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Bashore FM, Min SM, Chen X, Howell S, Rinderle CH, Morel G, Silvaroli JA, Wells CI, Bunnell BA, Drewry DH, Pabla NS, Ultanir SK, Bullock AN, Axtman AD. Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593776. [PMID: 38798634 PMCID: PMC11118373 DOI: 10.1101/2024.05.12.593776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Acylaminoindazole-based inhibitors of CDKL2 were identified via analyses of cell-free binding and selectivity data. Compound 9 was selected as a CDKL2 chemical probe based on its potent inhibition of CDKL2 enzymatic activity, engagement of CDKL2 in cells, and excellent kinome-wide selectivity, especially when used in cells. Compound 16 was designed as a negative control to be used alongside compound 9 in experiments to interrogate CDKL2-mediated biology. A solved co-crystal structure of compound 9 bound to CDKL2 highlighted key interactions it makes within its ATP-binding site. Inhibition of downstream phosphorylation of EB2, a CDKL2 substrate, in rat primary neurons provided evidence that engagement of CDKL2 by compound 9 in cells resulted in inhibition of its activity. When used at relevant concentrations, compound 9 does not impact the viability of rat primary neurons or certain breast cancer cells nor elicit consistent changes in the expression of proteins involved in epithelial-mesenchymal transition.
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Affiliation(s)
- Frances M. Bashore
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sophia M. Min
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiangrong Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Stefanie Howell
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caroline H. Rinderle
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Gabriel Morel
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Josie A. Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bruce A. Bunnell
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Navjot S. Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Sila K. Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Alex N. Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Gong J, Kim DM, Freeman MR, Kim H, Ellis L, Smith B, Theodorescu D, Posadas E, Figlin R, Bhowmick N, Freedland SJ. Genetic and biological drivers of prostate cancer disparities in Black men. Nat Rev Urol 2024; 21:274-289. [PMID: 37964070 DOI: 10.1038/s41585-023-00828-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 11/16/2023]
Abstract
Black men with prostate cancer have historically had worse outcomes than white men with prostate cancer. The causes of this disparity in outcomes are multi-factorial, but a potential basis is that prostate cancers in Black men are biologically distinct from prostate cancers in white men. Evidence suggests that genetic and ancestral factors, molecular pathways involving androgen and non-androgen receptor signalling, inflammation, epigenetics, the tumour microenvironment and tumour metabolism are contributing factors to the racial disparities observed. Key genetic and molecular pathways linked to prostate cancer risk and aggressiveness have potential clinical relevance. Describing biological drivers of prostate cancer disparities could inform efforts to improve outcomes for Black men with prostate cancer.
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Affiliation(s)
- Jun Gong
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Daniel M Kim
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael R Freeman
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hyung Kim
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Leigh Ellis
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bethany Smith
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Edwin Posadas
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert Figlin
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Neil Bhowmick
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephen J Freedland
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Section of Urology, Durham VA Medical Center, Durham, NC, USA
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Waseem M, Gujrati H, Wang BD. Tumor suppressive miR-99b-5p as an epigenomic regulator mediating mTOR/AR/SMARCD1 signaling axis in aggressive prostate cancer. Front Oncol 2023; 13:1184186. [PMID: 38023145 PMCID: PMC10661933 DOI: 10.3389/fonc.2023.1184186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction African American (AA) men exhibited 2.3-fold higher PCa incidence and 1.7-fold higher PCa mortality rates when compared to the European American (EA) men. Besides the socioeconomic factors, emerging evidence has highlighted that biological risk factors may play critical roles in the AA PCa disparities. Previously, we have shown that downregulated miR-99b-5p and upregulated mTOR cooperatively promotes the AA PCa aggressiveness and drug resistance. Methods In this study, we aimed to explore the miR-99b-5p/mTOR/AR/SMARCD1 signaling axis in AA PCa aggressiveness. The analyses used in the study included immunofluorescence, western blot, in-vitro functional assays (TUNEL, colony forming, and MTT), and chromatin immunoprecipitation (ChIP)-qPCR assays in 2D and/or 3D culture model of EA PCa and AA PCa cell lines. Results Specifically, the immunofluorescence staining, and western blot analysis has revealed that nuclear mTOR, AR, and SMARCD1 were highly expressed in AA PCa (MDA PCa 2b) compared to EA PCa (LNCaP) cell line. Western blot analysis further revealed that miR-99b-5p inhibited protein levels of mTOR, AR/AR-V7 and SMARCD1 in cytoplasm and nuclei of EA and AA PCa. The in-vitro functional (MTT, TUNEL, and clonogenic) assays have demonstrated that miR-99b-5p effectively inhibited cell proliferation/survival and induced cell apoptosis in EA and AA PCa cells. Moreover, combination of miR-99b-5p and enzalutamide (Enz) synergistically enhances the cytotoxicity against aggressive AA PCa and castration-resistant prostate cancer (CRPC). mTOR ChIP-qPCR assays further demonstrated that miR-99b-5p or miR-99b-5p/Enz significantly reduces the recruitment of mTOR to the genes involved in the metabolic reprogramming in CRPC. Discussion Taken together, miR-99b-5p may function as an epigenomic driver to modulate the mTOR/AR/SMARCD1 signaling axis in AA PCa and resistant CRPC.
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Affiliation(s)
- Mohammad Waseem
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy and Health Professions, Princess Anne, MD, United States
| | - Himali Gujrati
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy and Health Professions, Princess Anne, MD, United States
| | - Bi-Dar Wang
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy and Health Professions, Princess Anne, MD, United States
- Hormone Related Cancers Program, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
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Craddock J, Jiang J, Patrick SM, Mutambirwa SBA, Stricker PD, Bornman MSR, Jaratlerdsiri W, Hayes VM. Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities. Cancers (Basel) 2023; 15:3462. [PMID: 37444571 DOI: 10.3390/cancers15133462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Prostate cancer is driven by acquired genetic alterations, including those impacting the epigenetic machinery. With African ancestry as a significant risk factor for aggressive disease, we hypothesize that dysregulation among the roughly 656 epigenetic genes may contribute to prostate cancer health disparities. Investigating prostate tumor genomic data from 109 men of southern African and 56 men of European Australian ancestry, we found that African-derived tumors present with a longer tail of epigenetic driver gene candidates (72 versus 10). Biased towards African-specific drivers (63 versus 9 shared), many are novel to prostate cancer (18/63), including several putative therapeutic targets (CHD7, DPF3, POLR1B, SETD1B, UBTF, and VPS72). Through clustering of all variant types and copy number alterations, we describe two epigenetic PCa taxonomies capable of differentiating patients by ancestry and predicted clinical outcomes. We identified the top genes in African- and European-derived tumors representing a multifunctional "generic machinery", the alteration of which may be instrumental in epigenetic dysregulation and prostate tumorigenesis. In conclusion, numerous somatic alterations in the epigenetic machinery drive prostate carcinogenesis, but African-derived tumors appear to achieve this state with greater diversity among such alterations. The greater novelty observed in African-derived tumors illustrates the significant clinical benefit to be derived from a much needed African-tailored approach to prostate cancer healthcare aimed at reducing prostate cancer health disparities.
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Affiliation(s)
- Jenna Craddock
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Jue Jiang
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Sean M Patrick
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Shingai B A Mutambirwa
- Department of Urology, Sefako Makgatho Health Science University, Dr George Mukhari Academic Hospital, Medunsa 0208, South Africa
| | - Phillip D Stricker
- Department of Urology, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - M S Riana Bornman
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
| | - Weerachai Jaratlerdsiri
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
| | - Vanessa M Hayes
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria 0084, South Africa
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia
- Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
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Stevens C, Hightower A, Buxbaum SG, Falzarano SM, Rhie SK. Genomic, epigenomic, and transcriptomic signatures of prostate cancer between African American and European American patients. Front Oncol 2023; 13:1079037. [PMID: 36937425 PMCID: PMC10018228 DOI: 10.3389/fonc.2023.1079037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Prostate cancer is the second most common cancer in men in the United States, and racial disparities are greatly observed in the disease. Specifically, African American (AA) patients have 60% higher incidence and mortality rates, in addition to higher grade and stage prostate tumors, than European American (EA) patients. In order to narrow the gap between clinical outcomes for these two populations, genetic and molecular signatures contributing to this disparity have been characterized. Over the past decade, profiles of prostate tumor samples from different ethnic groups have been developed using molecular and functional assays coupled with next generation sequencing or microarrays. Comparative genome-wide analyses of genomic, epigenomic, and transcriptomic profiles from prostate tumor samples have uncovered potential race-specific mutations, copy number alterations, DNA methylation, and gene expression patterns. In this study, we reviewed over 20 published studies that examined the aforementioned molecular contributions to racial disparities in AA and EA prostate cancer patients. The reviewed genomic studies revealed mutations, deletions, amplifications, duplications, or fusion genes differentially enriched in AA patients relative to EA patients. Commonly reported genomic alterations included mutations or copy number alterations of FOXA1, KMT2D, SPOP, MYC, PTEN, TP53, ZFHX3, and the TMPRSS2-ERG fusion. The reviewed epigenomic studies identified that CpG sites near the promoters of PMEPA1, RARB, SNRPN, and TIMP3 genes were differentially methylated between AA and EA patients. Lastly, the reviewed transcriptomic studies identified genes (e.g. CCL4, CHRM3, CRYBB2, CXCR4, GALR1, GSTM3, SPINK1) and signaling pathways dysregulated between AA and EA patients. The most frequently found dysregulated pathways were involved in immune and inflammatory responses and neuroactive ligand signaling. Overall, we observed that the genomic, epigenomic, and transcriptomic alterations evaluated between AA and EA prostate cancer patients varied between studies, highlighting the impact of using different methods and sample sizes. The reported genomic, epigenomic, and transcriptomic alterations do not only uncover molecular mechanisms of tumorigenesis but also provide researchers and clinicians valuable resources to identify novel biomarkers and treatment modalities to improve the disparity of clinical outcomes between AA and EA patients.
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Affiliation(s)
- Claire Stevens
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Alexandria Hightower
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Sarah G. Buxbaum
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Epidemiology and Biostatistics, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL, United States
| | - Sara M. Falzarano
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
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Ha S, Wang BD. Molecular Insight into Drug Resistance Mechanism Conferred by Aberrant PIK3CD Splice Variant in African American Prostate Cancer. Cancers (Basel) 2023; 15:1337. [PMID: 36831678 PMCID: PMC9954641 DOI: 10.3390/cancers15041337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 02/22/2023] Open
Abstract
Targeting PI3Kδ has emerged as a promising therapy for hematologic and non-hematologic malignancies. Previously, we identified an oncogenic splice variant, PIK3CD-S, conferring Idelalisib resistance in African American (AA) prostate cancer (PCa). In the current study, we employed a comprehensive analysis combining molecular biology, biochemistry, histology, in silico simulation, and in vitro functional assays to investigate the PIK3CD-S expression profiles in PCa samples and to elucidate the drug resistance mechanism mediated by PI3Kδ-S (encoded by PIK3CD-S). The immunohistochemistry, RT-PCR, and Western blot assays first confirmed that PI3Kδ-S is highly expressed in AA PCa. Compared with PCa expressing the full-length PI3Kδ-L, PCa expressing PI3Kδ-S exhibits enhanced drug resistance properties, including a higher cell viability, more antiapoptotic and invasive capacities, and constitutively activated PI3K/AKT signaling, in the presence of PI3Kδ/PI3K inhibitors (Idelalisib, Seletalisib, Wortmannin, and Dactolisib). Molecular docking, ATP-competitive assays, and PI3 kinase assays have further indicated a drastically reduced affinity of PI3Kδ inhibitors with PI3Kδ-S vs. PI3Kδ-L, attributed to the lack of core binding residues in the PI3Kδ-S catalytic domain. Additionally, SRSF2 has been identified as a critical splicing factor mediating exon 20 skipping in PIK3CD pre-mRNA. The inhibition of the SRSF2 activity by SRPIN340 successfully sensitizes AA PCa cells to PI3Kδ inhibitors, suggesting a novel therapeutic option for Idelalisib-resistant tumors.
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Affiliation(s)
- Siyoung Ha
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy and Health Professions, Princess Anne, MD 21853, USA
| | - Bi-Dar Wang
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy and Health Professions, Princess Anne, MD 21853, USA
- Hormone Related Cancers Program, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
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Miyahira AK, Hawley JE, Adelaiye-Ogala R, Calais J, Nappi L, Parikh R, Seibert TM, Wasmuth EV, Wei XX, Pienta KJ, Soule HR. Exploring new frontiers in prostate cancer research: Report from the 2022 Coffey-Holden prostate cancer academy meeting. Prostate 2023; 83:207-226. [PMID: 36443902 DOI: 10.1002/pros.24461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022]
Abstract
INTRODUCTION The 2022 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, "Exploring New Frontiers in Prostate Cancer Research," was held from June 23 to 26, 2022, at the University of California, Los Angeles, Luskin Conference Center, in Los Angeles, CA. METHODS The CHPCA Meeting is an annual discussion-oriented scientific conference organized by the Prostate Cancer Foundation, that focuses on emerging and next-step topics deemed critical for making the next major advances in prostate cancer research and clinical care. The 2022 CHPCA Meeting included 35 talks over 10 sessions and was attended by 73 academic investigators. RESULTS Major topic areas discussed at the meeting included: prostate cancer diversity and disparities, the impact of social determinants on research and patient outcomes, leveraging real-world and retrospective data, development of artificial intelligence biomarkers, androgen receptor (AR) signaling biology and new strategies for targeting AR, features of homologous recombination deficient prostate cancer, and future directions in immunotherapy and nuclear theranostics. DISCUSSION This article summarizes the scientific presentations from the 2022 CHPCA Meeting, with the goal that dissemination of this knowledge will contribute to furthering global prostate cancer research efforts.
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Affiliation(s)
| | - Jessica E Hawley
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Remi Adelaiye-Ogala
- Department of Medicine, Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Jeremie Calais
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, California, USA
| | - Lucia Nappi
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, British Columbia, Canada
- Department of Medical Oncology, BC Cancer, British Columbia, Canada
| | - Ravi Parikh
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
| | - Tyler M Seibert
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California, USA
- Department of Radiology, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Research Service, VA San Diego Healthcare System, San Diego, California, USA
| | - Elizabeth V Wasmuth
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, Texas, USA
| | - Xiao X Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Howard R Soule
- Prostate Cancer Foundation, Santa Monica, California, USA
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Samtal C, El Jaddaoui I, Hamdi S, Bouguenouch L, Ouldim K, Nejjari C, Ghazal H, Bekkari H. Review of prostate cancer genomic studies in Africa. Front Genet 2022; 13:911101. [DOI: 10.3389/fgene.2022.911101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is the second most commonly diagnosed in men worldwide and one of the most frequent cancers in men in Africa. The heterogeneity of this cancer fosters the need to identify potential genetic risk factors/biomarkers. Omics variations may significantly contribute to early diagnosis and personalized treatment. However, there are few genomic studies of this disease in African populations. This review sheds light on the status of genomics research on PCa in Africa and outlines the common variants identified thus far. The allele frequencies of the most significant SNPs in Afro-native, Afro-descendants, and European populations were compared. We advocate how these few but promising data will aid in understanding, better diagnosing, and precisely treating this cancer and the need for further collaborative research on the genomics of PCa in the African continent.
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Cauchi LM, Houston BJ, Nagirnaja L, O'Connor AE, Merriner DJ, Aston KI, Schlegel PN, Conrad DF, Burke R, O'Bryan MK. Zinc finger RNA binding protein 2 (ZFR2) is not required for male fertility in the mouse. Dev Biol 2022; 489:55-61. [PMID: 35679955 DOI: 10.1016/j.ydbio.2022.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Thousands of genes are expressed during spermatogenesis and male infertility has a strong genetic component. Within this study, we focus on the role of Zfr2 in male fertility, a gene previously implicated in human male fertility. To date, very little is known about the role of ZFR2 in either humans or mice. To this end, the requirement for ZFR2 in male fertility was assessed using a knockout mouse model. RESULTS Zfr2 was found to be expressed in the testes of both humans and mice. Deletion of Zfr2 was achieved via removal of exon 2 using CRISPR-Cas9 methods. The absence of Zfr2 did not result in a reduction in any fertility parameters assessed. Knockout males were capable of fostering litter sizes equal to wild type males, and there were no effects of Zfr2 knockout on sperm number or motility. We note Zfr2 knockout females were also fertile. CONCLUSIONS The absence of Zfr2 alone is not sufficient to cause a reduction in male fertility in mice.
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Affiliation(s)
- Lachlan M Cauchi
- School of Biological Sciences, Monash University, Clayton, Australia; Institute for Veterinary Anatomy, Histology and Embryology, Justus-Liebig University, Giessen, Germany
| | - Brendan J Houston
- The School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Australia.
| | - Liina Nagirnaja
- Oregon National Primate Research Center, Oregon Health & Science University, Oregon, USA
| | - Anne E O'Connor
- The School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - D Jo Merriner
- The School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Utah, USA
| | | | - Don F Conrad
- Oregon National Primate Research Center, Oregon Health & Science University, Oregon, USA
| | - Richard Burke
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Moira K O'Bryan
- The School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Australia
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Berchuck JE, Adib E, Abou Alaiwi S, Dash AK, Shin JN, Lowder D, McColl C, Castro P, Carelli R, Benedetti E, Deng J, Robertson M, Baca SC, Bell C, McClure HM, El Zarif T, Davidsohn MP, Lakshminarayanan G, Rizwan K, Skapura DG, Grimm SL, Davis CM, Ehli EA, Kelleher KM, Seo JH, Mitsiades N, Coarfa C, Pomerantz MM, Loda M, Ittmann M, Freedman ML, Kaochar S. The Prostate Cancer Androgen Receptor Cistrome in African American Men Associates with Upregulation of Lipid Metabolism and Immune Response. Cancer Res 2022; 82:2848-2859. [PMID: 35731919 PMCID: PMC9379363 DOI: 10.1158/0008-5472.can-21-3552] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/03/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
African-American (AA) men are more likely to be diagnosed with and die from prostate cancer than European American (EA) men. Despite the central role of the androgen receptor (AR) transcription factor in prostate cancer, little is known about the contribution of epigenetics to observed racial disparities. We performed AR chromatin immunoprecipitation sequencing on primary prostate tumors from AA and EA men, finding that sites with greater AR binding intensity in AA relative to EA prostate cancer are enriched for lipid metabolism and immune response genes. Integration with transcriptomic and metabolomic data demonstrated coinciding upregulation of lipid metabolism gene expression and increased lipid levels in AA prostate cancer. In a metastatic prostate cancer cohort, upregulated lipid metabolism associated with poor prognosis. These findings offer the first insights into ancestry-specific differences in the prostate cancer AR cistrome. The data suggest a model whereby increased androgen signaling may contribute to higher levels of lipid metabolism, immune response, and cytokine signaling in AA prostate tumors. Given the association of upregulated lipogenesis with prostate cancer progression, our study provides a plausible biological explanation for the higher incidence and aggressiveness of prostate cancer observed in AA men. SIGNIFICANCE With immunotherapies and inhibitors of metabolic enzymes in clinical development, the altered lipid metabolism and immune response in African-American men provides potential therapeutic opportunities to attenuate racial disparities in prostate cancer.
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Affiliation(s)
- Jacob E. Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elio Adib
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sarah Abou Alaiwi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Amit K. Dash
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jin Na Shin
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Dallin Lowder
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Collin McColl
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Patricia Castro
- Department of Pathology, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Ryan Carelli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - Elisa Benedetti
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - Jenny Deng
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Matthew Robertson
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Sylvan C. Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Heather M. McClure
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Talal El Zarif
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew P. Davidsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gitanjali Lakshminarayanan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kinza Rizwan
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | - Sandra L. Grimm
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Christel M. Davis
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Erik A. Ehli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Kaitlin M. Kelleher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nicholas Mitsiades
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Cristian Coarfa
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Mark M. Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Massimo Loda
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - Michael Ittmann
- Department of Pathology, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Salma Kaochar
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
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11
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R Peter M, Bilenky M, Shi Y, Pu J, Kamdar S, R Hansen A, E Fleshner N, S Sridhar S, M Joshua A, Hirst M, Xu W, Bapat B. A novel methylated cell-free DNA marker panel to monitor treatment response in metastatic prostate cancer. Epigenomics 2022; 14:811-822. [PMID: 35818933 DOI: 10.2217/epi-2022-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study examined circulating cell-free DNA (cfDNA) biomarkers associated with androgen treatment resistance in metastatic castration resistance prostate cancer (mCRPC). Materials & methods: We designed a panel of nine candidate cfDNA methylation markers using droplet digital PCR (Methyl-ddPCR) and assessed methylation levels in sequentially collected cfDNA samples from patients with mCRPC. Results: Increased cfDNA methylation in eight out of nine markers during androgen-targeted treatment correlated with a faster time to clinical progression. Cox proportional hazards modeling and logistic regression analysis further confirmed that higher cfDNA methylation during treatment was significantly associated with clinical progression. Conclusion: Overall, our findings have revealed a novel methylated cfDNA marker panel that could aid in the clinical management of metastatic prostate cancer.
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Affiliation(s)
- Madonna R Peter
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Misha Bilenky
- Canada's Michael Smith Genome Science Center, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Yuliang Shi
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Jiajie Pu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Shivani Kamdar
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Aaron R Hansen
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Neil E Fleshner
- Division of Urology, Department of Surgical Oncology, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Srikala S Sridhar
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Anthony M Joshua
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada.,Department of Medical Oncology, Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Martin Hirst
- Canada's Michael Smith Genome Science Center, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.,Department of Microbiology & Immunology & Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Bharati Bapat
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
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12
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Mo L, Su Y, Yuan J, Xiao Z, Zhang Z, Lan X, Huang D. Comparisons of Forecasting for Survival Outcome for Head and Neck Squamous Cell Carcinoma by using Machine Learning Models based on Multi-omics. Curr Genomics 2022; 23:94-108. [PMID: 36778975 PMCID: PMC9878835 DOI: 10.2174/1389202923666220204153744] [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] [Received: 12/03/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Machine learning methods showed excellent predictive ability in a wide range of fields. For the survival of head and neck squamous cell carcinoma (HNSC), its multi-omics influence is crucial. This study attempts to establish a variety of machine learning multi-omics models to predict the survival of HNSC and find the most suitable machine learning prediction method. Methods: The HNSC clinical data and multi-omics data were downloaded from the TCGA database. The important variables were screened by the LASSO algorithm. We used a total of 12 supervised machine learning models to predict the outcome of HNSC survival and compared the results. In vitro qPCR was performed to verify core genes predicted by the random forest algorithm. Results: For omics of HNSC, the results of the twelve models showed that the performance of multi-omics was better than each single-omic alone. Results were presented, which showed that the Bayesian network(BN) model (area under the curve [AUC] 0.8250, F1 score=0.7917) and random forest(RF) model (area under the curve [AUC] 0.8002,F1 score=0.7839) played good prediction performance in HNSC multi-omics data. The results of in vitro qPCR were consistent with the RF algorithm. Conclusion: Machine learning methods could better forecast the survival outcome of HNSC. Meanwhile, this study found that the BN model and the RF model were the most superior. Moreover, the forecast result of multi-omics was better than single-omic alone in HNSC.
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Affiliation(s)
- Liying Mo
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China;,These authors contributed equally to this work
| | - Yuangang Su
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China;,Research Centre for Regenerative Medicine, Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning, Guangxi, China;,These authors contributed equally to this work
| | - Jianhui Yuan
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China;,The Laboratory of Biomedical Photonics and Engineering, Guangxi Medical University, Nanning, China
| | - Zhiwei Xiao
- School of Information and Management, Guangxi Medical University, Nanning, Guangxi, China
| | - Ziyan Zhang
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiuwan Lan
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China;,These authors contributed equally to this work
| | - Daizheng Huang
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China;,The Laboratory of Biomedical Photonics and Engineering, Guangxi Medical University, Nanning, China;,Address correspondence to this author at the School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China; The Laboratory of Biomedical Photonics and Engineering, Guangxi Medical University, Nanning, China; Tel: +867715358270; E-mail:
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13
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Ye F, Han X, Shao Y, Lo J, Zhang F, Wang J, Melamed J, Deng FM, Sfanos KS, De Marzo A, Ren G, Wang D, Zhang D, Lee P. Identification of novel biomarkers differentially expressed between African-American and Caucasian-American prostate cancer patients. Am J Cancer Res 2022; 12:1660-1670. [PMID: 35530298 PMCID: PMC9077070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023] Open
Abstract
Prostate cancer (PCa) incidence and mortality rate vary among racial and ethnic groups with the highest occurrence in African American (AA) men who have mortality rates twice that of Caucasians (CA). In this study, we focused on differential expression of proteins in AA prostate cancer compared to CA using Protein Pathway Array Analysis (PPAA), in order to identify protein biomarkers associated with PCa racial disparity. Fresh frozen prostate samples (n=90) obtained from radical prostatectomy specimens with PCa, including 25 AA tumor, 21 AA benign, 23 CA tumor, 21 CA benign samples were analyzed. A total of 286 proteins and phosphoproteins were assessed using PPAA. By PPAA analysis, 33 proteins were found to be significantly differentially expressed in tumor tissue (n=48, including both CA and AA) in comparison to benign tissue (n=42). We further compared protein expression levels between AA and CA tumor groups and found that 3 proteins were differentially expressed (P<0.05 and q<5%). Aurora was found to be significantly increased in AA tumors, while Cyclin D1 and HNF-3a proteins were downregulated in AA tumors. Predicted risk score was significantly different between AA and CA ethnic groups using logistic regression analysis. In conclusion, we identified Aurora, Cyclin D1 and HNF-3a proteins as being differentially expressed between AA and CA in PCa tissue. Our study suggests that these proteins might be involved in different pathways that lead to aggressive PCa behavior in AA patients, potentially serving as biomarkers for the PCa racial disparity.
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Affiliation(s)
- Fei Ye
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer CenterNew York, USA
| | - Xiaoxia Han
- Department of Biostatstics, New York University School of MedicineNew York, USA
| | - Yonzhao Shao
- Department of Biostatstics, New York University School of MedicineNew York, USA
| | - Jingzhi Lo
- Department of Genomic Medicine Unit, SanofiWaltham, MA, USA
| | - Fengxia Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer CenterNew York, USA
| | - Jinhua Wang
- Department of Pathology, New York University School of MedicineNew York, USA
| | - Jonathan Melamed
- Department of Pathology, New York University School of MedicineNew York, USA
| | - Fang-Ming Deng
- Department of Pathology, New York University School of MedicineNew York, USA
| | - Karen S Sfanos
- Department of Pathology, Johns Hopkins UniversityBaltimore, MD, USA
| | - Angelo De Marzo
- Department of Pathology, Johns Hopkins UniversityBaltimore, MD, USA
| | - Guoping Ren
- Department of Pathology, First Hospital of Zhejiang UniversityZhejiang, China
| | - Dongwen Wang
- Department of Urology, Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen CenterGuangdong, China
| | - David Zhang
- Department of Urology, New York University School of MedicineNew York, USA
| | - Peng Lee
- Department of Pathology, New York University School of MedicineNew York, USA
- Department of Urology, New York University School of MedicineNew York, USA
- Department of New York Harbor Healthcare System, New York University School of MedicineNew York, USA
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14
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Nelson WG, Brawley OW, Isaacs WB, Platz EA, Yegnasubramanian S, Sfanos KS, Lotan TL, De Marzo AM. Health inequity drives disease biology to create disparities in prostate cancer outcomes. J Clin Invest 2022; 132:e155031. [PMID: 35104804 PMCID: PMC8803327 DOI: 10.1172/jci155031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Prostate cancer exerts a greater toll on African American men than on White men of European descent (hereafter referred to as European American men): the disparity in incidence and mortality is greater than that of any other common cancer. The disproportionate impact of prostate cancer on Black men has been attributed to the genetics of African ancestry, to diet and lifestyle risk factors, and to unequal access to quality health care. In this Review, all of these influences are considered in the context of the evolving understanding that chronic or recurrent inflammatory processes drive prostatic carcinogenesis. Studies of inherited susceptibility highlight the contributions of genes involved in prostate cell and tissue repair (BRCA1/2, ATM) and regeneration (HOXB13 and MYC). Social determinants of health appear to accentuate these genetic influences by fueling prostate inflammation and associated cell and genome damage. Molecular characterization of the prostate cancers that arise in Black versus White men further implicates this inflammatory microenvironment in disease behavior. Yet, when Black and White men with similar grade and stage of prostate cancer are treated equally, they exhibit equivalent outcomes. The central role of prostate inflammation in prostate cancer development and progression augments the impact of the social determinants of health on disease pathogenesis. And, when coupled with poorer access to high-quality treatment, these inequities result in a disparate burden of prostate cancer on African American men.
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15
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Chen Z, Lv Y, He L, Wu S, Wu Z. Decreased CDKL2 Expression in Clear Cell Renal Cell Carcinoma Predicts Worse Overall Survival. Front Mol Biosci 2022; 8:657672. [PMID: 35096961 PMCID: PMC8793634 DOI: 10.3389/fmolb.2021.657672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
Background: Clear cell renal cell carcinoma (ccRCC) is the most frequent and lethal type of kidney cancer. Although differential expression of cyclin-dependent kinase-like 2 (CDKL2) has been reported to be associated with tumor progression in other cancers, its prognostic value, and potential mechanism in patients with ccRCC still remain unknown. Methods: Gene expression analysis was conducted using The Cancer Genome Atlas (TCGA), Gene Expression Omnibus, and International Cancer Genome Consortium databases. Further, clinicopathologic analysis; Kaplan–Meier survival analysis; weighted gene co-expression network analysis; gene set enrichment analysis; gene ontology enrichment; methylation; and immune infiltration analyses were performed using TCGA-kidney renal clear cell carcinoma profiles. CDKL2 translational levels were analyzed using The Human Protein Atlas database. Results:CDKL2 expression was decreased in ccRCC samples retrieved from the four databases. Gender, survival status, histologic grade, clinical stage, TNM classification, and tumor status were closely related to CDKL2 expression. In addition, CDKL2 downregulation was an independent prognostic factor for poor prognosis in multivariate analysis. Enrichment analyses using multiple tests revealed that CDKL2 is not just closely related to immune response but this association is highly correlated as well. Further, we found that CDKL2 expression was significantly correlated with the infiltration levels of T cell CD4 memory resting; monocytes; macrophages M0, M1, and M2; dendritic cells resting; mast cells resting; plasma cells; T cell CD8; and T cell regulatory. Conclusion: This is the first report to study the expression of CDKL2 in ccRCC, wherein we suggest that decreased CDKL2 expression is closely correlated with poor prognosis in ccRCC. We consider that CDKL2 is a novel and potential prognostic biomarker associated with immune infiltrates in ccRCC.
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16
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Lima T, Ferreira R, Freitas M, Henrique R, Vitorino R, Fardilha M. Integration of Automatic Text Mining and Genomic and Proteomic Analysis to Unravel Prostate Cancer Biomarkers. J Proteome Res 2022; 21:447-458. [DOI: 10.1021/acs.jproteome.1c00763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Tânia Lima
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
| | - Rita Ferreira
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marina Freitas
- Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-513 Porto, Portugal
| | - Rui Vitorino
- Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- Cardiovascular Research Centre (UnIC), Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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17
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Dovey ZS, Nair SS, Chakravarty D, Tewari AK. Racial disparity in prostate cancer in the African American population with actionable ideas and novel immunotherapies. Cancer Rep (Hoboken) 2021; 4:e1340. [PMID: 33599076 PMCID: PMC8551995 DOI: 10.1002/cnr2.1340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/22/2020] [Accepted: 12/02/2020] [Indexed: 12/28/2022] Open
Abstract
Background African Americans (AAs) in the United States are known to have a higher incidence and mortality for Prostate Cancer (PCa). The drivers of this epidemiological disparity are multifactorial, including socioeconomic factors leading to lifestyle and dietary issues, healthcare access problems, and potentially tumor biology. Recent findings Although recent evidence suggests once access is equal, AA men have equal outcomes to Caucasian American (CA) men, differences in PCa incidence remain, and there is much to do to reverse disparities in mortality across the USA. A deeper understanding of these issues, both at the clinical and molecular level, can facilitate improved outcomes in the AA population. This review first discusses PCa oncogenesis in the context of its diverse hallmarks before benchmarking key molecular and genomic differences for PCa in AA men that have emerged in the recent literature. Studies have emphasized the importance of tumor microenvironment that contributes to both the unequal cancer burden and differences in clinical outcome between the races. Management of comorbidities like obesity, hypertension, and diabetes will provide an essential means of reducing prostate cancer incidence in AA men. Although requiring further AA specific research, several new treatment strategies such as immune checkpoint inhibitors used in combination PARP inhibitors and other emerging vaccines, including Sipuleucel‐T, have demonstrated some proven efficacy. Conclusion Genomic profiling to integrate clinical and genomic data for diagnosis, prognosis, and treatment will allow physicians to plan a “Precision Medicine” approach to AA men. There is a pressing need for further research for risk stratification, which may allow early identification of AA men with higher risk disease based on their unique clinical, genomic, and immunological profiles, which can then be mapped to appropriate clinical trials. Treatment options are outlined, with a concise description of recent work in AA specific populations, detailing several targeted therapies, including immunotherapy. Also, a summary of current clinical trials involving AA men is presented, and it is important that policies are adopted to ensure that AA men are actively recruited. Although it is encouraging that many of these explore the lifestyle and educational initiatives and therapeutic interventions, there is much still work to be done to reduce incidence and mortality in AA men and equalize current racial disparities.
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Affiliation(s)
- Zachary S Dovey
- The Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sujit S Nair
- The Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dimple Chakravarty
- The Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ashutosh K Tewari
- The Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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18
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Hua T, Kang S, Li XF, Tian YJ, Li Y. DNA methylome profiling identifies novel methylated genes in epithelial ovarian cancer patients with platinum resistance. J Obstet Gynaecol Res 2021; 47:1031-1039. [PMID: 33403724 DOI: 10.1111/jog.14634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/23/2020] [Accepted: 12/17/2020] [Indexed: 12/28/2022]
Abstract
AIM Platinum-based chemotherapy is widely used for epithelial ovarian cancer (EOC). As high as 20-25% of EOC patients will not respond to the initial chemotherapy. Accumulated evidences have implied that DNA methylation may serve as a potential bio-marker for chemotherapy-resistant phenotypic screening; however, the pattern underlying primary platinum resistance remains unclear. METHODS Reduced representation bisulfite sequencing (RRBS) analysis was performed to identify differences in methylation status between primary platinum-resistant patients Progression free survival (PFS) (PFS < 6 months, n = 8) and extreme sensitive patients (PFS ≥ 24 months, n = 8). The Qubit 3.0 Fluorometer was used for the quantification of RRBS library. The RRBS library was sequenced on Illumina HiSeq2500 sequencer as 50 bp paired-end reads. RESULTS After screening, 94 valid hyper-/hypo-methylated regions were identified to be located within 94 gene promoter and exon regions (adjusted q ≤ 0.5), which were primarily associated with cell-cell adhesion, B cell activation and lymphocyte activation according to GO analysis. The 19 differentially methylated regions (DMR) located in the promoter region including TRC-GCA11-1, LOC105370912, ANO7P1, DHX4,MSH2, CDCP2, CCNL1, ARHGAP42P2, PRDM13, LOC101928344, USP29, ZIC5,IL1RAPL1, EVX2, ABR, MGRN1, UBALD1, LINC00261, and ISL2 were identified according to the order of P-values from low to high, of which MSH2, LINC00261, MGRN1, ZIC5, EVX2, CCNL1, and DHX40 were presented to play a variety of roles in cancers process based on the previous studies. CONCLUSION DNA methylome profiling based on RRBS assay is an effective method for screening aberrantly methylated genes in primary platinum-resistant patients, which may serve as a potential epigenetic bio-marker for the prediction of primary platinum resistance.
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Affiliation(s)
- Tian Hua
- Department of Gynaecology, Affiliated Xing Tai People Hospital of Hebei Medial University, Xingtai, China
| | - Shan Kang
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Xiao-Fei Li
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Yun-Jie Tian
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Yan Li
- Department of Molecular Biology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
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El Jaddaoui I, Allali I, Sehli S, Ouldim K, Hamdi S, Al Idrissi N, Nejjari C, Amzazi S, Bakri Y, Ghazal H. Cancer Omics in Africa: Present and Prospects. Front Oncol 2020; 10:606428. [PMID: 33425763 PMCID: PMC7793679 DOI: 10.3389/fonc.2020.606428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022] Open
Abstract
During the last century, cancer biology has been arguably one of the most investigated research fields. To gain deeper insight into cancer mechanisms, scientists have been attempting to integrate multi omics data in cancer research. Cancer genomics, transcriptomics, metabolomics, proteomics, and metagenomics are the main multi omics strategies used currently in the diagnosis, prognosis, treatment, and biomarker discovery in cancer. In this review, we describe the use of different multi omics strategies in cancer research in the African continent and discuss the main challenges facing the implementation of these approaches in African countries such as the lack of training programs in bioinformatics in general and omics strategies in particular and suggest paths to address deficiencies. As a way forward, we advocate for the establishment of an "African Cancer Genomics Consortium" to promote intracontinental collaborative projects and enhance engagement in research activities that address indigenous aspects for cancer precision medicine.
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Affiliation(s)
- Islam El Jaddaoui
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Sofia Sehli
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | | | - Salsabil Hamdi
- Environmental Health Laboratory, Pasteur Institute, Casablanca, Morocco
| | - Najib Al Idrissi
- Department of Surgery, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Chakib Nejjari
- Department of Medicine, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Hassan Ghazal
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- National Center for Scientific and Technical Research, Rabat, Morocco
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20
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Decreased CDKL2 expression is correlated with the progression and poor prognosis of glioma. Pathol Res Pract 2020; 216:152920. [DOI: 10.1016/j.prp.2020.152920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/19/2020] [Accepted: 03/07/2020] [Indexed: 01/23/2023]
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Casamassimi A, Rienzo M, Di Zazzo E, Sorrentino A, Fiore D, Proto MC, Moncharmont B, Gazzerro P, Bifulco M, Abbondanza C. Multifaceted Role of PRDM Proteins in Human Cancer. Int J Mol Sci 2020; 21:ijms21072648. [PMID: 32290321 PMCID: PMC7177584 DOI: 10.3390/ijms21072648] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
The PR/SET domain family (PRDM) comprise a family of genes whose protein products share a conserved N-terminal PR [PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1)] homologous domain structurally and functionally similar to the catalytic SET [Su(var)3-9, enhancer-of-zeste and trithorax] domain of histone methyltransferases (HMTs). These genes are involved in epigenetic regulation of gene expression through their intrinsic HMTase activity or via interactions with other chromatin modifying enzymes. In this way they control a broad spectrum of biological processes, including proliferation and differentiation control, cell cycle progression, and maintenance of immune cell homeostasis. In cancer, tumor-specific dysfunctions of PRDM genes alter their expression by genetic and/or epigenetic modifications. A common characteristic of most PRDM genes is to encode for two main molecular variants with or without the PR domain. They are generated by either alternative splicing or alternative use of different promoters and play opposite roles, particularly in cancer where their imbalance can be often observed. In this scenario, PRDM proteins are involved in cancer onset, invasion, and metastasis and their altered expression is related to poor prognosis and clinical outcome. These functions strongly suggest their potential use in cancer management as diagnostic or prognostic tools and as new targets of therapeutic intervention.
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Affiliation(s)
- Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maria Chiara Proto
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Bruno Moncharmont
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
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Gohlke JH, Lloyd SM, Basu S, Putluri V, Vareed SK, Rasaily U, Piyarathna DWB, Fuentes H, Rajendiran TM, Dorsey TH, Ambati CR, Sonavane R, Karanam B, Bhowmik SK, Kittles R, Ambs S, Mims MP, Ittmann M, Jones JA, Palapattu G, Putluri N, Michailidis G, Sreekumar A. Methionine-Homocysteine Pathway in African-American Prostate Cancer. JNCI Cancer Spectr 2019; 3:pkz019. [PMID: 31360899 PMCID: PMC6489686 DOI: 10.1093/jncics/pkz019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/13/2019] [Accepted: 03/07/2019] [Indexed: 11/14/2022] Open
Abstract
African American (AA) men have a 60% higher incidence and two times greater risk of dying of prostate cancer (PCa) than European American men, yet there is limited insight into the molecular mechanisms driving this difference. To our knowledge, metabolic alterations, a cancer-associated hallmark, have not been reported in AA PCa, despite their importance in tumor biology. Therefore, we measured 190 metabolites across ancestry-verified AA PCa/benign adjacent tissue pairs (n = 33 each) and identified alterations in the methionine-homocysteine pathway utilizing two-sided statistical tests for all comparisons. Consistent with this finding, methionine and homocysteine were elevated in plasma from AA PCa patients using case-control (AA PCa vs AA control, methionine: P = .0007 and homocysteine: P < .0001), biopsy cohorts (AA biopsy positive vs AA biopsy negative, methionine: P = .0002 and homocysteine: P < .0001), and race assignments based on either self-report (AA PCa vs European American PCa, methionine: P = .001, homocysteine: P < .0001) or West African ancestry (upper tertile vs middle tertile, homocysteine: P < .0001; upper tertile vs low tertile, homocysteine: P = .002). These findings demonstrate reprogrammed metabolism in AA PCa patients and provide a potential biological basis for PCa disparities.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Arun Sreekumar
- Correspondence to: Arun Sreekumar, PhD, Department of Molecular and Cell Biology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 (e-mail: )
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23
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Zhang Y, Yan L, Yao W, Chen K, Xu H, Ye Z. Integrated Analysis of Genetic Abnormalities of the Histone Lysine Methyltransferases in Prostate Cancer. Med Sci Monit 2019; 25:193-239. [PMID: 30616239 PMCID: PMC6330996 DOI: 10.12659/msm.912294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background The histone methyltransferase (HMT) family includes histone lysine methyltransferases (HKMTs) and histone/protein arginine methyltransferases (PRMTs). The role of HMT gene variants in prostate cancer remains unknown. Therefore, this study aimed to evaluate HMT gene variants in the pathogenesis and prognosis of human prostate cancer, using in vitro cell studies and bioinformatics analysis. Material/Methods Integrative bioinformatics analysis of the expression of 51 HMT genes in human prostate cancer was based on datasets from the Cancer Genome Atlas (TCGA). Correlation and regression analysis were used to identify critical HMTs in prostate cancer. Kaplan-Meier and the area under the receiver operating characteristics curve (AUROC) were performed to evaluate the function of the HMTs on prognosis. Gene expression and function of 22Rv1 human prostate carcinoma cells were studied. Results The HMT genes identified to have a role in the pathogenesis of prostate cancer included the EZH2, SETD5, PRDM12, NSD1, SETD6, SMYD1, and the WHSC1L1 gene. The EZH2, SETD5, and SMYD1 genes were selected as a prognostic panel, with the SUV420H2 HMT gene. SETD2, NSD1, and ASH1L were identified as critical genes in the development of castration-resistant prostate cancer (CRPC), similar to mixed-lineage leukemia (MLL) complex family members. Knockdown of the SETD5 gene in 22Rv1 prostate carcinoma cells in vitro inhibited cancer cell growth and migration. Conclusions HMT gene variants may have a role in the pathogenesis of prostate cancer. Future studies may determine the role of HMT genes as prognostic biomarkers in patients with prostate cancer.
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Affiliation(s)
- Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Libin Yan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Weimin Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
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24
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Zhou Y, Qiu XP, Li ZH, Zhang S, Rong Y, Yang GH, Fang-Zheng. Clinical significance of aberrant cyclin-dependent kinase-like 2 methylation in hepatocellular carcinoma. Gene 2019; 683:35-40. [DOI: 10.1016/j.gene.2018.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/20/2018] [Accepted: 10/04/2018] [Indexed: 12/24/2022]
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25
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Chu SH, Loucks EB, Kelsey KT, Gilman SE, Agha G, Eaton CB, Buka SL, Huang YT. Sex-specific epigenetic mediators between early life social disadvantage and adulthood BMI. Epigenomics 2018; 10:707-722. [PMID: 29888956 DOI: 10.2217/epi-2017-0146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM The objective of this study was to identify potential epigenetic mediating pathways linking early life social disadvantage (ELSD) to adulthood BMI. METHODS Sex-specific epigenome-wide two-stage mediation analyses were conducted in blood and adipose tissue, and mediation estimates were obtained using cross-product mediation analysis. Pathway analyses were conducted using GREAT software (Bejerano Lab, CA, USA). RESULTS Candidate mediation CpG sites were identified in adipose tissue, but not blood, and were sex-specific. Significant mediation sites in females included CpG loci in genes: PKHG1, BCAR3, ADAM5P, PIEZO1, FGFRL1, FASN and DPP9, among others. Pathway analyses revealed evidence of enrichment for processes associated with TFG-β signaling and immunologic signatures. In males, significant mediation loci included sites in MAP3K5 and RPTOR, which have previously been associated with adipogenesis, inflammation and insulin resistance. CONCLUSION Our findings provide supportive evidence for the mediating role of epigenetic mechanisms in the effect of early life social disadvantage on adulthood BMI.
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Affiliation(s)
- Su H Chu
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA.,Channing Division of Network Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - Eric B Loucks
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA.,Department of Pathology & Laboratory Medicine, Brown University Warren Alpert Medical School, Providence, RI, 02912, USA
| | - Stephen E Gilman
- Health Behavior Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, Bethesda, MD, 20892, USA.,Department of Social & Behavioral Sciences, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA.,Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Golareh Agha
- Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Charles B Eaton
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA.,Department of Family Medicine, Brown University Warren Alpert Medical School, Providence, RI, 02912, USA
| | - Stephen L Buka
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA
| | - Yen-Tsung Huang
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA.,Department of Biostatistics, Brown School of Public Health, Providence, RI, 02912, USA.,Institute of Statistical Science, Academia Sinica, Taipei, 11529, Taiwan
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26
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Yi R, Yang S, Wen E, Hu Z, Long H, Zeng Y, Wang X, Huang X, Liao Y, Luo M, Wang J, Zhou M, Wang W, Xu A, Lin J, Wu Z, Song Y. Negative nuclear expression of CDKL2 correlates with disease progression and poor prognosis of glioma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:712-719. [PMID: 31938157 PMCID: PMC6958001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 01/09/2018] [Indexed: 06/10/2023]
Abstract
AIMS This study aimed to investigate the nuclear expression status of cyclin dependent kinase like 2 (CDKL2) in glioma and its correlation with the characteristics of clinical pathology, including patient survival. METHODS AND RESULTS In the present study, the expression of CDKL2 mRNA was detected by real-time QPCR in freshly collected glioma and para-carcinoma tissues. Moreover, immunohistochemistry was used to identified nuclear expression of CDKL2, and the characteristics of clinical pathology from glioma cases (n = 144) and non-cancerous brain tissues (n = 32) were counted. Low mRNA and nuclear protein expression of CDKL2 was observed in glioma tissues compared to non-cancerous tissues. Glioma patients with negative nuclear expression of CDKL2 were correlated with histologic type, clinical World Health Organization (WHO) grade, tumor location, and KI-67 expression status. Negative nuclear expression of CDKL2 in glioma patients predicted an observably shorter overall survival time than did positive expression. However, as demonstrated by multivariate analysis, nuclear expression of CDKL2 was not an independent prognostic biomarker for the survival of patients with glioma. CONCLUSIONS Our study indicated that negative nuclear expression of CDKL2 may represent a potential unfavorable marker for progression and poor prognostic in glioma.
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Affiliation(s)
- Renhui Yi
- Gannan Medical UniversityGanzhou, Jiangxi, P. R. China
- Department of Neurosurgery, First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, P. R. China
| | - Shaochun Yang
- Department of Neurosurgery, First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, P. R. China
| | - Ersheng Wen
- Gannan Medical UniversityGanzhou, Jiangxi, P. R. China
| | - Zheng Hu
- Department of Neurosurgery, First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, P. R. China
| | - Hao Long
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Yu Zeng
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Xizhao Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Xiaoyu Huang
- Gannan Medical UniversityGanzhou, Jiangxi, P. R. China
| | - Yuanyuan Liao
- Department of Ultrasonography, First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, P. R. China
| | - Muyun Luo
- Department of Neurosurgery, First Affiliated Hospital of Gannan Medical UniversityGanzhou, Jiangxi, P. R. China
| | - Jizhou Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Mingfeng Zhou
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Wen Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Anqi Xu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Jie Lin
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Zhiyong Wu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
| | - Ye Song
- Department of Neurosurgery, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, P. R. China
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Karakas C, Wang C, Deng F, Huang H, Wang D, Lee P. Molecular mechanisms involving prostate cancer racial disparity. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2017; 5:34-48. [PMID: 29181436 PMCID: PMC5698597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Prostate cancer (PCa) is the second leading cause of cancer-related deaths in the United States. The African (AA) descent has greater incidence and mortality rates of PCa as compared to Caucasian (CA) men. While socioeconomic differences across racial groups contribute to disparity in PCa, increasing evidence points that genetic and molecular alterations play important roles in racial disparities associated with PCa. In this review, we focus on genetic and molecular influences that contribute to racial disparity between AA and CA men including: androgen and estrogen receptor signaling pathways, growth factors, apoptotic proteins, genetic, genomic and epigenetic alterations. Future translational studies will identify prognostic and predictive biomarkers for AA PCa and assist in the development of new targeted-therapies specifically for AA men with PCa.
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Affiliation(s)
- Cansu Karakas
- Department of Pathology, New York University School of MedicineNew York, NY, USA
| | - Cassie Wang
- Department of Bioengineering, University of PennsylvaniaPennsylvania, PA, USA
| | - Fangming Deng
- Department of Pathology, New York University School of MedicineNew York, NY, USA
| | - Hongying Huang
- Department of Pathology, New York University School of MedicineNew York, NY, USA
| | - Dongwen Wang
- Department of Urology, First Hospital of Shanxi Medical UniversityTaiyuan, Shanxi, China
| | - Peng Lee
- Department of Pathology, New York University School of MedicineNew York, NY, USA
- Department of Urology, New York University School of MedicineNew York, NY, USA
- Department of New York Harbor Healthcare System, New York University School of MedicineNew York, NY, USA
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28
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A multicenter, randomized study of decitabine as epigenetic priming with induction chemotherapy in children with AML. Clin Epigenetics 2017; 9:108. [PMID: 29034009 PMCID: PMC5629751 DOI: 10.1186/s13148-017-0411-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/25/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Decitabine is a deoxycytidine nucleoside derivative inhibitor of DNA-methyltransferases, which has been studied extensively and is approved for myelodysplastic syndrome in adults but with less focus in children. Accordingly, we conducted a phase 1 multicenter, randomized, open-label study to evaluate decitabine pre-treatment before standard induction therapy in children with newly diagnosed AML to assess safety and tolerability and explore a number of biologic endpoints. RESULTS Twenty-four patients were fully assessable for all study objectives per protocol (10 in Arm A = epigenetic priming induction, 14 in Arm B = standard induction). All patients experienced neutropenia and thrombocytopenia. The most common grade 3 and 4 non-hematologic adverse events observed were gastrointestinal toxicities and hypophosphatemia. Plasma decitabine PK were similar to previously reported adult data. Overall CR/CRi was similar for the two arms. MRD negativity at end-induction was 85% in Arm A versus 67% in Arm B patients. DNA methylation measured in peripheral blood over the course of treatment tracked with blast clearance and matched marrow aspirates at day 0 and day 21. Unlike end-induction marrow analyses, promoter methylation in blood identified an apparent reversal of response in the lone treatment failure, 1 week prior to the patient's marrow aspirate confirming non-response. Decitabine-induced effects on end-induction (day 35-43 following initiation of treatment) marrows in Arm A were reflected by changes in DNA methylation in matched paired marrow diagnostic aspirates. CONCLUSIONS This first-in-pediatrics trial demonstrates that decitabine prior to standard combination chemotherapy is feasible and well tolerated in children with newly diagnosed AML. Pre-treatment with decitabine may represent a newer therapeutic option for pediatric AML, especially as it appears to induce important epigenetic alterations. The novel biological correlates studied in this trial offer a clinically relevant window into disease progression and remission. Additional studies are needed to definitively assess whether decitabine can enhance durability responses in children with AML. TRIAL REGISTRATION NCT01177540.
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29
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Hashimoto Y, Shiina M, Kato T, Yamamura S, Tanaka Y, Majid S, Saini S, Shahryari V, Kulkarni P, Dasgupta P, Mitsui Y, Sumida M, Deng G, Tabatabai L, Kumar D, Dahiya R. The role of miR-24 as a race related genetic factor in prostate cancer. Oncotarget 2017; 8:16581-16593. [PMID: 28157714 PMCID: PMC5369986 DOI: 10.18632/oncotarget.15016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/24/2017] [Indexed: 02/02/2023] Open
Abstract
The incidence of prostate cancer (PCa) among African-Americans (AfA) is significantly higher than Caucasian-Americans (CaA) but the genetic basis for this disparity is not known. To address this problem, we analyzed miRNA expression in AfA (n = 81) and CaA (n = 51) PCa patients. Here, we found that miR-24 is differentially expressed in AfA and CaA PCa patients and attempt to clarify its role in AfA patients. Also, the public sequencing data of the miR-24 promoter confirmed that it was highly methylated and down-regulated in PCa patients. Utilizing a VAMCSF and NDRI patient cohorts, we discovered that miR-24 expression was linked to a racial difference between AfA/CaA PCa patients. Interestingly, miR-24 was restored after treatment of PCa cells with 5Aza-CdR in an AfA cell line (MDA-PCa-2b), while restoration of miR-24 was not observed in CaA cells, DU-145. Ectopic expression of miR-24 showed decreased growth and induced apoptosis, though the effect was less in the CaA cell line compared to the AfA cell line. Finally, we found unique changes in biological pathways and processes associated with miR-24 transfected AfA cells by quantitative PCR-based gene expression array. Evaluation of the altered pathways showed that AR, IGF1, IGFBP5 and ETV1 were markedly decreased in the AfA derived cell line compared with CaA cells, and there was a reciprocal regulatory relationship of miR-24/target expression in prostate cancer patients. These results demonstrate that miR-24 may be a central regulator of key events that contribute to race-related tumorigenesis and has potential to be a therapeutic agent for PCa treatment.
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Affiliation(s)
- Yutaka Hashimoto
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Marisa Shiina
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Taku Kato
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Soichiro Yamamura
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Yuichiro Tanaka
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Shahana Majid
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Sharanjot Saini
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Varahram Shahryari
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Priyanka Kulkarni
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Pritha Dasgupta
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Yozo Mitsui
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Mitsuho Sumida
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Guoren Deng
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
| | - Laura Tabatabai
- Department of Pathology, Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, CA 94121, USA
| | - Deepak Kumar
- Julius L. Chambers Biomedical/Biotechnology Research Institute (BBRI), Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA
| | - Rajvir Dahiya
- Department of Urology, VA Medical Center and UCSF, San Francisco, CA 94121, USA
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Epigenetic Mediators Between Childhood Socioeconomic Disadvantage and Mid-Life Body Mass Index: The New England Family Study. Psychosom Med 2016; 78:1053-1065. [PMID: 27768648 PMCID: PMC7380568 DOI: 10.1097/psy.0000000000000411] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Childhood socioeconomic disadvantage is associated with adulthood obesity risk; however, epigenetic mechanisms are poorly understood. This work's objective was to evaluate whether associations of childhood socioeconomic disadvantage with adulthood body mass index (BMI) are mediated by DNA methylation. METHODS Participants were 141 men and women from the New England Family Study, prospectively followed prenatally through a mean age of 47 years. Epigenomewide DNA methylation was evaluated in peripheral blood and adipose tissue obtained at adulthood, using the Infinium HumanMethylation450K BeadChip. Childhood socioeconomic status (SES) at age 7 years was assessed directly from parents' reports. Offspring adiposity was directly assessed using BMI at a mean age of 47 years. Associations of SES, DNA methylation, and BMI were estimated using least square estimators. Statistical mediation analyses were performed using joint significance test and bootstrapping. RESULTS Of CpG sites significant at the 25% false discovery rate level in epigenomewide methylation BMI analyses, 91 sites in men and 71 sites in women were additionally significant for SES-methylation associations (p < .001) in adipose tissue. Many involved genes biologically relevant for development of obesity, including fatty acid synthase, transmembrane protein 88, signal transducer and activator of transcription 3, and neuritin 1. There was no evidence of epigenetic mediation in peripheral blood leukocytes. CONCLUSIONS DNA methylation at specific genes may be mediators of associations between childhood socioeconomic disadvantage and mid-life BMI in adipose tissue. Findings motivate continued efforts to study if and how childhood socioeconomic disadvantage is biologically embedded at the level of the epigenome in regions etiologically relevant for adiposity.
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