano, Switzerland
- Department of Oncology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Charlotte K.Y. Ng
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Bern Center for Precision Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mark A. Rubin
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
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9
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Yu YP, Liu S, Ren BG, Nelson J, Jarrard D, Brooks JD, Michalopoulos G, Tseng G, Luo JH. Fusion Gene Detection in Prostate Cancer Samples Enhances the Prediction of Prostate Cancer Clinical Outcomes from Radical Prostatectomy through Machine Learning in a Multi-Institutional Analysis. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:392-403. [PMID: 36681188 PMCID: PMC10123524 DOI: 10.1016/j.ajpath.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 01/20/2023]
Abstract
Prostate cancer remains one of the most fatal malignancies in men in the United States. Predicting the course of prostate cancer is challenging given that only a fraction of prostate cancer patients experience cancer recurrence after radical prostatectomy or radiation therapy. This study examined the expressions of 14 fusion genes in 607 prostate cancer samples from the University of Pittsburgh, Stanford University, and the University of Wisconsin-Madison. The profiling of 14 fusion genes was integrated with Gleason score of the primary prostate cancer and serum prostate-specific antigen level to develop machine-learning models to predict the recurrence of prostate cancer after radical prostatectomy. Machine-learning algorithms were developed by analysis of the data from the University of Pittsburgh cohort as a training set using the leave-one-out cross-validation method. These algorithms were then applied to the data set from the combined Stanford/Wisconsin cohort (testing set). The results showed that the addition of fusion gene profiling consistently improved the prediction accuracy rate of prostate cancer recurrence by Gleason score, serum prostate-specific antigen level, or a combination of both. These improvements occurred in both the training and testing cohorts and were corroborated by multiple models.
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Affiliation(s)
- Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Bao-Guo Ren
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joel Nelson
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David Jarrard
- Department of Urology, University of Wisconsin School of Medicine, Madison, Wisconsin
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, California
| | - George Michalopoulos
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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10
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Kim SS, Lee SC, Lim B, Shin SH, Kim MY, Kim SY, Lim H, Charton C, Shin D, Moon HW, Kim J, Park D, Park WY, Lee JY. DNA methylation biomarkers distinguishing early-stage prostate cancer from benign prostatic hyperplasia. Prostate Int 2023. [DOI: 10.1016/j.prnil.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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11
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Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res 2022; 82:3888-3902. [PMID: 36251389 PMCID: PMC9627125 DOI: 10.1158/0008-5472.can-22-1123] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 07/29/2022] [Indexed: 02/03/2023]
Abstract
Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
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Affiliation(s)
- Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI
- William S. Middleton Memorial Veterans' Hospital, Madison, WI
| | | | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Corinne Maurice-Dror
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver, BC, Canada
| | - Ashutosh Maheshwari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wenbin Ye
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Jessica Petricca
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Marc D Perry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - William S Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Alicia K Morgans
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Robert E Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
| | - Matthew B Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Anders Bjartell
- Department of Translational Medicine, Medical Faculty, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin-Madison, Madison, WI
| | | | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
- Department of Urologic Surgery, University of California Davis, Sacramento, CA
| | - Phuoc T Tran
- Department of Radiation Oncology, University of Maryland, College Park, Baltimore, MD
| | - Edwin M Posadas
- Urologic Oncology Program & Uro-Oncology Research Laboratories, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Arc Institute, Palo Alto, CA
| | - Christopher A Maher
- Siteman Cancer Center, Washington University, St. Louis, MO
- McDonnell Genome Institute, Washington University, St. Louis, MO
- Department of Internal Medicine, Washington University, St. Louis, MO
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, Departments of Human Genetics and Urology, University of California Los Angeles, Los Angeles, CA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
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12
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Lu X, Fong KW, Gritsina G, Wang F, Baca SC, Brea LT, Berchuck JE, Spisak S, Ross J, Morrissey C, Corey E, Chandel NS, Catalona WJ, Yang X, Freedman ML, Zhao JC, Yu J. HOXB13 suppresses de novo lipogenesis through HDAC3-mediated epigenetic reprogramming in prostate cancer. Nat Genet 2022; 54:670-683. [PMID: 35468964 PMCID: PMC9117466 DOI: 10.1038/s41588-022-01045-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/28/2022] [Indexed: 01/16/2023]
Abstract
HOXB13, a homeodomain transcription factor, critically regulates androgen receptor (AR) activities and androgen-dependent prostate cancer (PCa) growth. However, its functions in AR-independent contexts remain elusive. Here we report HOXB13 interaction with histone deacetylase HDAC3, which is disrupted by the HOXB13 G84E mutation that has been associated with early-onset PCa. Independently of AR, HOXB13 recruits HDAC3 to lipogenic enhancers to catalyze histone deacetylation and suppress lipogenic regulators such as fatty acid synthase. Analysis of human tissues reveals that the HOXB13 gene is hypermethylated and downregulated in approximately 30% of metastatic castration-resistant PCa. HOXB13 loss or G84E mutation leads to lipid accumulation in PCa cells, thereby promoting cell motility and xenograft tumor metastasis, which is mitigated by pharmaceutical inhibition of fatty acid synthase. In summary, we present evidence that HOXB13 recruits HDAC3 to suppress de novo lipogenesis and inhibit tumor metastasis and that lipogenic pathway inhibitors may be useful to treat HOXB13-low PCa.
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Affiliation(s)
- Xiaodong Lu
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ka-wing Fong
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Galina Gritsina
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Fang Wang
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sylvan C. Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lourdes T. Brea
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jacob E. Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jenny Ross
- Department of Pathology, Northwestern University, Chicago, IL, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, USA
| | - Navdeep S. Chandel
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA,Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University, Chicago, IL, USA,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
| | - William J. Catalona
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA,Department of Urology, Northwestern University, Chicago, IL, USA
| | - Ximing Yang
- Department of Pathology, Northwestern University, Chicago, IL, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan C. Zhao
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA,Co-Corresponding Authors: Jindan Yu, M.D., Ph.D. , Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine; Jonathan C. Zhao,
| | - Jindan Yu
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA,Co-Corresponding Authors: Jindan Yu, M.D., Ph.D. , Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine; Jonathan C. Zhao,
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13
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Androgen receptor and MYC equilibration centralizes on developmental super-enhancer. Nat Commun 2021; 12:7308. [PMID: 34911936 PMCID: PMC8674345 DOI: 10.1038/s41467-021-27077-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Androgen receptor (AR) in prostate cancer (PCa) can drive transcriptional repression of multiple genes including MYC, and supraphysiological androgen is effective in some patients. Here, we show that this repression is independent of AR chromatin binding and driven by coactivator redistribution, and through chromatin conformation capture methods show disruption of the interaction between the MYC super-enhancer within the PCAT1 gene and the MYC promoter. Conversely, androgen deprivation in vitro and in vivo increases MYC expression. In parallel, global AR activity is suppressed by MYC overexpression, consistent with coactivator redistribution. These suppressive effects of AR and MYC are mitigated at shared AR/MYC binding sites, which also have markedly higher levels of H3K27 acetylation, indicating enrichment for functional enhancers. These findings demonstrate an intricate balance between AR and MYC, and indicate that increased MYC in response to androgen deprivation contributes to castration-resistant PCa, while decreased MYC may contribute to responses to supraphysiological androgen therapy. Androgen receptor in prostate cancer (PCa) transcriptionally represses multiple genes including MYC. Here, the authors suggest that increased MYC in response to androgen deprivation contributes to castration-resistant PCa, while decreased MYC may contribute to responses to supraphysiological androgen therapy.
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14
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Mazzu YZ, Liao Y, Nandakumar S, Sjöström M, Jehane LE, Ghale R, Govindarajan B, Gerke TA, Lee GSM, Luo JH, Chinni SR, Mucci LA, Feng FY, Kantoff PW. Dynamic expression of SNAI2 in prostate cancer predicts tumor progression and drug sensitivity. Mol Oncol 2021; 16:2451-2469. [PMID: 34792282 PMCID: PMC9251866 DOI: 10.1002/1878-0261.13140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/05/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Prostate cancer is a highly heterogeneous disease, understanding the crosstalk between complex genomic and epigenomic alterations will aid in developing targeted therapeutics. We demonstrate that, even though snail family transcriptional repressor 2 (SNAI2) is frequently amplified in prostate cancer, it is epigenetically silenced in this disease, with dynamic changes in SNAI2 levels showing distinct clinical relevance. Integrative clinical data from 18 prostate cancer cohorts and experimental evidence showed that gene fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2–ERG fusion) is involved in the silencing of SNAI2. We created a silencer score to evaluate epigenetic repression of SNAI2, which can be reversed by treatment with DNA methyltransferase inhibitors and histone deacetylase inhibitors. Silencing of SNAI2 facilitated tumor cell proliferation and luminal differentiation. Furthermore, SNAI2 has a major influence on the tumor microenvironment by reactivating tumor stroma and creating an immunosuppressive microenvironment in prostate cancer. Importantly, SNAI2 expression levels in part determine sensitivity to the cancer drugs dasatinib and panobinostat. For the first time, we defined the distinct clinical relevance of SNAI2 expression at different disease stages. We elucidated how epigenetic silencing of SNAI2 controls the dynamic changes of SNAI2 expression that are essential for tumor initiation and progression and discovered that restoring SNAI2 expression by treatment with panobinostat enhances dasatinib sensitivity, indicating a new therapeutic strategy for prostate cancer.
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Affiliation(s)
- Ying Z Mazzu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - YuRou Liao
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Subhiksha Nandakumar
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lina E Jehane
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Romina Ghale
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Travis A Gerke
- Prostate Cancer Clinical Trials Consortium, New York, NY, USA
| | - Gwo-Shu Mary Lee
- Department of Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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15
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Hawley JR, Zhou S, Arlidge C, Grillo G, Kron KJ, Hugh-White R, van der Kwast TH, Fraser M, Boutros PC, Bristow RG, Lupien M. Reorganization of the 3D genome pinpoints non-coding drivers of primary prostate tumors. Cancer Res 2021; 81:5833-5848. [PMID: 34642184 DOI: 10.1158/0008-5472.can-21-2056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/13/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
Prostate cancer is a heterogeneous disease whose progression is linked to genome instability. However, the impact of this instability on the non-coding genome and its three-dimensional organization to aid progression is unclear. Using primary benign and tumor tissue, we find a high concordance in higher order three-dimensional genome organization. This concordance argues for constraints to the topology of prostate tumor genomes. Nonetheless, we identified changes in focal chromatin interactions, typical of loops bridging non-coding cis-regulatory elements, and showed how structural variants can induce these changes to guide cis-regulatory element hijacking. Such events resulted in opposing differential expression of genes found at antipodes of rearrangements. Collectively, these results argue that changes to focal chromatin interactions, as opposed to higher order genome organization, allow for aberrant gene regulation and are repeatedly mediated by structural variants in primary prostate cancer.
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Affiliation(s)
- James R Hawley
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | - Stanley Zhou
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | | | - Giacomo Grillo
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | | | | | | | | | | | | | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network
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16
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Yu YP, Liu S, Nelson J, Luo JH. Detection of fusion gene transcripts in the blood samples of prostate cancer patients. Sci Rep 2021; 11:16995. [PMID: 34417538 PMCID: PMC8379170 DOI: 10.1038/s41598-021-96528-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/11/2021] [Indexed: 12/16/2022] Open
Abstract
Prostate cancer remains one of the most lethal cancers for men in the United States. The study aims to detect fusion transcripts in the blood samples of prostate cancer patients. We analyzed nine fusion transcripts including MAN2A1-FER, SLC45A2-AMACR, TRMT11-GRIK2, CCNH-C5orf30, mTOR-TP53BP1, KDM4-AC011523.2, TMEM135-CCDC67, LRRC59-FLJ60017 and Pten-NOLC1147 in the blood samples from 147 prostate cancer patients and 14 healthy individuals, using Taqman RT-PCR and Sanger's sequencing. Similar analyses were also performed on 25 matched prostate cancer samples for matched-sample evaluation. Eighty-two percent blood samples from the prostate cancer patients were positive for MAN2A1-FER transcript, while 41.5% and 38.8% blood samples from the prostate cancer patients were positive for SLC45A2-AMACR and Pten-NOLC1, respectively. CCNH-c5orf30 and mTOR-TP53BP1 had low detection rates, positive in only 5.4% and 4% of the blood samples from the prostate cancer patients. Only 2 blood samples were positive for KDM4B-AC011523.2 transcript. Overall, 89.8% patients were positive for at least one fusion transcript in their blood samples. The statistical analysis showed varied sensitivity of fusion transcript detection in the blood based on the types of fusions. In contrast, the blood samples from all healthy individuals were negative for the fusion transcripts. Detection of fusion transcripts in the blood samples of the prostate cancer patients may be a fast and cost-effective way to detect prostate cancer.
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Affiliation(s)
- Yan-Ping Yu
- Department of Pathology and Urology, School of Medicine, University of Pittsburgh, Scaife S-728, Pittsburgh, PA, 15261, USA
| | - Silvia Liu
- Department of Pathology and Urology, School of Medicine, University of Pittsburgh, Scaife S-728, Pittsburgh, PA, 15261, USA
| | - Joel Nelson
- Department of Pathology and Urology, School of Medicine, University of Pittsburgh, Scaife S-728, Pittsburgh, PA, 15261, USA
| | - Jian-Hua Luo
- Department of Pathology and Urology, School of Medicine, University of Pittsburgh, Scaife S-728, Pittsburgh, PA, 15261, USA.
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17
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Baca SC, Takeda DY, Seo JH, Hwang J, Ku SY, Arafeh R, Arnoff T, Agarwal S, Bell C, O'Connor E, Qiu X, Alaiwi SA, Corona RI, Fonseca MAS, Giambartolomei C, Cejas P, Lim K, He M, Sheahan A, Nassar A, Berchuck JE, Brown L, Nguyen HM, Coleman IM, Kaipainen A, De Sarkar N, Nelson PS, Morrissey C, Korthauer K, Pomerantz MM, Ellis L, Pasaniuc B, Lawrenson K, Kelly K, Zoubeidi A, Hahn WC, Beltran H, Long HW, Brown M, Corey E, Freedman ML. Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer. Nat Commun 2021; 12:1979. [PMID: 33785741 PMCID: PMC8010057 DOI: 10.1038/s41467-021-22139-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Lineage plasticity, the ability of a cell to alter its identity, is an increasingly common mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is the development of neuroendocrine prostate cancer (NEPC) after treatment of prostate adenocarcinoma (PRAD) with inhibitors of androgen signaling. NEPC is an aggressive variant of prostate cancer that aberrantly expresses genes characteristic of neuroendocrine (NE) tissues and no longer depends on androgens. Here, we investigate the epigenomic basis of this resistance mechanism by profiling histone modifications in NEPC and PRAD patient-derived xenografts (PDXs) using chromatin immunoprecipitation and sequencing (ChIP-seq). We identify a vast network of cis-regulatory elements (N~15,000) that are recurrently activated in NEPC. The FOXA1 transcription factor (TF), which pioneers androgen receptor (AR) chromatin binding in the prostate epithelium, is reprogrammed to NE-specific regulatory elements in NEPC. Despite loss of dependence upon AR, NEPC maintains FOXA1 expression and requires FOXA1 for proliferation and expression of NE lineage-defining genes. Ectopic expression of the NE lineage TFs ASCL1 and NKX2-1 in PRAD cells reprograms FOXA1 to bind to NE regulatory elements and induces enhancer activity as evidenced by histone modifications at these sites. Our data establish the importance of FOXA1 in NEPC and provide a principled approach to identifying cancer dependencies through epigenomic profiling.
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Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Y Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Justin Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sheng Yu Ku
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rand Arafeh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Taylor Arnoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Supreet Agarwal
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rosario I Corona
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcos A S Fonseca
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Istituto Italiano di Tecnologia, Genova, Italy
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anjali Sheahan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amin Nassar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Ilsa M Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Arja Kaipainen
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Keegan Korthauer
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leigh Ellis
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kate Lawrenson
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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18
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Elucidation of the Genomic-Epigenomic Interaction Landscape of Aggressive Prostate Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6641429. [PMID: 33511206 PMCID: PMC7825361 DOI: 10.1155/2021/6641429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022]
Abstract
Background Majority of prostate cancer (PCa) deaths are attributed to localized high-grade aggressive tumours which progress rapidly to metastatic disease. A critical unmet need in clinical management of PCa is discovery and characterization of the molecular drivers of aggressive tumours. The development and progression of aggressive PCa involve genetic and epigenetic alterations occurring in the germline, somatic (tumour), and epigenomes. To date, interactions between genes containing germline, somatic, and epigenetic mutations in aggressive PCa have not been characterized. The objective of this investigation was to elucidate the genomic-epigenomic interaction landscape in aggressive PCa to identify potential drivers aggressive PCa and the pathways they control. We hypothesized that aggressive PCa originates from a complex interplay between genomic (both germline and somatic mutations) and epigenomic alterations. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect gene expression, molecular networks, and signaling pathways which in turn drive aggressive PCa. Methods We addressed these hypotheses by performing integrative data analysis combining information on germline mutations from genome-wide association studies with somatic and epigenetic mutations from The Cancer Genome Atlas using gene expression as the intermediate phenotype. Results The investigation revealed signatures of genes containing germline, somatic, and epigenetic mutations associated with aggressive PCa. Aberrant DNA methylation had effect on gene expression. In addition, the investigation revealed molecular networks and signalling pathways enriched for germline, somatic, and epigenetic mutations including the STAT3, PTEN, PCa, ATM, AR, and P53 signalling pathways implicated in aggressive PCa. Conclusions The study demonstrated that integrative analysis combining diverse omics data is a powerful approach for the discovery of potential clinically actionable biomarkers, therapeutic targets, and elucidation of oncogenic interactions between genomic and epigenomic alterations in aggressive PCa.
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19
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Prostate cancer reactivates developmental epigenomic programs during metastatic progression. Nat Genet 2020; 52:790-799. [PMID: 32690948 PMCID: PMC10007911 DOI: 10.1038/s41588-020-0664-8] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/16/2020] [Indexed: 02/06/2023]
Abstract
Epigenetic processes govern prostate cancer (PCa) biology, as evidenced by the dependency of PCa cells on the androgen receptor (AR), a prostate master transcription factor. We generated 268 epigenomic datasets spanning two state transitions-from normal prostate epithelium to localized PCa to metastases-in specimens derived from human tissue. We discovered that reprogrammed AR sites in metastatic PCa are not created de novo; rather, they are prepopulated by the transcription factors FOXA1 and HOXB13 in normal prostate epithelium. Reprogrammed regulatory elements commissioned in metastatic disease hijack latent developmental programs, accessing sites that are implicated in prostate organogenesis. Analysis of reactivated regulatory elements enabled the identification and functional validation of previously unknown metastasis-specific enhancers at HOXB13, FOXA1 and NKX3-1. Finally, we observed that prostate lineage-specific regulatory elements were strongly associated with PCa risk heritability and somatic mutation density. Examining prostate biology through an epigenomic lens is fundamental for understanding the mechanisms underlying tumor progression.
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20
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Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nat Genet 2020; 52:778-789. [PMID: 32661416 PMCID: PMC7454228 DOI: 10.1038/s41588-020-0648-8] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023]
Abstract
Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes only detectable with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hyper-methylation and somatic mutations in TET2, DNMT3B, IDH1, and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer and provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Denise Playdle
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Travis J Barnard
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adina M Bailey
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA
| | - Marc D Perry
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Ruhollah Moussavi-Baygi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - S Laura Chang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Division of Hematology/Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew B Rettig
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA.,Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Yvonne Kim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hui Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tanushree Shenoy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Nupam P Mahajan
- Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Surgery, Washington University, St. Louis, MO, USA
| | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.,Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA.,Department of Urologic Surgery, University of California Davis, Sacramento, CA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Housheng H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Arul M Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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21
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Frame FM, Maitland NJ. Epigenetic Control of Gene Expression in the Normal and Malignant Human Prostate: A Rapid Response Which Promotes Therapeutic Resistance. Int J Mol Sci 2019; 20:E2437. [PMID: 31108832 PMCID: PMC6566891 DOI: 10.3390/ijms20102437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
A successful prostate cancer must be capable of changing its phenotype in response to a variety of microenvironmental influences, such as adaptation to treatment or successful proliferation at a particular metastatic site. New cell phenotypes emerge by selection from the large, genotypically heterogeneous pool of candidate cells present within any tumor mass, including a distinct stem cell-like population. In such a multicellular model of human prostate cancer, flexible responses are primarily governed not only by de novo mutations but appear to be dominated by a combination of epigenetic controls, whose application results in treatment resistance and tumor relapse. Detailed studies of these individual cell populations have resulted in an epigenetic model for epithelial cell differentiation, which is also instructive in explaining the reported high and inevitable relapse rates of human prostate cancers to a multitude of treatment types.
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Affiliation(s)
- Fiona M Frame
- The Cancer Research Unit, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - Norman J Maitland
- The Cancer Research Unit, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
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22
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Yu YP, Liu P, Nelson J, Hamilton RL, Bhargava R, Michalopoulos G, Chen Q, Zhang J, Ma D, Pennathur A, Luketich J, Nalesnik M, Tseng G, Luo JH. Identification of recurrent fusion genes across multiple cancer types. Sci Rep 2019; 9:1074. [PMID: 30705370 PMCID: PMC6355770 DOI: 10.1038/s41598-019-38550-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/27/2018] [Indexed: 01/21/2023] Open
Abstract
Chromosome changes are one of the hallmarks of human malignancies. Chromosomal rearrangement is frequent in human cancers. One of the consequences of chromosomal rearrangement is gene fusions in the cancer genome. We have previously identified a panel of fusion genes in aggressive prostate cancers. In this study, we showed that 6 of these fusion genes are present in 7 different types of human malignancies with variable frequencies. Among them, the CCNH-C5orf30 and TRMT11-GRIK2 gene fusions were found in breast cancer, colon cancer, non-small cell lung cancer, esophageal adenocarcinoma, glioblastoma multiforme, ovarian cancer and liver cancer, with frequencies ranging from 12.9% to 85%. In contrast, four other gene fusions (mTOR-TP53BP1, TMEM135-CCDC67, KDM4-AC011523.2 and LRRC59-FLJ60017) are less frequent. Both TRMT11-GRIK2 and CCNH-C5orf30 are also frequently present in lymph node metastatic cancer samples from the breast, colon and ovary. Thus, detecting these fusion transcripts may have significant biological and clinical implications in cancer patient management.
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Affiliation(s)
- Yan-Ping Yu
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Peng Liu
- Departments of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Joel Nelson
- Departments of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Ronald L Hamilton
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Rohit Bhargava
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - George Michalopoulos
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Qi Chen
- Department of Pharmacology, Toxicology & Therapeutics, University of Kansas, Kansas City, KS, 66160, USA
| | - Jun Zhang
- Department of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Deqin Ma
- Department of Pathology, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Arjun Pennathur
- Departments of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - James Luketich
- Departments of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Michael Nalesnik
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - George Tseng
- Departments of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Jian-Hua Luo
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
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23
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Phenotype-independent DNA methylation changes in prostate cancer. Br J Cancer 2018; 119:1133-1143. [PMID: 30318509 PMCID: PMC6219500 DOI: 10.1038/s41416-018-0236-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 12/17/2022] Open
Abstract
Background Human prostate cancers display numerous DNA methylation changes compared to normal tissue samples. However, definitive identification of features related to the cells’ malignant status has been compromised by the predominance of cells with luminal features in prostate cancers. Methods We generated genome-wide DNA methylation profiles of cell subpopulations with basal or luminal features isolated from matched prostate cancer and normal tissue samples. Results Many frequent DNA methylation changes previously attributed to prostate cancers are here identified as differences between luminal and basal cells in both normal and cancer samples. We also identified changes unique to each of the two cancer subpopulations. Those specific to cancer luminal cells were associated with regulation of metabolic processes, cell proliferation and epithelial development. Within the prostate cancer TCGA dataset, these changes were able to distinguish not only cancers from normal samples, but also organ-confined cancers from those with extraprostatic extensions. Using changes present in both basal and luminal cancer cells, we derived a new 17-CpG prostate cancer signature with high predictive power in the TCGA dataset. Conclusions This study demonstrates the importance of comparing phenotypically matched prostate cell populations from normal and cancer tissues to unmask biologically and clinically relevant DNA methylation changes.
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24
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Takeda DY, Spisák S, Seo JH, Bell C, O'Connor E, Korthauer K, Ribli D, Csabai I, Solymosi N, Szállási Z, Stillman DR, Cejas P, Qiu X, Long HW, Tisza V, Nuzzo PV, Rohanizadegan M, Pomerantz MM, Hahn WC, Freedman ML. A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer. Cell 2018; 174:422-432.e13. [PMID: 29909987 PMCID: PMC6046260 DOI: 10.1016/j.cell.2018.05.037] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/11/2018] [Accepted: 05/16/2018] [Indexed: 12/26/2022]
Abstract
Increased androgen receptor (AR) activity drives therapeutic resistance in advanced prostate cancer. The most common resistance mechanism is amplification of this locus presumably targeting the AR gene. Here, we identify and characterize a somatically acquired AR enhancer located 650 kb centromeric to the AR. Systematic perturbation of this enhancer using genome editing decreased proliferation by suppressing AR levels. Insertion of an additional copy of this region sufficed to increase proliferation under low androgen conditions and to decrease sensitivity to enzalutamide. Epigenetic data generated in localized prostate tumors and benign specimens support the notion that this region is a developmental enhancer. Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.
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Affiliation(s)
- David Y Takeda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Keegan Korthauer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dezső Ribli
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest 1117, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest 1117, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, István str. 2, Budapest 1078, Hungary
| | - Zoltán Szállási
- Computational Health Informatics Program (CHIP) Boston Children's Hospital Harvard Medical School, Boston, MA 02215, USA; Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark; 2nd Department of Pathology, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest 1091, Hungary
| | - David R Stillman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Viktória Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Computational Health Informatics Program (CHIP) Boston Children's Hospital Harvard Medical School, Boston, MA 02215, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Internal Medicine, School of Medicine, University of Genoa, Genoa, Lgo R. Benzi 10, 16132, Italy
| | - Mersedeh Rohanizadegan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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25
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Chen ZH, Yu YP, Tao J, Liu S, Tseng G, Nalesnik M, Hamilton R, Bhargava R, Nelson JB, Pennathur A, Monga SP, Luketich JD, Michalopoulos GK, Luo JH. MAN2A1-FER Fusion Gene Is Expressed by Human Liver and Other Tumor Types and Has Oncogenic Activity in Mice. Gastroenterology 2017; 153:1120-1132.e15. [PMID: 28245430 PMCID: PMC5572118 DOI: 10.1053/j.gastro.2016.12.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/16/2016] [Accepted: 12/23/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Human tumors and liver cancer cell lines express the product of a fusion between the first 13 exons in the mannosidase α class 2A member 1 gene (MAN2A1) and the last 6 exons in the FER tyrosine kinase gene (FER), called MAN2A1-FER. We investigated whether MAN2A1-FER is expressed by human liver tumors and its role in liver carcinogenesis. METHODS We performed reverse transcription polymerase chain reaction analyses of 102 non-small cell lung tumors, 61 ovarian tumors, 70 liver tumors, 156 glioblastoma multiform samples, 27 esophageal adenocarcinomas, and 269 prostate cancer samples, as well as 10 nontumor liver tissues and 20 nontumor prostate tissues, collected at the University of Pittsburgh. We also measured expression by 15 human cancer cell lines. We expressed a tagged form of MAN2A1-FER in NIH3T3 and HEP3B (liver cancer) cells; Golgi were isolated for analysis. MAN2A1-FER was also overexpressed in PC3 or DU145 (prostate cancer), NIH3T3 (fibroblast), H23 (lung cancer), and A-172 (glioblastoma multiforme) cell lines and knocked out in HUH7 (liver cancer) cells. Cells were analyzed for proliferation and in invasion assays, and/or injected into flanks of severe combined immunodeficient mice; xenograft tumor growth and metastasis were assessed. Mice with hepatic deletion of PTEN were given tail-vein injections of MAN2A1-FER. RESULTS We detected MAN2A1-FER messenger RNA and fusion protein (114 kD) in the hepatocellular carcinoma cell line HUH7, as well as in liver tumors, esophageal adenocarcinoma, glioblastoma multiforme, prostate tumors, non-small cell lung tumors, and ovarian tumors, but not nontumor prostate or liver tissues. MAN2A1-FER protein retained the signal peptide for Golgi localization from MAN2A1 and translocated from the cytoplasm to Golgi in cancer cell lines. MAN2A1-FER had tyrosine kinase activity almost 4-fold higher than that of wild-type FER, and phosphorylated the epidermal growth factor receptor at tyrosine 88 in its N-terminus. Expression of MAN2A1-FER in 4 cell lines led to epidermal growth factor receptor activation of BRAF, MEK, and AKT; HUH7 cells with MAN2A1-FER knockout had significant decreases in phosphorylation of these proteins. Cell lines that expressed MAN2A1-FER had increased proliferation, colony formation, and invasiveness and formed larger (>2-fold) xenograft tumors in mice, with more metastases, than cells not expressing the fusion protein. HUH7 cells with MAN2A1-FER knockout formed smaller xenograft tumors, with fewer metastases, than control HUH7 cells. HUH7, A-172, and PC3 cells that expressed MAN2A1-FER were about 2-fold more sensitive to the FER kinase inhibitor crizotinib and the epidermal growth factor receptor kinase inhibitor canertinib; these drugs slowed growth of xenograft tumors from MAN2A1-FER cells and prevented their metastasis in mice. Hydrodynamic tail-vein injection of MAN2A1-FER resulted in rapid development of liver cancer in mice with hepatic disruption of Pten. CONCLUSIONS Many human tumor types and cancer cell lines express the MAN2A1-FER fusion, which increases proliferation and invasiveness of cancer cell lines and has liver oncogenic activity in mice.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Crizotinib
- Dose-Response Relationship, Drug
- Enzyme Activation
- ErbB Receptors/genetics
- ErbB Receptors/metabolism
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Neoplastic
- Gene Fusion
- Golgi Apparatus/enzymology
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Mice
- Mice, Knockout
- Mice, SCID
- Morpholines/pharmacology
- NIH 3T3 Cells
- Neoplasm Invasiveness
- Neoplasm Transplantation
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Oncogenes
- PTEN Phosphohydrolase/deficiency
- PTEN Phosphohydrolase/genetics
- Phosphorylation
- Protein Kinase Inhibitors/pharmacology
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- Pyrazoles/pharmacology
- Pyridines/pharmacology
- RNA Interference
- Time Factors
- Transfection
- Tumor Burden
- alpha-Mannosidase/antagonists & inhibitors
- alpha-Mannosidase/genetics
- alpha-Mannosidase/metabolism
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Affiliation(s)
- Zhang-Hui Chen
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yan P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Junyan Tao
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Silvia Liu
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Michael Nalesnik
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ronald Hamilton
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Rohit Bhargava
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joel B Nelson
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Arjun Pennathur
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Satdarshan P Monga
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - James D Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George K Michalopoulos
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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26
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Oncogenic activity of amplified miniature chromosome maintenance 8 in human malignancies. Oncogene 2017; 36:3629-3639. [PMID: 28481876 PMCID: PMC5481462 DOI: 10.1038/onc.2017.123] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 01/02/2023]
Abstract
Miniature chromosome maintenance (MCM) proteins play critical roles in DNA replication licensing, initiation and elongation. MCM8, one of the MCM proteins playing a critical role in DNA repairing and recombination, was found to have over-expression and increased DNA copy number in a variety of human malignancies. The gain of MCM8 is associated with aggressive clinical features of several human cancers. Increased expression of MCM8 in prostate cancer is associated with cancer recurrence. Forced expression of MCM8 in RWPE1 cells, the immortalized but non-transformed prostate epithelial cell line, exhibited fast cell growth and transformation, while knocked down of MCM8 in PC3, DU145 and LNCaP cells induced cell growth arrest, and decreased tumor volumes and mortality of severe combined immunodeficiency mice xenografted with PC3 and DU145 cells. MCM8 bound cyclin D1 and activated Rb protein phosphorylation by cyclin-dependent kinase 4 in vitro and in vivo. The cyclin D1/MCM8 interaction is required for Rb phosphorylation and S phase entry in cancer cells. As a result, our study showed that copy number increase and overexpression of MCM8 may play critical roles in human cancer development.
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27
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Targeting genomic rearrangements in tumor cells through Cas9-mediated insertion of a suicide gene. Nat Biotechnol 2017; 35:543-550. [PMID: 28459452 PMCID: PMC5462845 DOI: 10.1038/nbt.3843] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 03/08/2017] [Indexed: 11/08/2022]
Abstract
Specifically targeting genomic rearrangements and mutations in tumor cells remains an elusive goal in cancer therapy. Here, we used Cas9-based genome editing to introduce the gene encoding the prodrug-converting enzyme herpes simplex virus type 1 thymidine kinase (HSV1-tk) into the genomes of cancer cells carrying unique sequences resulting from genome rearrangements. Specifically, we targeted the breakpoints of TMEM135-CCDC67 and MAN2A1-FER fusions in human prostate cancer or hepatocellular carcinoma cells in vitro and in mouse xenografts. We designed one adenovirus to deliver the nickase Cas9D10A and guide RNAs targeting the breakpoint sequences, and another to deliver an EGFP-HSV1-tk construct flanked by sequences homologous to those surrounding the breakpoint. Infection with both viruses resulted in breakpoint-dependent expression of EGFP-tk and ganciclovir-mediated apoptosis. When mouse xenografts were treated with adenoviruses and ganciclovir, all animals showed decreased tumor burden and no mortality during the study. Thus, Cas9-mediated suicide-gene insertion may be a viable genotype-specific cancer therapy.
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28
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Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients. Sci Rep 2017; 7:40636. [PMID: 28084441 PMCID: PMC5233981 DOI: 10.1038/srep40636] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 12/09/2016] [Indexed: 12/26/2022] Open
Abstract
Prostate cancer (PC) diagnosis is based on histological evaluation of prostate needle biopsies, which have high false negative rates. Here, we investigated if cancer-associated epigenetic field effects in histologically normal prostate tissue may be used to increase sensitivity for PC. We focused on nine genes (AOX1, CCDC181 (C1orf114), GABRE, GAS6, HAPLN3, KLF8, MOB3B, SLC18A2, and GSTP1) known to be hypermethylated in PC. Using quantitative methylation-specific PCR, we analysed 66 malignant and 134 non-malignant tissue samples from 107 patients, who underwent ultrasound-guided prostate biopsy (67 patients had at least one cancer-positive biopsy, 40 had exclusively cancer-negative biopsies). Hypermethylation was detectable for all genes in malignant needle biopsy samples (AUC: 0.80 to 0.98), confirming previous findings in prostatectomy specimens. Furthermore, we identified a four-gene methylation signature (AOX1xGSTP1xHAPLN3xSLC18A2) that distinguished histologically non-malignant biopsies from patients with vs. without PC in other biopsies (AUC = 0.65; sensitivity = 30.8%; specificity = 100%). This signature was validated in an independent patient set (59 PC, 36 adjacent non-malignant, and 9 normal prostate tissue samples) analysed on Illumina 450 K methylation arrays (AUC = 0.70; sensitivity = 40.6%; specificity = 100%). Our results suggest that a novel four-gene signature may be used to increase sensitivity for PC diagnosis through detection of epigenetic field effects in histologically non-malignant prostate tissue samples.
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29
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Ma R, Feng N, Yu X, Lin H, Zhang X, Shi O, Zhang H, Zhang S, Li L, Zheng M, Gao M, Yu H, Qian B. Promoter methylation of Wnt/β-Catenin signal inhibitor TMEM88 is associated with unfavorable prognosis of non-small cell lung cancer. Cancer Biol Med 2017; 14:377-386. [PMID: 29372104 PMCID: PMC5765437 DOI: 10.20892/j.issn.2095-3941.2017.0061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Objective: Recent research has indicated that altered promoter methylation of oncogenes and tumor suppressor genes is an important mechanism in lung cancer development and progression. In this study, we investigated the association between promoter methylation of TMEM88, a possible inhibitor of the Wnt/β-Catenin signaling, and the survival of patients with non-small cell lung cancer (NSCLC). Methods: Twelve pairs of tumor and adjacent non-tumor samples were used for microarray analyses of DNA methylation and gene expression. For validation, more than two hundred additional samples were analyzed for methylation using bisulfite pyrosequencing and for gene expression using qRT-PCR. Then the cell function were tested by wound healing, transwell, CCK8 and cell cycle assay. Results: Our analysis of patient specimens showed that TMEM88 methylation was higher in NSCLC tumors (82.2% ± 10.3, P < 0.01) compared with the adjacent normal tissues (65.9% ± 7.2). The survival analysis revealed that patients with high TMEM88 methylation had a shorter overall survival (46 months) compared with patients with low TMEM88 methylation (>56 months;P=0.021). In addition, we found that demethylation treatment could inhibit tumor cell proliferation, migration, and invasion, which was supportive of an association between methylation and survival. Conclusions: Based on these consistent observations, we concluded that TMEM88 may play an important role in NSCLC progression and that promoter methylation of TMEM88 may serve as a biomarker for NSCLC prognosis and treatment.
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Affiliation(s)
- Rongna Ma
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Nannan Feng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao Yu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hongyan Lin
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaohong Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Oumin Shi
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huan Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shuo Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lei Li
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Min Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ming Gao
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Herbert Yu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Biyun Qian
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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30
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Analysis of Microarray Data on Gene Expression and Methylation to Identify Long Non-coding RNAs in Non-small Cell Lung Cancer. Sci Rep 2016; 6:37233. [PMID: 27849024 PMCID: PMC5110979 DOI: 10.1038/srep37233] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/26/2016] [Indexed: 12/28/2022] Open
Abstract
To identify what long non-coding RNAs (lncRNAs) are involved in non-small cell lung cancer (NSCLC), we analyzed microarray data on gene expression and methylation. Gene expression chip and HumanMethylation450BeadChip were used to interrogate genome-wide expression and methylation in tumor samples. Differential expression and methylation were analyzed through comparing tumors with adjacent non-tumor tissues. LncRNAs expressed differentially and correlated with coding genes and DNA methylation were validated in additional tumor samples using RT-qPCR and pyrosequencing. In vitro experiments were performed to evaluate lncRNA’s effects on tumor cells. We identified 8,500 lncRNAs expressed differentially between tumor and non-tumor tissues, of which 1,504 were correlated with mRNA expression. Two of the lncRNAs, LOC146880 and ENST00000439577, were positively correlated with expression of two cancer-related genes, KPNA2 and RCC2, respectively. High expression of LOC146880 and ENST00000439577 were also associated with poor survival. Analysis of lncRNA expression in relation to DNA methylation showed that LOC146880 expression was down-regulated by DNA methylation in its promoter. Lowering the expression of LOC146880 or ENST00000439577 in tumor cells could inhibit cell proliferation, invasion and migration. Analysis of microarray data on gene expression and methylation allows us to identify two lncRNAs, LOC146880 and ENST00000439577, which may promote the progression of NSCLC.
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Zuo ZH, Yu YP, Martin A, Luo JH. Cellular stress response 1 down-regulates the expression of epidermal growth factor receptor and platelet-derived growth factor receptor through inactivation of splicing factor 3A3. Mol Carcinog 2016; 56:315-324. [PMID: 27148859 DOI: 10.1002/mc.22494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/19/2016] [Accepted: 04/13/2016] [Indexed: 12/19/2022]
Abstract
Cellular stress response 1 (CSR1) is a tumor suppressor gene that plays an important role in regulating cell death. In this report, we show that the N-terminus of CSR1 interacts with splicing factor 3A, subunit 3 (SF3A3). The SF3A3 binding motif was identified in the region of amino acids 62-91 of CSR1 through cell-free binding analyses. The interaction between CSR1 and SF3A3 led to migration of SF3A3 from nucleus to cytoplasm. The cytoplasmic redistribution of SF3A3 significantly reduced the splicing efficiency of epidermal growth factor receptor and platelet-derived growth factor receptor. Induction of CSR1 or down-regulation of SF3A3 also significantly reduced the splicing activity of oxytocin reporter gene both in vivo and in vitro. Mutant CSR1 that lacks the SF3A3 binding motif contained no RNA splicing regulatory activity, while the peptide corresponding to the SF3A3 binding motif in CSR1 interfered with the wild-type CSR1 mediated inhibition of RNA splicing. Interaction of CSR1 and SF3A3 is essential for CSR1 mediated cell death. To our knowledge, this is the first report demonstrating that RNA splicing is negatively regulated by redistribution of a splicing factor. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ze-Hua Zuo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yan P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Amantha Martin
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Yu YP, Ding Y, Chen Z, Liu S, Michalopoulos A, Chen R, Gulzar ZG, Yang B, Cieply KM, Luvison A, Ren BG, Brooks JD, Jarrard D, Nelson JB, Michalopoulos GK, Tseng GC, Luo JH. Novel fusion transcripts associate with progressive prostate cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 184:2840-9. [PMID: 25238935 DOI: 10.1016/j.ajpath.2014.06.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 12/21/2022]
Abstract
The mechanisms underlying the potential for aggressive behavior of prostate cancer (PCa) remain elusive. In this study, whole genome and/or transcriptome sequencing was performed on 19 specimens of PCa, matched adjacent benign prostate tissues, matched blood specimens, and organ donor prostates. A set of novel fusion transcripts was discovered in PCa. Eight of these fusion transcripts were validated through multiple approaches. The occurrence of these fusion transcripts was then analyzed in 289 prostate samples from three institutes, with clinical follow-up ranging from 1 to 15 years. The analyses indicated that most patients [69 (91%) of 76] positive for any of these fusion transcripts (TRMT11-GRIK2, SLC45A2-AMACR, MTOR-TP53BP1, LRRC59-FLJ60017, TMEM135-CCDC67, KDM4-AC011523.2, MAN2A1-FER, and CCNH-C5orf30) experienced PCa recurrence, metastases, and/or PCa-specific death after radical prostatectomy. These outcomes occurred in only 37% (58/157) of patients without carrying those fusion transcripts. Three fusion transcripts occurred exclusively in PCa samples from patients who experienced recurrence or PCaerelated death. The formation of these fusion transcripts may be the result of genome recombination. A combination of these fusion transcripts in PCa with Gleason's grading or with nomogram significantly improves the prediction rate of PCa recurrence. Our analyses suggest that formation of these fusion transcripts may underlie the aggressive behavior of PCa.
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Bhasin JM, Lee BH, Matkin L, Taylor MG, Hu B, Xu Y, Magi-Galluzzi C, Klein EA, Ting AH. Methylome-wide Sequencing Detects DNA Hypermethylation Distinguishing Indolent from Aggressive Prostate Cancer. Cell Rep 2015; 13:2135-46. [PMID: 26628371 DOI: 10.1016/j.celrep.2015.10.078] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 09/10/2015] [Accepted: 10/28/2015] [Indexed: 01/12/2023] Open
Abstract
A critical need in understanding the biology of prostate cancer is characterizing the molecular differences between indolent and aggressive cases. Because DNA methylation can capture the regulatory state of tumors, we analyzed differential methylation patterns genome-wide among benign prostatic tissue and low-grade and high-grade prostate cancer and found extensive, focal hypermethylation regions unique to high-grade disease. These hypermethylation regions occurred not only in the promoters of genes but also in gene bodies and at intergenic regions that are enriched for DNA-protein binding sites. Integration with existing RNA-sequencing (RNA-seq) and survival data revealed regions where DNA methylation correlates with reduced gene expression associated with poor outcome. Regions specific to aggressive disease are proximal to genes with distinct functions from regions shared by indolent and aggressive disease. Our compendium of methylation changes reveals crucial molecular distinctions between indolent and aggressive prostate cancer.
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Affiliation(s)
- Jeffrey M Bhasin
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Byron H Lee
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Lars Matkin
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Margaret G Taylor
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bo Hu
- Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Cristina Magi-Galluzzi
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Angela H Ting
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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Ngollo M, Dagdemir A, Karsli-Ceppioglu S, Judes G, Pajon A, Penault-Llorca F, Boiteux JP, Bignon YJ, Guy L, Bernard-Gallon DJ. Epigenetic modifications in prostate cancer. Epigenomics 2015; 6:415-26. [PMID: 25333850 DOI: 10.2217/epi.14.34] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer is the most common cancer in men and the second leading cause of cancer deaths in men in France. Apart from the genetic alterations in prostate cancer, epigenetics modifications are involved in the development and progression of this disease. Epigenetic events are the main cause in gene regulation and the three most epigenetic mechanisms studied include DNA methylation, histone modifications and microRNA expression. In this review, we summarized epigenetic mechanisms in prostate cancer. Epigenetic drugs that inhibit DNA methylation, histone methylation and histone acetylation might be able to reactivate silenced gene expression in prostate cancer. However, further understanding of interactions of these enzymes and their effects on transcription regulation in prostate cancer is needed and has become a priority in biomedical research. In this study, we summed up epigenetic changes with emphasis on pharmacologic epigenetic target agents.
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Affiliation(s)
- Marjolaine Ngollo
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand, France
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Luo JH, Liu S, Zuo ZH, Chen R, Tseng GC, Yu YP. Discovery and Classification of Fusion Transcripts in Prostate Cancer and Normal Prostate Tissue. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:1834-45. [PMID: 25963990 DOI: 10.1016/j.ajpath.2015.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/03/2015] [Accepted: 03/12/2015] [Indexed: 12/20/2022]
Abstract
Fusion transcript formation is one of the fundamental mechanisms that drives the development of prostate cancer. Because of the advance of high-throughput parallel sequencing, many fusion transcripts have been discovered. However, the discovery rate of fusion transcripts specific for prostate cancer is lagging behind the discoveries made on chromosome abnormalities of prostate cancer. Recent analyses suggest that many fusion transcripts are present in both benign and cancerous tissues. Some of these fusion transcripts likely represent important components of normal gene expression in cells. It is necessary to identify the criteria and features of fusion transcripts that are specific for cancer. In this review, we discuss optimization of RNA sequencing depth for fusion transcript discovery and the characteristics of fusion transcripts in normal prostate tissues and prostate cancer. We also propose a new classification of cancer-specific fusion transcripts on the basis of their tail gene fusion protein product and the roles that these fusions may play in cancer development.
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Affiliation(s)
- Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
| | - Silvia Liu
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ze-Hua Zuo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Rui Chen
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yan P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Zuo ZH, Yu YP, Ding Y, Liu S, Martin A, Tseng G, Luo JH. Oncogenic Activity of miR-650 in Prostate Cancer Is Mediated by Suppression of CSR1 Expression. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:1991-9. [PMID: 25956032 DOI: 10.1016/j.ajpath.2015.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 03/05/2015] [Accepted: 03/17/2015] [Indexed: 02/07/2023]
Abstract
Cellular stress response 1 (CSR1) is a tumor suppressor gene whose expression was frequently down-regulated in prostate cancer. The mechanism of its down-regulation, however, is not clear. Here, we show that the 3' untranslated region of CSR1 contains a target site of miR-650. High level of miR-650 was found in prostate cancer samples and cell lines. Degradation of miR-650 by specific inhibitor dramatically increased the expression levels of CSR1. Interaction between miR-650 and its target site in the 3' untranslated region was validated through luciferase reporter system. Mutation at the target site completely abrogated the activity of miR-650 on the 3' untranslated region of CSR1. Inhibition of miR-650 reversed the expression suppression of CSR1, suppressed colony formation, and blocked cell cycle entry to the S phase of both PC3 and DU145 cells. Animal model showed significant decrease of tumor volume, rate of metastasis, and mortality of severe combined immunodeficient mice xenografted with PC3 or DU145 cells transformed with inhibitor of miR-650. Our analyses demonstrate that suppression of CSR1 expression is a novel mechanism critical for the oncogenic activity of miR-650.
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Affiliation(s)
- Ze-Hua Zuo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yan P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Silvia Liu
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Amantha Martin
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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Karsli-Ceppioglu S, Ngollo M, Adjakly M, Dagdemir A, Judes G, Lebert A, Boiteux JP, Penault-LLorca F, Bignon YJ, Guy L, Bernard-Gallon D. Genome-wide DNA methylation modified by soy phytoestrogens: role for epigenetic therapeutics in prostate cancer? OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:209-19. [PMID: 25831061 DOI: 10.1089/omi.2014.0142] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In prostate cancer, DNA methylation is significantly associated with tumor initiation, progression, and metastasis. Previous studies have suggested that soy phytoestrogens might regulate DNA methylation at individual candidate gene loci and that they play a crucial role as potential therapeutic agents for prostate cancer. The purpose of our study was to examine the modulation effects of phytoestrogens on a genome-wide scale in regards to DNA methylation in prostate cancer. Prostate cancer cell lines DU-145 and LNCaP were treated with 40 μM of genistein and 110 μM of daidzein. DNMT inhibitor 5-azacytidine (2 μM) and the methylating agent budesonide (2 μM) were used to compare their demethylation/methylation effects with phytoestrogens. The regulatory effects of phytoestrogens on DNA methylation were analyzed by using a methyl-DNA immunoprecipitation method coupled with Human DNA Methylation Microarrays (MeDIP-chip). We observed that the methylation profiles of 58 genes were altered by genistein and daidzein treatments in DU-145 and LNCaP prostate cancer cells. In addition, the methylation frequencies of the MAD1L1, TRAF7, KDM4B, and hTERT genes were remarkably modified by genistein treatment. Our results suggest that the modulation effects of phytoestrogens on DNA methylation essentially lead to inhibition of cell growth and induction of apoptosis. Genome-wide methylation profiling reported here suggests that epigenetic regulation mechanisms and, by extension, epigenetics-driven novel therapeutic candidates warrant further consideration in future "omics" studies of prostate cancer.
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Affiliation(s)
- Seher Karsli-Ceppioglu
- 1 Department of Oncogenetics, Centre Jean Perrin-CBRV , Dunant, Clermont-Ferrand, France
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Liang YX, Mo RJ, He HC, Chen JH, Zou J, Han ZD, Lu JM, Cai C, Zeng YR, Zhong WD, Wu CL. Aberrant hypomethylation-mediated CD147 overexpression promotes aggressive tumor progression in human prostate cancer. Oncol Rep 2015; 33:2648-54. [PMID: 25813864 DOI: 10.3892/or.2015.3870] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/05/2015] [Indexed: 12/31/2022] Open
Abstract
Our previous study revealed the potential role of CD147 in human prostate cancer (PCa). Here, we investigated the CD147 promoter methylation status and the correlation with tumorigenicity in human PCa. CD147 mRNA and protein expression levels were both significantly higher in the 4 PCa cell lines, than in the 2 non-tumorigenic benign human prostatic epithelial cell lines (all P<0.01). We showed hypomethylation of promoter regions of CD147 in PCa cell lines with significant CD147 expression as compared to non-tumorigenic benign human prostatic epithelial cell lines slowly expressing CD147. Additionally, the treatment of methylated cell lines with 5-aza-2'-deoxycytidine increased CD147 expression significantly in low-expressing cell lines and also activated the expression of matrix metalloproteinase (MMP)-2, which may be one of the most important downstream targets of CD147. Furthermore, PCa tissues displayed decreased DNA methylation in the promoter region of CD147 compared to the corresponding non-cancerous prostate tissues, and methylation intensity correlated inversely with the CD147 mRNA levels. There was a significant negative correlation between CD147 mRNA levels and the number of methylated sites in PCa tissues (r=-0.467, P<0.01). In conclusion, our data offer convincing evidence for the first time that the DNA promoter hypomethylation of CD147 may be one of the regulatory mechanisms involved in the cancer-related overexpression of CD147 and may play a crucial role in the tumorigenesis of PCa.
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Affiliation(s)
- Yu-Xiang Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Ru-Jun Mo
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Hui-Chan He
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Jia-Hong Chen
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Jun Zou
- Department of Urology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Zhao-Dong Han
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Jian-Ming Lu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Chao Cai
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Yan-Ru Zeng
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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Lin IH, Chen DT, Chang YF, Lee YL, Su CH, Cheng C, Tsai YC, Ng SC, Chen HT, Lee MC, Chen HW, Suen SH, Chen YC, Liu TT, Chang CH, Hsu MT. Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes. PLoS One 2015; 10:e0118453. [PMID: 25706888 PMCID: PMC4338251 DOI: 10.1371/journal.pone.0118453] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 01/20/2015] [Indexed: 01/18/2023] Open
Abstract
Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.
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Affiliation(s)
- I-Hsuan Lin
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Dow-Tien Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Feng Chang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Ling Lee
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Hsin Su
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Ching Cheng
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chien Tsai
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Swee-Chuan Ng
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Hsiao-Tan Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Mei-Chen Lee
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Hong-Wei Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Hui Suen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Cheng Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Tze-Tze Liu
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Chuan-Hsiung Chang
- Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Ta Hsu
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
- * E-mail:
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Abstract
Cytosine methylation in DNA constitutes an important epigenetic layer of transcriptional and regulatory control in many eukaryotes. Profiling DNA methylation across the genome is critical to understanding the influence of epigenetics in normal biology and disease, such as cancer. Genome-wide analyses such as arrays and next-generation sequencing (NGS) technologies have been used to assess large fractions of the methylome at a single-base-pair resolution. However, the range of DNA methylation profiling techniques can make selecting the appropriate protocol a challenge. This chapter discusses the advantages and disadvantages of various methylome detection approaches to assess which is appropriate for the question at hand. Here, we focus on four prominent genome-wide approaches: whole-genome bisulfite sequencing (WGBS); methyl-binding domain capture sequencing (MBDCap-Seq); reduced-representation-bisulfite-sequencing (RRBS); and Infinium Methylation450 BeadChips (450 K, Illumina). We discuss some of the requirements, merits, and challenges that should be considered when choosing a methylome technology to ensure that it will be informative. In addition, we show how genome-wide methylation detection arrays and high-throughput sequencing have provided immense insight into ovarian cancer-specific methylation signatures that may serve as diagnostic biomarkers or predict patient response to epigenetic therapy.
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Prognostic DNA methylation markers for prostate cancer. Int J Mol Sci 2014; 15:16544-76. [PMID: 25238417 PMCID: PMC4200823 DOI: 10.3390/ijms150916544] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC.
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Wang L, Xie PG, Lin YL, Ma JG, Li WP. Aberrant methylation of PCDH10 predicts worse biochemical recurrence-free survival in patients with prostate cancer after radical prostatectomy. Med Sci Monit 2014; 20:1363-8. [PMID: 25086586 PMCID: PMC4136935 DOI: 10.12659/msm.891241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Prostate cancer is a common malignancy in men, and inevitably some patients experience biochemical recurrence after radical prostatectomy. To date, there are no reliable predictors for prostate cancer recurrence, and novel predictors are urgently needed. PCDH10 (protocadherin-10) is a novel tumor suppressor gene, which is down-regulated by promoter methylation in prostate cancer. The aim of this study was to evaluate the feasibility of using PCDH10 methylation to predict the biochemical recurrence (BCR) of prostate cancer after radical prostatectomy. Material/Methods Fresh tissue samples were obtained from 151 patients with primary prostate cancer, and from 34 patients with benign prostatic hyperplasia (BPH) as control. The methylation status of PCDH10 in prostate cancer tissues and controls were examined using methylation-specific PCR (MSP), and then associated with clinicopathological features and BCR-free survival of patients with prostate cancer. Results We found that PCDH10 methylation was detected in 79 (52.3%) patients with prostate cancer, but no methylation was found in controls (P<0.0001). Moreover, PCDH10 methylation was significantly associated with higher preoperative prostate-specific antigen (PSA) level (P <0.0001), higher Gleason Score (P<0.0001), advanced clinical stage (P=0.0002), lymph node metastasis (P=0.0389), angiolymphatic invasion (P=0.0303), and biochemical recurrence (P=0.0068). Moreover, PCDH10 methylation was associated with poor BCR-free survival (P<0.0001), and may be used as an independent predictor of BCR-free survival (P=0.0046). Conclusions Our results indicate that PCDH10 methylation in prostate cancer tissue is an independent prognostic biomarker of worse BCR-free survival of patients with prostate cancer after radical prostatectomy.
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Affiliation(s)
- Li Wang
- Department of Urology, Affiliated Hospital, Hebei University of Engineering, Handan, Chile
| | - Pei-Gen Xie
- Department of Spine Surgery, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China (mainland)
| | - Ying-Li Lin
- Department of Urology, Xuzhou Tumor Hospital (Affiliated Xuzhou Hospital of Jiangsu University), Xuzhou, China (mainland)
| | - Jian-Guo Ma
- Department of Urology, Third Hospital, Hebei Medical University, Shijiazhuang, China (mainland)
| | - Wen-Ping Li
- Department of Urology, Third Hospital, Hebei Medical University, Shijiazhuang, China (mainland)
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Naeem H, Wong NC, Chatterton Z, Hong MKH, Pedersen JS, Corcoran NM, Hovens CM, Macintyre G. Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array. BMC Genomics 2014; 15:51. [PMID: 24447442 PMCID: PMC3943510 DOI: 10.1186/1471-2164-15-51] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 01/15/2014] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The Illumina HumanMethylation450 BeadChip (HM450K) measures the DNA methylation of 485,512 CpGs in the human genome. The technology relies on hybridization of genomic fragments to probes on the chip. However, certain genomic factors may compromise the ability to measure methylation using the array such as single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), repetitive DNA, and regions with reduced genomic complexity. Currently, there is no clear method or pipeline for determining which of the probes on the HM450K bead array should be retained for subsequent analysis in light of these issues. RESULTS We comprehensively assessed the effects of SNPs, INDELs, repeats and bisulfite induced reduced genomic complexity by comparing HM450K bead array results with whole genome bisulfite sequencing. We determined which CpG probes provided accurate or noisy signals. From this, we derived a set of high-quality probes that provide unadulterated measurements of DNA methylation. CONCLUSIONS Our method significantly reduces the risk of false discoveries when using the HM450K bead array, while maximising the power of the array to detect methylation status genome-wide. Additionally, we demonstrate the utility of our method through extraction of biologically relevant epigenetic changes in prostate cancer.
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Affiliation(s)
- Haroon Naeem
- />NICTA Victoria Research Laboratory, Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, Victoria 3010 Australia
- />Department of Computing and Information Systems, Melbourne School of Engineering, The University of Melbourne, Melbourne, Victoria 3010 Australia
| | - Nicholas C Wong
- />Cancer, Disease and Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children’s Hospital, Department of Paediatrics, The University of Melbourne, Melbourne, Australia
- />Ludwig Institute of Cancer Research, Olivia Newton John Cancer and Wellness Centre, Austin Hospital, Heidelberg, Victoria Australia
| | - Zac Chatterton
- />Cancer, Disease and Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children’s Hospital, Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Matthew K H Hong
- />Australian Prostate Cancer Research Centre Epworth, Richmond, Australia and Division of Urology, Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, Australia
| | - John S Pedersen
- />TissuPath Specialist Pathology, Mount Waverley, Victoria 3149, Melbourne, Australia
- />Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, 3800 Australia
| | - Niall M Corcoran
- />Australian Prostate Cancer Research Centre Epworth, Richmond, Australia and Division of Urology, Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, Australia
| | - Christopher M Hovens
- />Australian Prostate Cancer Research Centre Epworth, Richmond, Australia and Division of Urology, Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, Australia
| | - Geoff Macintyre
- />NICTA Victoria Research Laboratory, Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, Victoria 3010 Australia
- />Department of Computing and Information Systems, Melbourne School of Engineering, The University of Melbourne, Melbourne, Victoria 3010 Australia
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