1
|
Wani SA, Hussain S, Gray JS, Nayak D, Tang H, Perez LM, Long MD, Siddappa M, McCabe CJ, Sucheston-Campbell LE, Freeman MR, Campbell MJ. Epigenetic disruption of the RARγ complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.15.571947. [PMID: 38168185 PMCID: PMC10760102 DOI: 10.1101/2023.12.15.571947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The current study in prostate cancer (PCa) focused on the genomic mechanisms at the cross-roads of pro-differentiation signals and the emergence of lineage plasticity. We explored an understudied cistromic mechanism involving RARγ's ability to govern AR cistrome-transcriptome relationships, including those associated with more aggressive PCa features. The RARγ complex in PCa cell models was enriched for canonical cofactors, as well as proteins involved in RNA processing and bookmarking. Identifying the repertoire of miR-96 bound and regulated gene targets, including those recognition elements marked by m6A, revealed their significant enrichment in the RARγ complex. RARγ significantly enhanced the AR cistrome, particularly in active enhancers and super-enhancers, and overlapped with the binding of bookmarking factors. Furthermore, RARγ expression led to nucleosome-free chromatin enriched with H3K27ac, and significantly enhanced the AR cistrome in G2/M cells. RARγ functions also antagonized the transcriptional actions of the lineage master regulator ONECUT2. Similarly, gene programs regulated by either miR-96 or antagonized by RARγ were enriched in alternative lineages and more aggressive PCa phenotypes. Together these findings reveal an under-investigated role for RARγ, modulated by miR-96, to bookmark enhancer sites during mitosis. These sites are required by the AR to promote transcriptional competence, and emphasize luminal differentiation, while antagonizing ONECUT2.
Collapse
Affiliation(s)
- Sajad A Wani
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Shahid Hussain
- Division of Cancer Biology, Cedars Sinai Cancer, and Los Angeles, CA 90048
- Board of Governors Innovation Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Jaimie S Gray
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Debasis Nayak
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Hancong Tang
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Lillian M Perez
- Division of Cancer Therapeutics, Cedars Sinai Cancer, Departments of Urology and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Mark D Long
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263
| | - Manjunath Siddappa
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Christopher J McCabe
- Institute of Metabolism and Systems Research (IMSR), and Centre of Endocrinology, Diabetes and Metabolism (CEDAM), University of Birmingham, Birmingham, UK
| | | | - Michael R Freeman
- Division of Cancer Therapeutics, Cedars Sinai Cancer, Departments of Urology and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Moray J Campbell
- Division of Cancer Biology, Cedars Sinai Cancer, and Los Angeles, CA 90048
- Board of Governors Innovation Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| |
Collapse
|
2
|
Crumbaker M, Goldstein LD, Murray DH, Tao J, Pathmanandavel S, Boulter N, Ratnayake L, Joshua AM, Kummerfeld S, Emmett L. Circulating Tumour DNA Biomarkers Associated with Outcomes in Metastatic Prostate Cancer Treated with Lutetium-177-PSMA-617. EUR UROL SUPPL 2023; 57:30-36. [PMID: 38020530 PMCID: PMC10658415 DOI: 10.1016/j.euros.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2023] [Indexed: 12/01/2023] Open
Abstract
Background Lutetium-177-prostate-specific membrane antigen- 617 (Lu-PSMA) is an effective therapy for metastatic castration-resistant prostate cancer (mCRPC). However, treatment responses are heterogeneous despite stringent positron emission tomography (PET)-based imaging selection criteria. Molecularly based biomarkers have potential to refine patient selection and optimise outcomes. Objective To identify circulating tumour DNA (ctDNA) features associated with treatment outcomes for men treated with Lu-PSMA. Design setting and participants ctDNA from men treated with Lu-PSMA in combination with idronoxil for progressive mCRPC were analysed using an 85-gene customised sequencing assay. ctDNA fractions, molecular profiles, and the presence of alterations in aggressive-variant prostate cancer (AVPC) genes were analysed at baseline, cycle 3 and at disease progression. Intervention Men received Lu-PSMA with idronoxil every 6 wk for up to six cycles. Outcome measurements and statistical analysis Baseline and exit PSMA and fluorodeoxyglucose PET/computed tomography (CT) imaging was conducted at baseline and study exit. Single-photon emission CT (SPECT) scans were performed 24 h after Lu-PSMA. Blood samples were collected at baseline,cycle 3 and at disease progression. Cox proportional-hazards models were used to assess associations and derive hazard ratios (HRs) and confidence intervals (CIs) for associations between molecular factors, imaging features, and clinical outcomes. Results and limitations Sixty samples from 32 men were sequenced (32 at baseline, 24 at cycle 3, four from patients with disease progression); two samples (baseline, on-treatment) from one individual were excluded from analysis owing to poor quality of the baseline sequencing data. Alterations in AVPC genes were associated with shorter prostate-specific antigen (PSA) progression-free survival (PFS) and overall survival (OS) in univariate (HR 3.4, 95% CI 1.5-7.7; p = 0.0036; and HR 3.3, 95% CI 1.4-7.7; p = 0.0063, respectively) and multivariate analyses (HR 4.8, 95% CI 1.8-13; p = 0.0014; and HR 4.1, 95% CI 1.6-11; p = 0.004). Conclusions ctDNA alterations in AVPC genes were associated with shorter PSA PFS and OS among men treated with Lu-PSMA and intermittent idronoxil. These candidate molecular biomarkers warrant further study to determine whether they have predictive value and potential to guide synergistic combination strategies to enhance outcomes for men treated with Lu-PSMA for mCRPC. Patient summary Certain DNA/gene changes detected in the blood of men with advanced prostate cancer were associated with shorter benefit from lutetium PSMA, a targeted radioactive therapy. This information may be useful in determining which men may benefit most from this treatment, but additional research is needed.
Collapse
Affiliation(s)
- Megan Crumbaker
- The Kinghorn Cancer Centre, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
- St. Vincent’s Clinical School, University of New South Wales, Kensington, Australia
- Garvan Institute of Medical Research, Darlinghurst, Australia
- Department of Theranostics and Nuclear Medicine, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
| | - Leonard D. Goldstein
- St. Vincent’s Clinical School, University of New South Wales, Kensington, Australia
- Garvan Institute of Medical Research, Darlinghurst, Australia
| | - David H. Murray
- Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Jiang Tao
- Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Sarennya Pathmanandavel
- St. Vincent’s Clinical School, University of New South Wales, Kensington, Australia
- Department of Theranostics and Nuclear Medicine, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
| | - Nicky Boulter
- Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Lalith Ratnayake
- The Kinghorn Cancer Centre, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
| | - Anthony M. Joshua
- The Kinghorn Cancer Centre, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
- St. Vincent’s Clinical School, University of New South Wales, Kensington, Australia
- Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Sarah Kummerfeld
- St. Vincent’s Clinical School, University of New South Wales, Kensington, Australia
- Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Louise Emmett
- St. Vincent’s Clinical School, University of New South Wales, Kensington, Australia
- Garvan Institute of Medical Research, Darlinghurst, Australia
- Department of Theranostics and Nuclear Medicine, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
| |
Collapse
|
3
|
Jafari H, Hussain S, Campbell MJ. Nuclear Receptor Coregulators in Hormone-Dependent Cancers. Cancers (Basel) 2022; 14:2402. [PMID: 35626007 PMCID: PMC9139824 DOI: 10.3390/cancers14102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 12/10/2022] Open
Abstract
Nuclear receptors (NRs) function collectively as a transcriptional signaling network that mediates gene regulatory actions to either maintain cellular homeostasis in response to hormonal, dietary and other environmental factors, or act as orphan receptors with no known ligand. NR complexes are large and interact with multiple protein partners, collectively termed coregulators. Coregulators are essential for regulating NR activity and can dictate whether a target gene is activated or repressed by a variety of mechanisms including the regulation of chromatin accessibility. Altered expression of coregulators contributes to a variety of hormone-dependent cancers including breast and prostate cancers. Therefore, understanding the mechanisms by which coregulators interact with and modulate the activity of NRs provides opportunities to develop better prognostic and diagnostic approaches, as well as novel therapeutic targets. This review aims to gather and summarize recent studies, techniques and bioinformatics methods used to identify distorted NR coregulator interactions that contribute as cancer drivers in hormone-dependent cancers.
Collapse
Affiliation(s)
- Hedieh Jafari
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA;
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Shahid Hussain
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Moray J. Campbell
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| |
Collapse
|
4
|
Epigenetic Coregulation of Androgen Receptor Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:277-293. [DOI: 10.1007/978-3-031-11836-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
5
|
Lei H, Wang Z, Jiang D, Liu F, Liu M, Lei X, Yang Y, He B, Yan M, Huang H, Liu Q, Pang J. CRISPR screening identifies CDK12 as a conservative vulnerability of prostate cancer. Cell Death Dis 2021; 12:740. [PMID: 34315855 PMCID: PMC8316367 DOI: 10.1038/s41419-021-04027-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022]
Abstract
Androgen receptor (AR) signaling inhibitors provide limited survival benefits to patients with prostate cancer (PCa), and worse, few feasible genomic lesions restrict targeted treatment to PCa. Thus, a better understanding of the critical dependencies of PCa may enable more feasible therapeutic approaches to the dilemma. We performed a kinome-scale CRISPR/Cas9 screen and identified cyclin-dependent kinase 12 (CDK12) as being conservatively required for PCa cell survival. Suppression of CDK12 by the covalent inhibitor THZ531 led to an obvious anti-PCa effect. Mechanistically, THZ531 downregulated AR signaling and preferentially repressed a distinct class of CDK12 inhibition-sensitive transcripts (CDK12-ISTs), including prostate lineage-specific genes, and contributed to cellular survival processes. Integration of the super-enhancer (SE) landscape and CDK12-ISTs indicated a group of potential PCa oncogenes, further conferring the sensitivity of PCa cells to CDK12 inhibition. Importantly, THZ531 strikingly synergized with multiple AR antagonists. The synergistic effect may be driven by attenuated H3K27ac signaling on AR targets and an intensive SE-associated apoptosis pathway. In conclusion, we highlight the validity of CDK12 as a druggable target in PCa. The synergy of THZ531 and AR antagonists suggests a potential combination therapy for PCa.
Collapse
Affiliation(s)
- Hanqi Lei
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Department of Urology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zifeng Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Donggen Jiang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Fang Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Meiling Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xinxing Lei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yafei Yang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Bin He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Min Yan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hai Huang
- Department of Urology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Quentin Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Jun Pang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.
| |
Collapse
|
6
|
Mondal D, Narwani D, Notta S, Ghaffar D, Mardhekar N, Quadri SSA. Oxidative stress and redox signaling in CRPC progression: therapeutic potential of clinically-tested Nrf2-activators. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2021; 4:96-124. [PMID: 35582006 PMCID: PMC9019181 DOI: 10.20517/cdr.2020.71] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022]
Abstract
Androgen deprivation therapy (ADT) is the mainstay regimen in patients with androgen-dependent prostate cancer (PCa). However, the selection of androgen-independent cancer cells leads to castrate resistant prostate cancer (CRPC). The aggressive phenotype of CRPC cells underscores the need to elucidate mechanisms and therapeutic strategies to suppress CRPC outgrowth. Despite ADT, the activation of androgen receptor (AR) transcription factor continues via crosstalk with parallel signaling pathways. Understanding of how these signaling cascades are initiated and amplified post-ADT is lacking. Hormone deprivation can increase oxidative stress and the resultant reactive oxygen species (ROS) may activate both AR and non-AR signaling. Moreover, ROS-induced inflammatory cytokines may further amplify these redox signaling pathways to augment AR function. However, clinical trials using ROS quenching small molecule antioxidants have not suppressed CRPC progression, suggesting that more potent and persistent suppression of redox signaling in CRPC cells will be needed. The transcription factor Nrf2 increases the expression of numerous antioxidant enzymes and downregulates the function of inflammatory transcription factors, e.g., nuclear factor kappa B. We documented that Nrf2 overexpression can suppress AR-mediated transcription in CRPC cell lines. Furthermore, two Nrf2 activating agents, sulforaphane (a phytochemical) and bardoxolone-methyl (a drug in clinical trial) suppress AR levels and sensitize CRPC cells to anti-androgens. These observations implicate the benefits of potent Nrf2-activators to suppress the lethal signaling cascades that lead to CRPC outgrowth. This review article will address the redox signaling networks that augment AR signaling during PCa progression to CRPC, and the possible utility of Nrf2-activating agents as an adjunct to ADT.
Collapse
Affiliation(s)
- Debasis Mondal
- Debusk College of Osteopathic Medicine, Lincoln Memorial University, Knoxville, TN 37932, USA
| | - Devin Narwani
- Debusk College of Osteopathic Medicine, Lincoln Memorial University, Knoxville, TN 37932, USA
| | - Shahnawaz Notta
- Debusk College of Osteopathic Medicine, Lincoln Memorial University, Knoxville, TN 37932, USA
| | - Dawood Ghaffar
- Debusk College of Osteopathic Medicine, Lincoln Memorial University, Knoxville, TN 37932, USA
| | - Nikhil Mardhekar
- Debusk College of Osteopathic Medicine, Lincoln Memorial University, Knoxville, TN 37932, USA
| | - Syed S A Quadri
- Debusk College of Osteopathic Medicine, Lincoln Memorial University, Knoxville, TN 37932, USA
| |
Collapse
|
7
|
Blatt EB, Kopplin N, Kumar S, Mu P, Conzen SD, Raj GV. Overcoming oncogene addiction in breast and prostate cancers: a comparative mechanistic overview. Endocr Relat Cancer 2021; 28:R31-R46. [PMID: 33263560 PMCID: PMC8218927 DOI: 10.1530/erc-20-0272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023]
Abstract
Prostate cancer (PCa) and breast cancer (BCa) are both hormone-dependent cancers that require the androgen receptor (AR) and estrogen receptor (ER, ESR1) for growth and proliferation, respectively. Endocrine therapies that target these nuclear receptors (NRs) provide significant clinical benefit for metastatic patients. However, these therapeutic strategies are seldom curative and therapy resistance is prevalent. Because the vast majority of therapy-resistant PCa and BCa remain dependent on the augmented activity of their primary NR driver, common mechanisms of resistance involve enhanced NR signaling through overexpression, mutation, or alternative splicing of the receptor, coregulator alterations, and increased intracrine hormonal synthesis. In addition, a significant subset of endocrine therapy-resistant tumors become independent of their primary NR and switch to alternative NR or transcriptional drivers. While these hormone-dependent cancers generally employ similar mechanisms of endocrine therapy resistance, distinct differences between the two tumor types have been observed. In this review, we compare and contrast the most frequent mechanisms of antiandrogen and antiestrogen resistance, and provide potential therapeutic strategies for targeting both advanced PCa and BCa.
Collapse
Affiliation(s)
- Eliot B Blatt
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Noa Kopplin
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shourya Kumar
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ping Mu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Suzanne D Conzen
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
8
|
Gray JS, Campbell MJ. Challenges and Opportunities of Genomic Approaches in Therapeutics Development. Methods Mol Biol 2021; 2194:107-126. [PMID: 32926364 DOI: 10.1007/978-1-0716-0849-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The magnitude of all therapeutic responses is significantly determined by genome structure, variation, and functional interactions. This determination occurs at many levels which are discussed in the current review. Well-established examples of structural variation between individuals are known to dictate an individual's response to numerous drugs, as clearly illustrated by warfarin. The exponential rate of genomic-based interrogation is coupled with an expanding repertoire of genomic technologies and applications. This is leading to an ever more sophisticated appreciation of how structural variation, regulation of transcription and genomic structure, both individually and collectively, define cell therapeutic responses.
Collapse
Affiliation(s)
- Jaimie S Gray
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
9
|
Tang L, Zhang L, Liu L, Dong L, Dong Y, Zhu W, Wang H. NCOR1 may be a potential biomarker of a novel molecular subtype of prostate cancer. FEBS Open Bio 2020; 10:2678-2686. [PMID: 33058520 PMCID: PMC7714081 DOI: 10.1002/2211-5463.13004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/18/2020] [Accepted: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
Prostate cancer (PCa) is the most frequently diagnosed male cancer. An earlier study of a cohort of 333 primary prostate carcinomas showed that 74% of these tumors fell into one of seven subtypes of a molecular taxonomy defined by specific gene fusions (ERG, ETV1/4 and FLI1) or mutations (SPOP, FOXA1 and IDH1). Molecular subtypes may aid in distinguishing indolent cases from aggressive cases and improving management of the disease. However, molecular features of PCa outside the seven subtypes are still not well studied. Here we report molecular features of PCa cases without typical features of the established subtypes. We performed comprehensive genomic analysis of 91 patients, including 54 primary and 37 metastatic cases, by whole‐exome sequencing. TP53, SPOP, FOXA1, AR (androgen receptor) and a TMPRSS2–ERG fusion emerged as the most commonly altered genes in primary cases, whereas AR, FOXA1, PTEN, CDK12, APC and TP53 were the most commonly altered genes in metastatic cases. Nuclear receptor corepressor (NCOR1) genomic alterations have been identified in 5% of cases, which are nontypical molecular features of PCa subtypes. A novel NCOR1 c.2182G>C (p.Val728Leu) was identified in tumor. RT‐PCR was used to show that this mutation caused loss of NCOR1 exon 19 and might be oncogenic in PCa. NCOR1 is involved in maintenance of mitochondrial membrane potential in PCa cells, and loss of NCOR1 might contribute to PCa progression. Therefore, NCOR1 may be a potential molecular marker of a subtype of PCa.
Collapse
Affiliation(s)
- Lu Tang
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin, China
| | - Lixia Zhang
- School of Landscape, Jiangxi Agricultural University, Nanchang, China
| | - Lei Liu
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin, China
| | - Liping Dong
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin, China
| | - Yuan Dong
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin, China
| | - Wenhe Zhu
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin, China
| | - Huiyan Wang
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin, China
| |
Collapse
|
10
|
Crumbaker M, Chan EKF, Gong T, Corcoran N, Jaratlerdsiri W, Lyons RJ, Haynes AM, Kulidjian AA, Kalsbeek AMF, Petersen DC, Stricker PD, Jamieson CAM, Croucher PI, Hovens CM, Joshua AM, Hayes VM. The Impact of Whole Genome Data on Therapeutic Decision-Making in Metastatic Prostate Cancer: A Retrospective Analysis. Cancers (Basel) 2020; 12:E1178. [PMID: 32392735 PMCID: PMC7280976 DOI: 10.3390/cancers12051178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND While critical insights have been gained from evaluating the genomic landscape of metastatic prostate cancer, utilizing this information to inform personalized treatment is in its infancy. We performed a retrospective pilot study to assess the current impact of precision medicine for locally advanced and metastatic prostate adenocarcinoma and evaluate how genomic data could be harnessed to individualize treatment. METHODS Deep whole genome-sequencing was performed on 16 tumour-blood pairs from 13 prostate cancer patients; whole genome optical mapping was performed in a subset of 9 patients to further identify large structural variants. Tumour samples were derived from prostate, lymph nodes, bone and brain. RESULTS Most samples had acquired genomic alterations in multiple therapeutically relevant pathways, including DNA damage response (11/13 cases), PI3K (7/13), MAPK (10/13) and Wnt (9/13). Five patients had somatic copy number losses in genes that may indicate sensitivity to immunotherapy (LRP1B, CDK12, MLH1) and one patient had germline and somatic BRCA2 alterations. CONCLUSIONS Most cases, whether primary or metastatic, harboured therapeutically relevant alterations, including those associated with PARP inhibitor sensitivity, immunotherapy sensitivity and resistance to androgen pathway targeting agents. The observed intra-patient heterogeneity and presence of genomic alterations in multiple growth pathways in individual cases suggests that a precision medicine model in prostate cancer needs to simultaneously incorporate multiple pathway-targeting agents. Our whole genome approach allowed for structural variant assessment in addition to the ability to rapidly reassess an individual's molecular landscape as knowledge of relevant biomarkers evolve. This retrospective oncological assessment highlights the genomic complexity of prostate cancer and the potential impact of assessing genomic data for an individual at any stage of the disease.
Collapse
Affiliation(s)
- Megan Crumbaker
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
- Kinghorn Cancer Centre, Department of Medical Oncology, St. Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
| | - Eva K. F. Chan
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
| | - Tingting Gong
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- Central Clinical School, University of Sydney, Sydney, Camperdown, NSW 2050, Australia
| | - Niall Corcoran
- Australian Prostate Cancer Research Centre Epworth, Richmond, VIC 3121, Australia;
- Department of Surgery, University of Melbourne, Melbourne, VIC 3010, Australia
- Division of Urology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Weerachai Jaratlerdsiri
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
| | - Ruth J. Lyons
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
| | - Anne-Maree Haynes
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
| | - Anna A. Kulidjian
- Department of Orthopedic Surgery, Scripps Clinic, La Jolla, CA 92037, USA.;
- Orthopedic Oncology Program, Scripps MD Anderson Cancer Center, La Jolla, CA 92037, USA
| | - Anton M. F. Kalsbeek
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
| | - Desiree C. Petersen
- The Centre for Proteomic and Genomic Research, Cape Town 7925, South Africa;
| | - Phillip D. Stricker
- Department of Urology, St. Vincent’s Hospital, Darlinghurst, NSW 2010, Australia;
| | - Christina A. M. Jamieson
- Department of Urology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92037, USA;
| | - Peter I. Croucher
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
| | - Christopher M. Hovens
- Australian Prostate Cancer Research Centre Epworth, Richmond, VIC 3121, Australia;
- Department of Surgery, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Anthony M. Joshua
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
- Kinghorn Cancer Centre, Department of Medical Oncology, St. Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
| | - Vanessa M. Hayes
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; (M.C.); (E.K.F.C.); (T.G.); (W.J.); (R.J.L.); (A.-M.H.); (A.M.F.K.); (P.I.C.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Randwick, NSW 2031, Australia
- Central Clinical School, University of Sydney, Sydney, Camperdown, NSW 2050, Australia
| |
Collapse
|
11
|
Cai Q, Kang J, Yu T. Bayesian Network Marker Selection via the Thresholded Graph Laplacian Gaussian Prior. BAYESIAN ANALYSIS 2020; 15:79-102. [PMID: 32802246 PMCID: PMC7428197 DOI: 10.1214/18-ba1142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Selecting informative nodes over large-scale networks becomes increasingly important in many research areas. Most existing methods focus on the local network structure and incur heavy computational costs for the large-scale problem. In this work, we propose a novel prior model for Bayesian network marker selection in the generalized linear model (GLM) framework: the Thresholded Graph Laplacian Gaussian (TGLG) prior, which adopts the graph Laplacian matrix to characterize the conditional dependence between neighboring markers accounting for the global network structure. Under mild conditions, we show the proposed model enjoys the posterior consistency with a diverging number of edges and nodes in the network. We also develop a Metropolis-adjusted Langevin algorithm (MALA) for efficient posterior computation, which is scalable to large-scale networks. We illustrate the superiorities of the proposed method compared with existing alternatives via extensive simulation studies and an analysis of the breast cancer gene expression dataset in the Cancer Genome Atlas (TCGA).
Collapse
Affiliation(s)
- Qingpo Cai
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Jian Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
12
|
Petanidis S, Domvri K, Porpodis K, Anestakis D, Freitag L, Hohenforst-Schmidt W, Tsavlis D, Zarogoulidis K. Inhibition of kras-derived exosomes downregulates immunosuppressive BACH2/GATA-3 expression via RIP-3 dependent necroptosis and miR-146/miR-210 modulation. Biomed Pharmacother 2020; 122:109461. [PMID: 31918262 DOI: 10.1016/j.biopha.2019.109461] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
Immunosuppressive chemoresistance is a major challenge in lung cancer treatment. Exosomes present in the tumor microenviroment are implicated in chemoresistant-related immune suppression, and metastasis but the exact pathogenic role of lung-derived exosomes is still uncertain. Recent reports reveal that lung cancer pathogenesis is strictly associated with a exosomal tumor supportive status and a dysfunctional immune system. In this study, we investigate the role of Kras-derived exosomes in chemoresistant immunosuppression in which neoplastic cells create a metabolic-sustained microenvironment. Findings reveal that Kras-derived exosomes induce regulation of SMARCE1/NCOR1 chromatin remodeling genes promoting pre-metastatic niche formation in naive mice and consequently increase lung metastatic burden. Furthermore, exosomal Kras inhibition downregulated transcription factor BACH2/GATA-3 expression in lung tumor tissues by shifting pyruvate/PKM2 dependent metabolism, contributing to a tumor-restraining status. Further co-treatment with carboplatin triggered RIP3/TNFa dependent necroptosis in ex vivo cells accompanied by differential expression of immunosuppressive miR-146/miR-210 regulators in metastatic lung cancer patients. Overall, these findings demonstrate the multifaceted roles of Kras-derived exosomes in sustaining lung immunosuppressive metastasis and provide new opportunities for effective metastasis inhibition, especially in chemoresistant tumors.
Collapse
Affiliation(s)
- Savvas Petanidis
- Department of Medicine, Laboratory of Medical Biology and Genetics, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece; Department of Pulmonology, I.M. Sechenov First Moscow State Medical University, Moscow, 119992, Russian Federation
| | - Kalliopi Domvri
- Pulmonary Department-Oncology Unit, "G. Papanikolaou" General Hospital, Aristotle University of Thessaloniki, Thessaloniki, 57010, Greece
| | - Konstantinos Porpodis
- Pulmonary Department-Oncology Unit, "G. Papanikolaou" General Hospital, Aristotle University of Thessaloniki, Thessaloniki, 57010, Greece
| | - Doxakis Anestakis
- Department of Medicine, Laboratory of Forensic Medicine and Toxicology, Aristotle University of Thessaloniki, 54124, Greece
| | - Lutz Freitag
- Department of Pulmonology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich Switzerland
| | | | - Drosos Tsavlis
- Department of Medicine, Laboratory of Experimental Physiology, Aristotle University of Thessaloniki, 54124, Greece
| | - Konstantinos Zarogoulidis
- Department of Medicine, Laboratory of Medical Biology and Genetics, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece.
| |
Collapse
|
13
|
Interaction between androgen receptor and coregulator SLIRP is regulated by Ack1 tyrosine kinase and androgen. Sci Rep 2019; 9:18637. [PMID: 31819114 PMCID: PMC6901447 DOI: 10.1038/s41598-019-55057-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/23/2019] [Indexed: 12/16/2022] Open
Abstract
Aberrant activation of the androgen receptor (AR) may play a critical role in castration resistant prostate cancer. After ligand binding, AR is recruited to the androgen responsive element (ARE) sequences on the DNA where AR interaction with coactivators and corepressors modulates transcription. We demonstrated that phosphorylation of AR at Tyr-267 by Ack1/TNK2 tyrosine kinase results in nuclear translocation, DNA binding, and androgen-dependent gene transcription in a low androgen environment. In order to dissect downstream mechanisms, we searched for proteins whose interaction with AR was regulated by Ack1. SLIRP (SRA stem-loop interacting RNA binding protein) was identified as a candidate protein. Interaction between AR and SLIRP was disrupted by Ack1 kinase activity as well as androgen or heregulin treatment. The noncoding RNA, SRA, was required for AR-SLIRP interaction. SLIRP was bound to ARE’s of AR target genes in the absence of androgen. Treatment with androgen or heregulin led to dissociation of SLIRP from the ARE. Whole transcriptome analysis of SLIRP knockdown in androgen responsive LNCaP cells showed that SLIRP affects a significant subset of androgen-regulated genes. Our data suggest that Ack1 kinase and androgen regulate interaction between AR and SLIRP and that SLIRP functions as a coregulator of AR with properties of a corepressor in a context-dependent manner.
Collapse
|
14
|
Yin L, He N, Chen C, Zhang N, Lin Y, Xia Q. Identification of novel blood-based HCC-specific diagnostic biomarkers for human hepatocellular carcinoma. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:1908-1916. [PMID: 31072138 DOI: 10.1080/21691401.2019.1613421] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) ranks fourth in global cancer mortality, accounting for 8.2% of all cancer deaths. Early detection of HCC has a significant impact on clinical outcomes. The aim of this study was to identify blood-based biomarkers which are HCC-specific. METHODS Comprehensive gene expression raw data of purified RNA of peripheral blood mononuclear cells (PBMC) was downloaded from GEO and was then analyzed. Differentially expressed genes (DEGs) in HCC were screened and the method of weighted gene co-expression network analysis was applied to identify candidate blood-based biomarkers associated with HCC. RESULTS Three modules closely related to HCC were screened using WGCNA. Nuclear localization signal (NLS)-bearing protein import into nucleus biological process was the most significant enriched physiological process identified by MCODE, and 3 genes (DICER1, GMPS and NCOR1) were selected as biomarkers. CONCLUSION In our study, three novel blood-based HCC-specific diagnostic biomarkers for human hepatocellular carcinoma were identified. These findings may contribute to the non-invasive detection of early HCC patients.
Collapse
Affiliation(s)
- Li Yin
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| | - Na He
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| | - Chuizhe Chen
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| | - Nan Zhang
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| | - Yingzi Lin
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| | - Qianfeng Xia
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| |
Collapse
|
15
|
Wu J, Gao FX, Wang C, Qin M, Han F, Xu T, Hu Z, Long Y, He XM, Deng X, Ren DL, Dai TY. IL-6 and IL-8 secreted by tumour cells impair the function of NK cells via the STAT3 pathway in oesophageal squamous cell carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:321. [PMID: 31324197 PMCID: PMC6642486 DOI: 10.1186/s13046-019-1310-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022]
Abstract
Background Recurrence and metastasis are the leading causes of tumour-related death in patients with oesophageal squamous cell carcinoma (ESCC). Tumour-infiltrating natural killer cells (NK cells) display powerful cytotoxicity to tumour cells and play a pivotal role in tumour therapy. However, the phenotype and functional regulation of NK cells in oesophageal squamous cell carcinoma (ESCC) remains largely unknown. Methods Single cell suspensions from blood and tissue samples were isolated by physical dissociation and filtering through a 70 μm cell strainer. Flow cytometry was applied to profile the activity and function of NK cells, and an antibody chip experiment was used to identify and quantitate cytokine levels. We studied IL-6 and IL-8 function in primary oesophageal squamous carcinoma and NK cell co-cultures in vitro and by a xenograft tumour model in vivo. Western blotting was used to quantitate STAT3 (signal transducer and activator of transcription 3) and p-STAT3 levels. Finally, we performed an IHC array to analyse IL-6/IL-8 (interleukin 6/interleukin 8) expression in 103 pairs of tumours and matched adjacent tissues of patients with ESCC to elucidate the correlation between IL-6 or IL-8 and clinical characteristics. Results The percentages of NK cells in both peripheral blood and tumour tissues from patients with ESCC were significantly increased in comparison with those in the controls and correlated with the clinical characteristics. Furthermore, the decrease in activating receptors and increase in inhibitory receptors on the surface of tumour-infiltrating NK cells was confirmed by flow cytometry. The level of granzyme B, the effector molecule of tumour-infiltrating NK cells, was also decreased. Mechanistically, primary ESCC cells activated the STAT3 signalling pathway on NK cells through IL-6 and IL-8 secretion, leading to the downregulation of activating receptors (NKp30 and NKG2D) on the surface of NK cells. An ex vivo study showed that blockade of STAT3 attenuated the IL-6/IL-8-mediated impairment of NK cell function. Moreover, the expression of IL-6 or IL-8 in tumour tissues was validated by immunohistochemistry to be positively correlated with tumour progression and poor survival, respectively. Conclusions Tumour cell-secreted IL-6 and IL-8 impair the activity and function of NK cells via STAT3 signalling and contribute to oesophageal squamous cell carcinoma malignancy. Electronic supplementary material The online version of this article (10.1186/s13046-019-1310-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jian Wu
- Department of Thoracic Surgery, The Affiliated Hospital of South West Medical University, Luzhou, Sichuan, China
| | - Feng-Xia Gao
- Department of Immunology, Basic Medicine College, South West Medical University, Luzhou, Sichuan, China
| | - Chao Wang
- Department of Thoracic Surgery, The Affiliated Hospital of South West Medical University, Luzhou, Sichuan, China
| | - Mei Qin
- Department of Immunology, Basic Medicine College, South West Medical University, Luzhou, Sichuan, China
| | - Fei Han
- Department of Thoracic Surgery, The Affiliated Hospital of South West Medical University, Luzhou, Sichuan, China
| | - Tao Xu
- Department of Thoracic Surgery, The Affiliated Hospital of South West Medical University, Luzhou, Sichuan, China
| | - Zhi Hu
- Department of Thoracic Surgery, The Affiliated Hospital of South West Medical University, Luzhou, Sichuan, China
| | - Yang Long
- Experimental Medicine Center, The Affiliated Hospital of South West Medical University, Luzhou, Sichuan, China
| | - Xue-Mei He
- Experimental Medicine Center, The Affiliated Hospital of South West Medical University, Luzhou, Sichuan, China
| | - Xin Deng
- Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China.,Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, The School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - De-Lian Ren
- Department of Immunology, Basic Medicine College, South West Medical University, Luzhou, Sichuan, China.
| | - Tian-Yang Dai
- Department of Thoracic Surgery, The Affiliated Hospital of South West Medical University, Luzhou, Sichuan, China.
| |
Collapse
|
16
|
Chung JH, Dewal N, Sokol E, Mathew P, Whitehead R, Millis SZ, Frampton GM, Bratslavsky G, Pal SK, Lee RJ, Necchi A, Gregg JP, Lara P, Antonarakis ES, Miller VA, Ross JS, Ali SM, Agarwal N. Prospective Comprehensive Genomic Profiling of Primary and Metastatic Prostate Tumors. JCO Precis Oncol 2019; 3:PO.18.00283. [PMID: 31218271 PMCID: PMC6583915 DOI: 10.1200/po.18.00283] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2018] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Comprehensive genomic profiling (CGP) is increasingly used for routine clinical management of prostate cancer. To inform targeted treatment strategies, 3,476 clinically advanced prostate tumors were analyzed by CGP for genomic alterations (GAs) and signatures of genomic instability. METHODS Prostate cancer samples (1,660 primary site and 1,816 metastatic site tumors from unmatched patients) were prospectively analyzed by CGP (FoundationOne Assay; Foundation Medicine, Cambridge, MA) for GAs and genomic signatures (genome-wide loss of heterozygosity [gLOH], microsatellite instability [MSI] status, tumor mutational burden [TMB]). RESULTS Frequently altered genes were TP53 (44%), PTEN (32%), TMPRSS2-ERG (31%), and AR (23%). Potentially targetable GAs were frequently identified in DNA repair, phosphatidylinositol 3-kinase, and RAS/RAF/MEK pathways. DNA repair pathway GAs included homologous recombination repair (23%), Fanconi anemia (5%), CDK12 (6%), and mismatch repair (4%) GAs. BRCA1/2, ATR, and FANCA GAs were associated with high gLOH, whereas CDK12-altered tumors were infrequently gLOH high. Median TMB was low (2.6 mutations/Mb). A subset of cases (3%) had high TMB, of which 71% also had high MSI. Metastatic site tumors were enriched for the 11q13 amplicon (CCND1/FGF19/FGF4/FGF3) and GAs in AR, LYN, MYC, NCOR1, PIK3CB, and RB1 compared with primary tumors. CONCLUSION Routine clinical CGP in the real-world setting identified GAs that are investigational biomarkers for targeted therapies in 57% of cases. gLOH and MSI/TMB signatures could further inform selection of poly (ADP-ribose) polymerase inhibitors and immunotherapies, respectively. Correlation of DNA repair GAs with gLOH identified genes associated with homologous recombination repair deficiency. GAs enriched in metastatic site tumors suggest therapeutic strategies for metastatic prostate cancer. Lack of clinical outcome correlation was a limitation of this study.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Andrea Necchi
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Primo Lara
- University of California, Davis, Medical Center, Sacramento, CA
| | | | | | - Jeffrey S. Ross
- Foundation Medicine, Cambridge, MA
- Upstate Medical University, Syracuse, NY
| | | | | |
Collapse
|
17
|
Liu XD, Xie DF, Wang YL, Guan H, Huang RX, Zhou PK. Integrated analysis of lncRNA–mRNA co-expression networks in the α-particle induced carcinogenesis of human branchial epithelial cells. Int J Radiat Biol 2018; 95:144-155. [DOI: 10.1080/09553002.2019.1539880] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xiao-Dan Liu
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, PR China
| | - Da-Fei Xie
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, PR China
| | - Yi-Long Wang
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, PR China
| | - Hua Guan
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, PR China
| | - Rui-Xue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Heath, Central South University, Changsha, PR China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, PR China
- State Key Laboratory of Respiratory, School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| |
Collapse
|
18
|
Hewit K, Sandilands E, Martinez RS, James D, Leung HY, Bryant DM, Shanks E, Markert EK. A functional genomics screen reveals a strong synergistic effect between docetaxel and the mitotic gene DLGAP5 that is mediated by the androgen receptor. Cell Death Dis 2018; 9:1069. [PMID: 30341281 PMCID: PMC6195526 DOI: 10.1038/s41419-018-1115-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 09/10/2018] [Accepted: 09/12/2018] [Indexed: 01/31/2023]
Abstract
Based on a molecular classification of prostate cancer using gene expression pathway signatures, we derived a set of 48 genes in critical pathways that significantly predicts clinical outcome in all tested patient cohorts. We tested these genes in a functional genomics screen in a panel of three prostate cancer cell lines (LNCaP, PC3, DU145), using RNA interference. The screen revealed several genes whose knockdown caused strong growth inhibition in all cell lines. Additionally, we tested the gene set in the presence of docetaxel to see whether any gene exhibited additive or synergistic effects with the drug. We observed a strong synergistic effect between DLGAP5 knockdown and docetaxel in the androgen-sensitive line LNCaP, but not in the two other androgen-independent lines. We then tested whether this effect was connected to androgen pathways and found that knockdown of the androgen receptor by si-RNA attenuated the synergy significantly. Similarly, androgen desensitized LNCaP-AI cells had a higher IC50 to docetaxel and did not exhibit the synergistic interaction. Short-term exposure to enzalutamide did not significantly alter the behaviour of parental LNCaP cells. An immunofluorescence analysis in LNCaP cells suggests that under the double insult of DLGAP5 knockdown and docetaxel, cells predominantly arrest in metaphase. In contrast, the knockdown of the androgen receptor by siRNA appears to assist cells to progress through metaphase in to anaphase, even in the presence of docetaxel. Our data suggest that DLGAP5 has a unique function in stabilizing spindle formation and surviving microtubule assault from docetaxel, in an androgen-regulated cell cycle system.
Collapse
Affiliation(s)
- Kay Hewit
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Scottish National Blood Transfusion Service, NSS, Glasgow, UK
| | - Emma Sandilands
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Daniel James
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Hing Y Leung
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - David M Bryant
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Emma Shanks
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Elke K Markert
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
19
|
Zhang M, Suarez E, Vasquez JL, Nathanson L, Peterson LE, Rajapakshe K, Basil P, Weigel NL, Coarfa C, Agoulnik IU. Inositol polyphosphate 4-phosphatase type II regulation of androgen receptor activity. Oncogene 2018; 38:1121-1135. [PMID: 30228349 PMCID: PMC6377303 DOI: 10.1038/s41388-018-0498-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/05/2018] [Accepted: 08/24/2018] [Indexed: 11/18/2022]
Abstract
Activation and transcriptional reprogramming of AR in advanced prostate cancer frequently coincides with the loss of two tumor suppressors, INPP4B and PTEN, which are highly expressed in human and mouse prostate epithelium. While regulation of AR signaling by PTEN has been described by multiple groups, it is not known whether the loss of INPP4B affects AR activity. Using prostate cancer cell lines we showed that INPP4B regulates AR transcriptional activity and the oncogenic signaling pathways Akt and PKC. Analysis of gene expression in prostate cancer patient cohorts showed a positive correlation between INPP4B expression and both AR mRNA levels and AR transcriptional output. Using an Inpp4b-/- mouse model, we demonstrated that INPP4B suppresses Akt and PKC signaling pathways and modulates AR transcriptional activity in normal mouse prostate. Remarkably, PTEN protein levels and phosphorylation of S380 were the same in Inpp4b-/- and WT males, suggesting that the observed changes were due exclusively to the loss of INPP4B. Our data show that INPP4B modulates AR activity in normal prostate and its loss contributes to the AR-dependent transcriptional profile in prostate cancer.
Collapse
Affiliation(s)
- Manqi Zhang
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA
| | - Egla Suarez
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Judy L Vasquez
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | | | - Leif E Peterson
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX, USA
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Paul Basil
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nancy L Weigel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Irina U Agoulnik
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Biomolecular Science Institute, School of Integrated Science and Humanity, Florida International University, Miami, FL, 33199, USA.
| |
Collapse
|
20
|
Zhang M, Krause WC, Agoulnik IU. Techniques for Evaluation of AR Transcriptional Output and Recruitment to DNA. Methods Mol Biol 2018; 1786:219-236. [PMID: 29786796 DOI: 10.1007/978-1-4939-7845-8_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Steroid receptors are ligand activated transcription factors whose promoter specificity is regulated by a broad set of coregulators and pioneer factors. Corepressors and coactivators determine receptors' recruitment to specific regulatory elements and ultimately their transcriptional output. Using androgen receptor (AR) and NCOR1 corepressor as examples, this chapter describes experimental approaches to evaluate recruitment of steroid receptors and their coregulators to DNA and to determine coregulator contribution to the transcriptional output of the receptor. The chromatin immunoprecipitation assay, or ChIP, quantifies protein-DNA interaction in the cellular chromatin environment. Here, we describe a protocol to measure NCOR1 recruitment to AR binding sites of interest using ChIP. Gene Set Enrichment Analysis, GSEA, is a computational technique to determine whether a defined gene set is significantly represented among changes in gene expression between two biological groups. As an example, we examine whether AR repressed genes are significantly represented among genes altered by the NCOR1 knockout.
Collapse
Affiliation(s)
- Manqi Zhang
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - William C Krause
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Irina U Agoulnik
- Biomolecular Sciences Institute, FIU, Miami, FL, USA. .,Baylor College of Medicine, Houston, TX, USA. .,Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Miami, FL, USA.
| |
Collapse
|
21
|
Naderi A. C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. Oncotarget 2017; 8:57907-57933. [PMID: 28915724 PMCID: PMC5593696 DOI: 10.18632/oncotarget.17826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
This study investigated the network of genes that are co-expressed with androgen receptor (AR) to discover novel AR targets in breast cancer. Bioinformatics analysis of two datasets from breast cancer cell lines resulted in the identification of an AR-gene signature constituted of 98 genes that highly correlated with AR expression. Notably, C1orf64 showed the highest positive correlation with AR across the datasets with a correlation coefficient (CC) of 0.737. In addition, C1orf64 closely correlated with AR expression in primary and metastatic breast tumors and C1orf64 expression was relatively higher in breast tumors with a lower grade and lobular histology. Furthermore, there is a functional interplay between AR and C1orf64 in breast cancer. In this process, AR activation directly represses C1orf64 transcription and C1orf64, in turn, interacts with AR as a corepressor and negatively regulates the AR-mediated induction of prolactin-induced protein (PIP) and AR reporter activity. Moreover, the corepressor effect of C1orf64 results in a reduction of AR binding to PIP promoter. The other aspect of this interplay involves a cross-talk between AR and estrogen receptor (ER) signaling in which C1orf64 silencing intensifies the AR-mediated down-regulation of ER target gene, progesterone receptor. Therefore, the repression of C1orf64 by AR provides an underlying mechanism for the AR inhibitory effects on ER signaling. To elucidate the biochemical mechanisms of C1orf64 function, this study demonstrates that C1orf64 is a phosphothreonine protein that interacts with the chaperone protein 14-3-3. In summary, C1orf64 is a novel AR coregulator and a 14-3-3 binding partner in breast cancer.
Collapse
Affiliation(s)
- Ali Naderi
- University of Hawaii Cancer Center, Cancer Biology Program, Honolulu, Hawaii 96813, USA
| |
Collapse
|
22
|
Wong N, Major P, Kapoor A, Wei F, Yan J, Aziz T, Zheng M, Jayasekera D, Cutz JC, Chow MJ, Tang D. Amplification of MUC1 in prostate cancer metastasis and CRPC development. Oncotarget 2016; 7:83115-83133. [PMID: 27825118 PMCID: PMC5347757 DOI: 10.18632/oncotarget.13073] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 10/16/2016] [Indexed: 01/06/2023] Open
Abstract
Evidence supports the upregulation of MUC1 in prostate cancer (PC). However, this has not been thoroughly investigated. We report here an association of MUC1 upregulation with PC metastasis and the development of castration resistant PC (CRPC). MUC1 expression was specifically increased in DU145 cell-derived PC stem-like cells (PCSLCs) in comparison to their non-PCSLCs counterparts. While immunohistochemistry staining of 34 primary PCs revealed variability in MUC1 expression, Nanostring technology demonstrated elevated MUC1 mRNA levels in 4 of 7 PCs compared to their normal matched tissues. By analyzing MUC1 mRNA levels and gene copy number (GCN) using the OncomineTM database, elevations in MUC1 mRNA in 82 metastases versus 280 primary PCs and in MUC1 GCN in 37 metastases over 181 primary tumors were demonstrated. Analysis of genomic datasets within cBioPortal revealed increases in MUC1 GCN in 2% (6/333) of primary PCs, 6% (9/150) of metastatic PCs, and 33% (27/82) of CRPCs; in comparison, the respective increase in androgen receptor (AR) GCN was 1%, 63%, and 56%, revealing a specific increase in MUC1 GCN for CRPC. Furthermore, a 25-gene MUC1 network was amplified in 52% of CRPCs compared to 69% of CRPCs displaying increases in an AR co-regulator group. While genomic alterations in the MUC1 network largely overlap with those in the AR group, 18 CRPCs (66.7% being neuroendocrine PC) showed genomic alterations only in the MUC1 network. Moreover, genomic alterations in the MUC1 network correlated with PC relapse. Collectively, our observations suggest a combination therapy involving MUC1-based immunotherapy and androgen deprivation.
Collapse
MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Adenocarcinoma/secondary
- Adenocarcinoma/therapy
- Aged
- Aged, 80 and over
- Animals
- Antineoplastic Agents, Phytogenic/pharmacology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cell Movement/drug effects
- Computational Biology
- Databases, Genetic
- Disease Progression
- Disease-Free Survival
- Docetaxel
- Gene Amplification
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Male
- Mice, Inbred NOD
- Mice, SCID
- Middle Aged
- Mucin-1/genetics
- Mucin-1/metabolism
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Neuroendocrine Tumors/genetics
- Neuroendocrine Tumors/metabolism
- Neuroendocrine Tumors/secondary
- Neuroendocrine Tumors/therapy
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Prostatic Neoplasms/therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Prostatic Neoplasms, Castration-Resistant/pathology
- Prostatic Neoplasms, Castration-Resistant/therapy
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Androgen/metabolism
- Signal Transduction
- Survival Analysis
- Taxoids/pharmacology
- Time Factors
- Up-Regulation
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Nicholas Wong
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Father Sean O'sullivan Research Institute, Hamilton, Ontario, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
| | - Pierre Major
- Division of Medical Oncology, Department of Oncology, McMaster University, Hamilton, Ontario, Canada
| | - Anil Kapoor
- Father Sean O'sullivan Research Institute, Hamilton, Ontario, Canada
- Department of Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Fengxiang Wei
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Father Sean O'sullivan Research Institute, Hamilton, Ontario, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
- The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital, Longgang District, Shenzhen, Guangdong, P.R. China
| | - Judy Yan
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Father Sean O'sullivan Research Institute, Hamilton, Ontario, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
| | - Tariq Aziz
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Mingxing Zheng
- Department of Respiratory Medicine, Shenzhen 2nd People's Hospital, Shenzhen, Guangdong, China
- Department of Respiratory Disease, The First Affiliated Hospital of Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Dulitha Jayasekera
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Father Sean O'sullivan Research Institute, Hamilton, Ontario, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
| | - Jean-Claude Cutz
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Mathilda Jing Chow
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Father Sean O'sullivan Research Institute, Hamilton, Ontario, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
| | - Damu Tang
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Father Sean O'sullivan Research Institute, Hamilton, Ontario, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
| |
Collapse
|