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Zhang H, Huang C, Gordon J, Yu S, Morton G, Childers W, Abou-Gharbia M, Zhang Y, Jelinek J, Issa JPJ. MC180295 is a highly potent and selective CDK9 inhibitor with preclinical in vitro and in vivo efficacy in cancer. Clin Epigenetics 2024; 16:3. [PMID: 38172923 PMCID: PMC10765884 DOI: 10.1186/s13148-023-01617-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Inhibition of cyclin-dependent kinase 9 (CDK9), a novel epigenetic target in cancer, can reactivate epigenetically silenced genes in cancer by dephosphorylating the SWI/SNF chromatin remodeler BRG1. Here, we characterized the anti-tumor efficacy of MC180295, a newly developed CDK9 inhibitor. METHODS In this study, we explored the pharmacokinetics of MC180295 in mice and rats, and tested the anti-tumor efficacy of MC180295, and its enantiomers, in multiple cancer cell lines and mouse models. We also combined CDK9 inhibition with a DNA methyltransferase (DNMT) inhibitor, decitabine, in multiple mouse models, and tested MC180295 dependence on T cells. Drug toxicity was measured by checking body weights and complete blood counts. RESULTS MC180295 had high specificity for CDK9 and high potency against multiple neoplastic cell lines (median IC50 of 171 nM in 46 cell lines representing 6 different malignancies), with the highest potency seen in AML cell lines derived from patients with MLL translocations. MC180295 is a racemic mixture of two enantiomers, MC180379 and MC180380, with MC180380 showing higher potency in a live-cell epigenetic assay. Both MC180295 and MC180380 showed efficacy in in vivo AML and colon cancer xenograft models, and significant synergy with decitabine in both cancer models. Lastly, we found that CDK9 inhibition-mediated anti-tumoral effects were partially dependent on CD8 + T cells in vivo, indicating a significant immune component to the response. CONCLUSIONS MC180380, an inhibitor of cyclin-dependent kinase 9 (CDK9), is an efficacious anti-cancer agent worth advancing further toward clinical use.
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Affiliation(s)
- Hanghang Zhang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chen Huang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - John Gordon
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, 19140, USA
| | - Sijia Yu
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - George Morton
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, 19140, USA
| | - Wayne Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, 19140, USA
| | - Magid Abou-Gharbia
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, 19140, USA
| | - Yi Zhang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ, 08103, USA
- Cooper Medical School at Rowan University, Camden, NJ, 08103, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ, 08103, USA.
- Cooper Medical School at Rowan University, Camden, NJ, 08103, USA.
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2
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Sun A, Park P, Cole L, Vaidya H, Maegawa S, Keith K, Calendo G, Madzo J, Jelinek J, Jobin C, Issa JPJ. Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa. Epigenetics 2023; 18:2160568. [PMID: 36572998 PMCID: PMC9980687 DOI: 10.1080/15592294.2022.2160568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/11/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic process altered in cancer and ageing. Age-related methylation drift can be used to estimate lifespan and can be influenced by extrinsic factors such as diet. Here, we report that non-pathogenic microbiota accelerate age-related methylation drift in the colon when compared with germ-free mice. DNA methylation analyses showed that microbiota and IL10KO were associated with changes in 5% and 4.1% of CpG sites, while mice with both factors had 18% alterations. Microbiota, IL10KO, and their combination altered 0.4%, 0.4%, and 4% of CpG island methylation, respectively. These are comparable to what is seen in colon cancer. Ageing changes were accelerated in the IL10KO mice with microbiota, and the affected genes were more likely to be altered in colon cancer. Thus, the microbiota affect DNA methylation of the colon in patterns reminiscent of what is observed in ageing and colorectal cancer.
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Affiliation(s)
- Ang Sun
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
| | - Pyounghwa Park
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Lauren Cole
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
| | - Himani Vaidya
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Shinji Maegawa
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Research Department of Pediatrics, University of Texas, MD Anderson Cancer Center Department of Pediatrics, University of Texas, MD Anderson Cancer CenterHouston, TX, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Gennaro Calendo
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Christian Jobin
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
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3
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Kusic DM, Heil J, Zajic S, Brangan A, Dairo O, Heil S, Feigin G, Kacinko S, Buono RJ, Ferraro TN, Rafeq R, Haroz R, Baston K, Bodofsky E, Sabia M, Salzman M, Resch A, Madzo J, Scheinfeldt LB, Issa JPJ, Jelinek J. Postmortem toxicology findings from the Camden Opioid Research Initiative. PLoS One 2023; 18:e0292674. [PMID: 37910493 PMCID: PMC10619848 DOI: 10.1371/journal.pone.0292674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
The United States continues to be impacted by decades of an opioid misuse epidemic, worsened by the COVID-19 pandemic and by the growing prevalence of highly potent synthetic opioids (HPSO) such as fentanyl. In instances of a toxicity event, first-response administration of reversal medications such as naloxone can be insufficient to fully counteract the effects of HPSO, particularly when there is co-occurring substance use. In an effort to characterize and study this multi-faceted problem, the Camden Opioid Research Initiative (CORI) has been formed. The CORI study has collected and analyzed post-mortem toxicology data from 42 cases of decedents who expired from opioid-related toxicity in the South New Jersey region to characterize substance use profiles. Co-occurring substance use, whether by intent or through possible contamination of the illicit opioid supply, is pervasive among deaths due to opioid toxicity, and evidence of medication-assisted treatment is scarce. Nearly all (98%) of the toxicology cases show the presence of the HPSO, fentanyl, and very few (7%) results detected evidence of medication-assisted treatment for opioid use disorder, such as buprenorphine or methadone, at the time of death. The opioid toxicity reversal drug, naloxone, was detected in 19% of cases, but 100% of cases expressed one or more stimulants, and sedatives including xylazine were detected in 48% of cases. These results showing complex substance use profiles indicate that efforts at mitigating the opioid misuse epidemic must address the complications presented by co-occurring stimulant and other substance use, and reduce barriers to and stigmas of seeking effective medication-assisted treatments.
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Affiliation(s)
- Dara M. Kusic
- Research, Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Jessica Heil
- Clinical Research Office, Cooper University Health Care, Camden, New Jersey, United States of America
| | - Stefan Zajic
- Research, Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Andrew Brangan
- Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Oluseun Dairo
- Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Stacey Heil
- Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Gerald Feigin
- Office of the Medical Examiner, Gloucester County Health Department, Sewell, New Jersey, United States of America
| | - Sherri Kacinko
- Forensic Toxicology, NMS Labs, Horsham, Pennsylvania, United States of America
| | - Russell J. Buono
- Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, United States of America
| | - Thomas N. Ferraro
- Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, United States of America
| | - Rachel Rafeq
- Department of Emergency Medicine, Cooper University Health Care, Camden, New Jersey, United States of America
| | - Rachel Haroz
- Department of Emergency Medicine, Cooper University Health Care, Camden, New Jersey, United States of America
| | - Kaitlan Baston
- Cooper Medical School of Rowan University, Camden, New Jersey, United States of America
| | - Elliot Bodofsky
- Neurological Institute, Cooper University Health Care, Camden, New Jersey, United States of America
| | - Michael Sabia
- Anesthesiology, Cooper University Health Care, Camden, New Jersey, United States of America
| | - Matthew Salzman
- Department of Emergency Medicine, Cooper University Health Care, Camden, New Jersey, United States of America
| | - Alissa Resch
- Research, Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Jozef Madzo
- Research, Coriell Institute for Medical Research, Camden, New Jersey, United States of America
- Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, United States of America
| | - Laura B. Scheinfeldt
- Research, Coriell Institute for Medical Research, Camden, New Jersey, United States of America
- Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, United States of America
| | - Jean-Pierre J. Issa
- Research, Coriell Institute for Medical Research, Camden, New Jersey, United States of America
- Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, United States of America
| | - Jaroslav Jelinek
- Research, Coriell Institute for Medical Research, Camden, New Jersey, United States of America
- Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, United States of America
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4
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Fenaux P, Gobbi M, Kropf PL, Issa JPJ, Roboz GJ, Mayer J, Krauter J, Robak T, Kantarjian H, Novak J, Jedrzejczak WW, Thomas X, Ojeda-Uribe M, Miyazaki Y, Min YH, Yeh SP, Brandwein J, Gercheva-Kyuchukova L, Demeter J, Griffiths E, Yee K, Döhner K, Hao Y, Keer H, Azab M, Döhner H. Guadecitabine vs treatment choice in newly diagnosed acute myeloid leukemia: a global phase 3 randomized study. Blood Adv 2023; 7:5027-5037. [PMID: 37276510 PMCID: PMC10471926 DOI: 10.1182/bloodadvances.2023010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
This phase 3 study evaluated the efficacy and safety of the new hypomethylating agent guadecitabine (n = 408) vs a preselected treatment choice (TC; n = 407) of azacitidine, decitabine, or low-dose cytarabine in patients with acute myeloid leukemia unfit to receive intensive induction chemotherapy. Half of the patients (50%) had poor Eastern Cooperative Oncology Group Performance Status (2-3). The coprimary end points were complete remission (19% and 17% of patients for guadecitabine and TC, respectively [stratified P = .48]) and overall survival (median survival 7.1 and 8.5 months for guadecitabine and TC, respectively [hazard ratio, 0.97; 95% confidence interval, 0.83-1.14; stratified log-rank P = .73]). One- and 2-year survival estimates were 37% and 18% for guadecitabine and 36% and 14% for TC, respectively. A large proportion of patients (42%) received <4 cycles of treatment in both the arms. In a post hoc analysis of patients who received ≥4 treatment cycles, guadecitabine was associated with longer median survival vs TC (15.6 vs 13.0 months [hazard ratio, 0.78; 95% confidence interval, 0.64-0.96; log-rank P = .02]). There was no significant difference in the proportion of patients with grade ≥3 adverse events (AEs) between guadecitabine (92%) and TC (88%); however, grade ≥3 AEs of febrile neutropenia, neutropenia, and pneumonia were higher with guadecitabine. In conclusion, no significant difference was observed in the efficacy of guadecitabine and TC in the overall population. This trial was registered at www.clinicaltrials.gov as #NCT02348489.
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Affiliation(s)
| | - Marco Gobbi
- Ospedale Policlinico San Martino, Genova, Italy
| | | | | | | | - Jiri Mayer
- Fakultní Nemocnice, Brno, Česká Republika
| | - Jürgen Krauter
- Städtisches Klinikum Braunschweig gGmbH, Braunschweig, Germany
| | - Tadeusz Robak
- Medical University of Lodz and Copernicus Memorial Hospital, Lodz, Poland
| | | | - Jan Novak
- Univerzita Karlova, Praha, Česká Republika
| | | | | | | | | | - Yoo Hong Min
- Severance Hospital, Yonsei University Health System, Seoul, Republic of Korea
| | - Su-Peng Yeh
- China Medical University Hospital, Taichung City, Taiwan
| | | | | | | | | | - Karen Yee
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Yong Hao
- Astex Pharmaceuticals Inc, Pleasanton, CA
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5
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Vaidya H, Jeong HS, Keith K, Maegawa S, Calendo G, Madzo J, Jelinek J, Issa JPJ. Author Correction: DNA methylation entropy as a measure of stem cell replication and aging. Genome Biol 2023; 24:104. [PMID: 37122020 PMCID: PMC10150501 DOI: 10.1186/s13059-023-02943-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Affiliation(s)
- Himani Vaidya
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
| | - Hye Seon Jeong
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
- Department of Neurology, Chungnam National University Hospital, Daejeon, South Korea
| | - Kelsey Keith
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Gennaro Calendo
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
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6
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Jang HJ, Hostetter G, MacFarlane AW, Madaj Z, Ross EA, Hinoue T, Kulchycki JR, Burgos RS, Tafseer M, Alpaugh RK, Schwebel CL, Kokate R, Geynisman DM, Zibelman MR, Ghatalia P, Nichols PW, Chung W, Madzo J, Hahn NM, Quinn DI, Issa JPJ, Topper MJ, Baylin SB, Shen H, Campbell KS, Jones PA, Plimack ER. A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy. Clin Cancer Res 2023:718801. [PMID: 36928921 DOI: 10.1158/1078-0432.ccr-22-3642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023]
Abstract
PURPOSE Based on preclinical evidence of epigenetic contribution to sensitivity and resistance to immune checkpoint inhibitors (ICI), we hypothesized that guadecitabine (hypomethylating agent) and atezolizumab (anti-PD-L1) together would potentiate a clinical response in patients with metastatic urothelial carcinoma (UC) unresponsive to initial immune checkpoint blockade therapy. PATIENTS AND METHODS We designed a single arm Phase II study (NCT03179943) with a safety run-in to identify the recommended phase II dose of the combination therapy of guadecitabine and atezolizumab. Patients with recurrent/advanced urothelial carcinoma who had previously progressed on ICI therapy with PD-1 or PD-L1 targeting agents were eligible. Pre-planned correlative analysis was performed to characterize peripheral immune dynamics and global DNA methylation, transcriptome, and immune infiltration dynamics of patient tumors. RESULTS Safety run-in enrolled 6 patients and Phase II enrolled 15 patients before the trial was closed for futility. No dose-limiting toxicity was observed. Four patients, with best response of stable disease, exhibited extended tumor control (8-11 months) and survival (>14 months). Correlative analysis revealed lack of DNA demethylation in tumors after 2 cycles of treatment. Increased peripheral immune activation and immune infiltration in tumors after treatment correlated with progression-free survival and stable disease. Furthermore, high IL-6 and IL-8 levels in the patients' plasma associates with short survival. CONCLUSIONS No RECIST responses were observed after combination therapy in this trial. Although we could not detect the anticipated tumor-intrinsic effects of guadecitabine, the addition of hypomethylating agent to ICI therapy induced immune activation in a few patients, which associated with longer patient survival.
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Affiliation(s)
- H Josh Jang
- Van Andel Institute, Grand Rapids, MI, United States
| | | | | | - Zachary Madaj
- Van Andel Institute, Grand Rapids, MI, United States
| | - Eric A Ross
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | | | | | - Ryan S Burgos
- Van Andel Institute, Grand Rapids, MI, United States
| | | | | | | | - Rutika Kokate
- Fox Chase Cancer Center, Philadelphia, United States
| | | | | | | | - Peter W Nichols
- University of Southern California, Keck School of Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, CA, United States
| | - Woonbok Chung
- Coriell Institute For Medical Research, Camden, NJ, United States
| | - Jozef Madzo
- Coriell Institute For Medical Research, Camden, NJ, United States
| | - Noah M Hahn
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States
| | - David I Quinn
- University of Southern California, Los Angeles, CA, United States
| | | | | | - Stephen B Baylin
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hui Shen
- Van Andel Institute, Los Angeles, United States
| | | | - Peter A Jones
- Van Andel Institute, Grand Rapids, MI, United States
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7
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Vaidya H, Jeong HS, Keith K, Maegawa S, Calendo G, Madzo J, Jelinek J, Issa JPJ. DNA methylation entropy as a measure of stem cell replication and aging. Genome Biol 2023; 24:27. [PMID: 36797759 PMCID: PMC9933260 DOI: 10.1186/s13059-023-02866-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 02/05/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Epigenetic marks are encoded by DNA methylation and accumulate errors as organisms age. This drift correlates with lifespan, but the biology of how this occurs is still unexplained. We analyze DNA methylation with age in mouse intestinal stem cells and compare them to nonstem cells. RESULTS Age-related changes in DNA methylation are identical in stem and nonstem cells, affect most prominently CpG islands and correlate weakly with gene expression. Age-related DNA methylation entropy, measured by the Jensen-Shannon Distribution, affects up to 25% of the detectable CpG sites and is a better measure of aging than individual CpG methylation. We analyze this entropy as a function of age in seven other tissues (heart, kidney, skeletal muscle, lung, liver, spleen, and blood) and it correlates strikingly with tissue-specific stem cell division rates. Thus, DNA methylation drift and increased entropy with age are primarily caused by and are sensors for, stem cell replication in adult tissues. CONCLUSIONS These data have implications for the mechanisms of tissue-specific functional declines with aging and for the development of DNA-methylation-based biological clocks.
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Affiliation(s)
- Himani Vaidya
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Hye Seon Jeong
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA ,grid.411665.10000 0004 0647 2279Department of Neurology, Chungnam National University Hospital, Daejeon, South Korea
| | - Kelsey Keith
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Shinji Maegawa
- grid.240145.60000 0001 2291 4776Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX USA
| | - Gennaro Calendo
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Jozef Madzo
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Jaroslav Jelinek
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Jean-Pierre J. Issa
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
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8
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Kim JY, Jelinek J, Lee YH, Kim DH, Kang K, Ryu SH, Moon HR, Cho K, Rha SH, Cha JK, Issa JPJ, Kim J. Hypomethylation in MTNR1B: a novel epigenetic marker for atherosclerosis profiling using stenosis radiophenotype and blood inflammatory cells. Clin Epigenetics 2023; 15:11. [PMID: 36658621 PMCID: PMC9854223 DOI: 10.1186/s13148-023-01423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Changes in gene-specific promoter methylation may result from aging and environmental influences. Atherosclerosis is associated with aging and environmental effects. Thus, promoter methylation profiling may be used as an epigenetic tool to evaluate the impact of aging and the environment on atherosclerosis development. However, gene-specific methylation changes are currently inadequate epigenetic markers for predicting atherosclerosis and cardiovascular disease pathogenesis. RESULTS We profiled and validated changes in gene-specific promoter methylation associated with atherosclerosis using stenosis radiophenotypes of cranial vessels and blood inflammatory cells rather than direct sampling of atherosclerotic plaques. First, we profiled gene-specific promoter methylation changes using digital restriction enzyme analysis of methylation (DREAM) sequencing in peripheral blood mononuclear cells from eight samples each of cranial vessels with and without severe-stenosis radiophenotypes. Using DREAM sequencing profiling, 11 tags were detected in the promoter regions of the ACVR1C, ADCK5, EFNA2, ENOSF1, GLS2, KNDC1, MTNR1B, PACSIN3, PAX8-AS1, TLDC1, and ZNF7 genes. Using methylation evaluation, we found that EFNA2, ENOSF1, GLS2, KNDC1, MTNR1B, PAX8-AS1, and TLDC1 showed > 5% promoter methylation in non-plaque intima, atherosclerotic vascular tissues, and buffy coats. Using logistic regression analysis, we identified hypomethylation of MTNR1B as an independent variable for the stenosis radiophenotype prediction model by combining it with traditional atherosclerosis risk factors including age, hypertension history, and increases in creatinine, lipoprotein (a), and homocysteine. We performed fivefold cross-validation of the prediction model using 384 patients with ischemic stroke (50 [13%] no-stenosis and 334 [87%] > 1 stenosis radiophenotype). For the cross-validation, the training dataset included 70% of the dataset. The prediction model showed an accuracy of 0.887, specificity to predict stenosis radiophenotype of 0.940, sensitivity to predict no-stenosis radiophenotype of 0.533, and area under receiver operating characteristic curve of 0.877 to predict stenosis radiophenotype from the test dataset including 30% of the dataset. CONCLUSIONS We identified and validated MTNR1B hypomethylation as an epigenetic marker to predict cranial vessel atherosclerosis using stenosis radiophenotypes and blood inflammatory cells rather than direct atherosclerotic plaque sampling.
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Affiliation(s)
- Jee Yeon Kim
- grid.254230.20000 0001 0722 6377Department of Neurology and Neuroepigenetics Laboratory, College of Medicine and Hospital, Chungnam National University, 282 Moonhwaro, Joongku, Daejeon, 35015 South Korea
| | - Jaroslav Jelinek
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ USA
| | - Young Ho Lee
- grid.254230.20000 0001 0722 6377Department of Anatomy, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Dae Hyun Kim
- grid.412048.b0000 0004 0647 1081Department of Neurology, Dong-A University Hospital, Busan, South Korea
| | - Keunsoo Kang
- grid.411982.70000 0001 0705 4288Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, South Korea
| | - Su Hyun Ryu
- grid.254230.20000 0001 0722 6377Department of Neurology and Neuroepigenetics Laboratory, College of Medicine and Hospital, Chungnam National University, 282 Moonhwaro, Joongku, Daejeon, 35015 South Korea
| | - Hye Rin Moon
- grid.254230.20000 0001 0722 6377Department of Neurology and Neuroepigenetics Laboratory, College of Medicine and Hospital, Chungnam National University, 282 Moonhwaro, Joongku, Daejeon, 35015 South Korea
| | - Kwangjo Cho
- grid.412048.b0000 0004 0647 1081Department of Thoracic and Cardiovascular Surgery, Dong-A University Hospital, Busan, South Korea
| | - Seo Hee Rha
- grid.412048.b0000 0004 0647 1081Department of Pathology, Dong-A University Hospital, Busan, South Korea
| | - Jae Kwan Cha
- grid.254230.20000 0001 0722 6377Department of Anatomy, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Jean-Pierre J. Issa
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ USA
| | - Jei Kim
- grid.254230.20000 0001 0722 6377Department of Neurology and Neuroepigenetics Laboratory, College of Medicine and Hospital, Chungnam National University, 282 Moonhwaro, Joongku, Daejeon, 35015 South Korea ,grid.411665.10000 0004 0647 2279Daejeon-Chungnam Regional Cerebrovascular Center, Chungnam National University Hospital, Daejeon, South Korea
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9
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Ghosh J, Schultz BM, Chan J, Wultsch C, Singh R, Shureiqi I, Chow S, Doymaz A, Varriano S, Driscoll M, Muse J, Kleiman FE, Krampis K, Issa JPJ, Sapienza C. Epigenome-Wide Study Identifies Epigenetic Outliers in Normal Mucosa of Patients with Colorectal Cancer. Cancer Prev Res (Phila) 2022; 15:755-766. [PMID: 36219239 PMCID: PMC9623234 DOI: 10.1158/1940-6207.capr-22-0258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 01/31/2023]
Abstract
Nongenetic predisposition to colorectal cancer continues to be difficult to measure precisely, hampering efforts in targeted prevention and screening. Epigenetic changes in the normal mucosa of patients with colorectal cancer can serve as a tool in predicting colorectal cancer outcomes. We identified epigenetic changes affecting the normal mucosa of patients with colorectal cancer. DNA methylation profiling on normal colon mucosa from 77 patients with colorectal cancer and 68 controls identified a distinct subgroup of normally-appearing mucosa with markedly disrupted DNA methylation at a large number of CpGs, termed as "Outlier Methylation Phenotype" (OMP) and are present in 15 of 77 patients with cancer versus 0 of 68 controls (P < 0.001). Similar findings were also seen in publicly available datasets. Comparison of normal colon mucosa transcription profiles of patients with OMP cancer with those of patients with non-OMP cancer indicates genes whose promoters are hypermethylated in the OMP patients are also transcriptionally downregulated, and that many of the genes most affected are involved in interactions between epithelial cells, the mucus layer, and the microbiome. Analysis of 16S rRNA profiles suggests that normal colon mucosa of OMPs are enriched in bacterial genera associated with colorectal cancer risk, advanced tumor stage, chronic intestinal inflammation, malignant transformation, nosocomial infections, and KRAS mutations. In conclusion, our study identifies an epigenetically distinct OMP group in the normal mucosa of patients with colorectal cancer that is characterized by a disrupted methylome, altered gene expression, and microbial dysbiosis. Prospective studies are needed to determine whether OMP could serve as a biomarker for an elevated epigenetic risk for colorectal cancer development. PREVENTION RELEVANCE Our study identifies an epigenetically distinct OMP group in the normal mucosa of patients with colorectal cancer that is characterized by a disrupted methylome, altered gene expression, and microbial dysbiosis. Identification of OMPs in healthy controls and patients with colorectal cancer will lead to prevention and better prognosis, respectively.
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Affiliation(s)
- Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Bryant M. Schultz
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Joe Chan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Claudia Wultsch
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, New York.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Rajveer Singh
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, New York
| | - Imad Shureiqi
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Stephanie Chow
- Nutrition Department, School of Urban Public Health at Hunter College, New York, New York
| | - Ahmet Doymaz
- Department of Chemistry, Hunter College, City University of New York, New York, New York
| | - Sophia Varriano
- The Graduate Center, City University of New York, New York, New York
| | | | - Jennifer Muse
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Frida E. Kleiman
- Department of Chemistry, Hunter College, City University of New York, New York, New York
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, New York.,Department of Biological Sciences, Hunter College, City University of New York, New York, New York.,Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | | | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania.,Corresponding Author: Carmen Sapienza, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, 3307 N. Broad Street, Room 300, Philadelphia, PA 19140. Phone: 215-707-7373; E-mail:
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10
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Zeidan AM, Fenaux P, Gobbi M, Mayer J, Roboz GJ, Krauter J, Robak T, Kantarjian HM, Novák J, Jedrzejczak WW, Thomas X, Ojeda-Uribe M, Miyazaki Y, Min YH, Yeh SP, Brandwein JM, Gercheva L, Demeter J, Griffiths EA, Yee KWL, Issa JPJ, Bewersdorf JP, Keer H, Hao Y, Azab M, Döhner H. Prospective comparison of outcomes with azacitidine and decitabine in patients with AML ineligible for intensive chemotherapy. Blood 2022; 140:285-289. [PMID: 35507690 PMCID: PMC9305088 DOI: 10.1182/blood.2022015832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/27/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Amer M Zeidan
- Section of Hematology, Department of Medicine, Yale University, New Haven, CT
- Yale Cancer Center, New Haven, CT
| | | | - Marco Gobbi
- Ospedale Policlinico San Martino, Genova, Italy
| | - Jiří Mayer
- Fakultní Nemocnice, Brno, Czech Republic
| | - Gail J Roboz
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, Cornell University, New York, NY
- NewYork-Presbyterian Hospital, New York, NY
| | - Jürgen Krauter
- Städtisches Klinikum Braunschweig, Braunschweig, Germany
| | - Tadeusz Robak
- Copernicus Memorial Hospital, Lodz, Poland; Department of Hematology, Medical University of Lodz, Lodz, Poland
| | | | - Jan Novák
- Fakultní Nemocnice Královské Vinohrady, Praha, Czech Republic
| | - Wieslaw W Jedrzejczak
- Uniwersyteckie Centrum Kliniczne, Warszawskiego Uniwersytetu Medycznego, Warsaw, Poland
| | | | - Mario Ojeda-Uribe
- Groupe Hospitalier de la Région Mulhouse Sud-Alsace, Mulhouse, France
| | | | - Yoo Hong Min
- Severance Hospital, Yonsei University Health System, Seoul, Republic of Korea
| | - Su-Peng Yeh
- China Medical University Hospital, Taichung, Taiwan, Republic of China
| | | | - Liana Gercheva
- Multiprofile Hospital for Active Treatment Sveta Marina EAD, Varna, Bulgaria
| | | | | | | | | | - Jan Philipp Bewersdorf
- Section of Hematology, Department of Medicine, Yale University, New Haven, CT
- Yale Cancer Center, New Haven, CT
- Leukemia Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Harold Keer
- Astex Pharmaceuticals, Inc., Pleasanton, CA; and
| | - Yong Hao
- Astex Pharmaceuticals, Inc., Pleasanton, CA; and
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11
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Plimack ER, Campbell K, Issa JPJ, Hahn NM, Quinn DI, Jang HS, Hostetter G, Nichols PW, Chung W, Madzo J, Ohtani H, Shen H, Hinoue T, Baylin SB, Jones PA. Abstract CT121: A Phase II trial of guadecitabine (G) plus atezolizumab (A) in patients with metastatic urothelial carcinoma (UC) progressing after initial checkpoint inhibitor therapy. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-ct121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: We report the results of a phase II trial testing the hypothesis that adding the hypomethylating agent G to the PDL1 inhibitor A in patients with mUC who developed primary or acquired resistance to checkpoint blockade (CB) will overcome this resistance by (1) eliciting viral mimicry in the tumor tissue to potentiate and reinvigorate anti-tumor immunity, (2) epigenetic reprogramming of T lymphocytes to overcome exhaustion.
Methods: Pts with mUC resistant to CB accrued at 3 centers were treated with G 45mg/m2 daily days 1-5 every 6 wks and A 1200mg every 3 wks. After initial safety lead in with 6 patients, trial was designed to add 37 additional patients. The primary endpoint was ORR. Correlative analyses included analysis of peripheral blood T cells and tumor tissue collected at baseline and once during treatment.
Results: 21 pts were enrolled. 20 pts were evaluable for response. Best response was PD (16), SD (4). 10 patients progressed clinically prompting earlier than scheduled (12 wk) imaging. Four pts exhibited a “hyperprogression” phenotype exhibiting rapid acceleration of tumor growth rate starting with initiation of therapy. At presepcified interim analysis it was determined that the trial would not meet its primary endpoint and it closed early. Median PFS 2.6 mo, median OS 8 mo. The 4 patients with SD maintained that status for median 13 months (range 9-15 mo). Global DNA methylome and transcriptome profiles from pre- and post-treatment tumor samples revealed a lack of transposable element-induced viral mimicry activation, which correlated with minimal DNA demethylation being induced in the tumors. Of note, flow cytometry-based immune profiling of peripheral blood from patients suggests a correlation between increased progression-free survival (PFS) with 1) lower expression of DNAM-1 on mature NK cells and 2) lower expression of CD39 on CD8+ effector T cells at time of inclusion on the trial.
Conclusions: While no responses were seen, both prolonged SD and hyperprogression were seen. Further tissue and peripheral blood based analyses are ongoing to elucidate the biological determinates of this dichotomy.
Citation Format: Elizabeth R. Plimack, Kerry Campbell, Jean-Pierre J. Issa, Noah M. Hahn, David I. Quinn, Hyo Sik Jang, Galen Hostetter, Peter W. Nichols, Woonbok Chung, Jozef Madzo, Hitoshi Ohtani, Hui Shen, Toshinori Hinoue, Stephen B. Baylin, Peter A. Jones. A Phase II trial of guadecitabine (G) plus atezolizumab (A) in patients with metastatic urothelial carcinoma (UC) progressing after initial checkpoint inhibitor therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT121.
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Affiliation(s)
| | | | | | - Noah M. Hahn
- 3The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David I. Quinn
- 4USC Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | | | | | | | - Jozef Madzo
- 2Coriell Institute for Medical Research, Camden, NJ
| | | | - Hui Shen
- 5Van Andel Research Institute, Grand Rapids, MI
| | | | - Stephen B. Baylin
- 3The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
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12
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Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JPJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun 2021; 12:687. [PMID: 33514726 PMCID: PMC7846738 DOI: 10.1038/s41467-021-20907-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied. We perform reduced representation bisulfite sequencing of invasive lung adenocarcinoma and its precursors, atypical adenomatous hyperplasia, adenocarcinoma in situ and minimally invasive adenocarcinoma. We observe gradual increase of methylation aberrations and significantly higher level of methylation ITH in later-stage lesions. The phylogenetic patterns inferred from methylation aberrations resemble those based on somatic mutations suggesting parallel methylation and genetic evolution. De-convolution reveal higher ratio of T regulatory cells (Tregs) versus CD8 + T cells in later-stage diseases, implying progressive immunosuppression with neoplastic progression. Furthermore, increased global hypomethylation is associated with higher mutation burden, copy number variation burden and AI burden as well as higher Treg/CD8 ratio, highlighting the potential impact of methylation on chromosomal instability, mutagenesis and tumor immune microenvironment during early carcinogenesis of lung adenocarcinomas.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Runzhe Chen
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jian Carrot-Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Nicholas McGranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, SW73RP, UK
| | - Lisha Ying
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, 310022, Hangzhou, China
- Zhejiang Cancer Research Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Chi-Wan Chow
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Myrna C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Brett W Carter
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carmen Behrens
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mara B Antonoff
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Boris Sepesi
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Humam Kadara
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ara A Vaporciyan
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Dan Su
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China.
| | | | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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13
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Leclerc D, Jelinek J, Christensen KE, Issa JPJ, Rozen R. High folic acid intake increases methylation-dependent expression of Lsr and dysregulates hepatic cholesterol homeostasis. J Nutr Biochem 2020; 88:108554. [PMID: 33220403 DOI: 10.1016/j.jnutbio.2020.108554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/17/2020] [Accepted: 11/12/2020] [Indexed: 12/12/2022]
Abstract
Food fortification with folic acid and increased use of vitamin supplements have raised concerns about high folic acid intake. We previously showed that high folic acid intake was associated with hepatic degeneration, decreased levels of methylenetetrahydrofolate reductase (MTHFR), lower methylation potential, and perturbations of lipid metabolism. MTHFR synthesizes the folate derivative for methylation reactions. In this study, we assessed the possibility that high folic acid diets, fed to wild-type and Mthfr+/- mice, could alter DNA methylation and/or deregulate hepatic cholesterol homeostasis. Digital restriction enzyme analysis of methylation in liver revealed DNA hypomethylation of a CpG in the lipolysis-stimulated lipoprotein receptor (Lsr) gene, which is involved in hepatic uptake of cholesterol. Pyrosequencing confirmed this methylation change and identified hypomethylation of several neighboring CpG dinucleotides. Lsr expression was increased and correlated negatively with DNA methylation and plasma cholesterol. A putative binding site for E2F1 was identified. ChIP-qPCR confirmed reduced E2F1 binding when methylation at this site was altered, suggesting that it could be involved in increasing Lsr expression. Expression of genes in cholesterol synthesis, transport or turnover (Abcg5, Abcg8, Abcc2, Cyp46a1, and Hmgcs1) was perturbed by high folic acid intake. We also observed increased hepatic cholesterol and increased expression of genes such as Sirt1, which might be involved in a rescue response to restore cholesterol homeostasis. Our work suggests that high folic acid consumption disturbs cholesterol homeostasis in liver. This finding may have particular relevance for MTHFR-deficient individuals, who represent ~10% of many populations.
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Affiliation(s)
- Daniel Leclerc
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Karen E Christensen
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Rima Rozen
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada.
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14
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Kim JY, Choi BG, Jelinek J, Kim DH, Lee SH, Cho K, Rha SH, Lee YH, Jin HS, Choi DK, Kim GE, Kwon SU, Hwang J, Cha JK, Lee S, Issa JPJ, Kim J. Promoter methylation changes in ALOX12 and AIRE1: novel epigenetic markers for atherosclerosis. Clin Epigenetics 2020; 12:66. [PMID: 32398127 PMCID: PMC7218560 DOI: 10.1186/s13148-020-00846-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Atherosclerosis is the main cause of cardiovascular diseases such as ischemic stroke and coronary heart disease. Gene-specific promoter methylation changes have been suggested as one of the causes underlying the development of atherosclerosis. We aimed to identify and validate specific genes that are differentially expressed through promoter methylation in atherosclerotic plaques. We performed the present study in four steps: (1) profiling and identification of gene-specific promoter methylation changes in atherosclerotic tissues; (2) validation of the promoter methylation changes of genes in plaques by comparison with non-plaque intima; (3) evaluation of promoter methylation status of the genes in vascular cellular components composing atherosclerotic plaques; and (4) evaluation of promoter methylation differences in genes among monocytes, T cells, and B cells isolated from the blood of ischemic stroke patients. RESULTS Upon profiling, AIRE1, ALOX12, FANK1, NETO1, and SERHL2 were found to have displayed changes in promoter methylation. Of these, AIRE1 and ALOX12 displayed higher methylation levels in plaques than in non-plaque intima, but lower than those in the buffy coat of blood. Between inflammatory cells, the three genes were significantly less methylated in monocytes than in T and B cells. In the vascular cells, AIRE1 methylation was lower in endothelial and smooth muscle cells. ALOX12 methylation was higher in endothelial, but lower in smooth muscle cells. Immunofluorescence staining showed that co-localization of ALOX12 and AIRE1 was more frequent in CD14(+)-monocytes than in CD4(+)-T cell in plaque than in non-plaque intima. CONCLUSIONS Promoter methylation changes in AIRE1 and ALOX12 occur in atherosclerosis and can be considered as novel epigenetic markers.
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Affiliation(s)
- Jee Yeon Kim
- Department of Neurology and Neuroepigenetics Laboratory, School of Medicine and Hospital, Chungnam National University, Daejeon, South Korea
| | - Bong-Geun Choi
- Department of Neurology and Neuroepigenetics Laboratory, School of Medicine and Hospital, Chungnam National University, Daejeon, South Korea
- Biomedical Research Center, Chungnam National University Hospital, Daejeon, South Korea
| | | | - Dae Hyun Kim
- Department of Neurology, Dong-A University Hospital, Busan, South Korea
| | - Seo Hyun Lee
- Division of Medical Mathematics Researches, National Institute for Mathematical Sciences, Daejeon, South Korea
| | - Kwangjo Cho
- Department of Thoracic and Cardiovascular Surgery, Dong-A University Hospital, Busan, South Korea
| | - Seo Hee Rha
- Department of Pathology, Dong-A University Hospital, Busan, South Korea
| | - Young Ho Lee
- Department of Anatomy, School of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hyo Sun Jin
- Biomedical Research Center, Chungnam National University Hospital, Daejeon, South Korea
| | - Dae-Kyoung Choi
- Biomedical Research Center, Chungnam National University Hospital, Daejeon, South Korea
| | - Geun-Eun Kim
- Department of Vascular Surgery, Asan Medical Center, Seoul, South Korea
| | - Sun U Kwon
- Department of Neurology, Asan Medical Center, Seoul, South Korea
| | - Junha Hwang
- Department of Neurology and Neuroepigenetics Laboratory, School of Medicine and Hospital, Chungnam National University, Daejeon, South Korea
| | - Jae Kwan Cha
- Department of Neurology, Dong-A University Hospital, Busan, South Korea
| | - Sukhoon Lee
- Division of Medical Mathematics Researches, National Institute for Mathematical Sciences, Daejeon, South Korea
| | | | - Jei Kim
- Department of Neurology and Neuroepigenetics Laboratory, School of Medicine and Hospital, Chungnam National University, Daejeon, South Korea.
- Department of Neurology, Chungnam National University Hospital, 282 Moonhwaro, Joongku, Daejeon, 35015, South Korea.
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15
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Kim JY, Choi BG, Jelinek J, Kim DH, Cho K, Rha SH, Lee YH, Kim GE, Kwon SU, Hwang J, Cha JK, Issa JPJ, Kim J. Abstract 139: Promoter Methylation Changes in
ALOX12, AIRE1, and NETO1
: Novel Epigenetic Markers for Atherosclerosis. Stroke 2020. [DOI: 10.1161/str.51.suppl_1.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background and Objective:
We aimed to identify and validate specific genes developing changes in promoter methylation in atherosclerotic plaques.
Methods:
We initially profiled DNA methylation signatures via a high-throughput sequencing platform from 5 carotid endarterectomy (CEA) plaques to identify genes with altered promoter methylation. The significances of the identified gene-specific promoter methylations were validated by the comparison between 1) plaques and non-plaque intima of the common carotid artery harvested from 20 cadavers, 2) cellular components composing atherosclerosis including plaques and buffy coats of blood of 27 CEA patients, 5 human umbilical vein endothelial cells (HUVEC), 2 human aortic endothelial (HAEC) and 2 smooth muscle (HASMC) cell lines, and, 3) monocytes, T- and B-cell circulating in blood of 19 ischemic stroke patients. Finally, the localization pattern the genes was compared by the inflammatory cell types infiltrated into atherosclerotic plaque and non-plaque intima using immunofluorescence stain.
Results:
Upon the profiling, five genes (
AIRE1
,
ALOX12
,
FANK1
,
NETO1
, and
SERHL2
) displayed changes in promoter methylation. Of these,
AIRE1
,
ALOX12, and NETO1
displayed higher methylation in plaques than in non-plaque intima, but lower than buffy coat of blood. In vascular cells,
AIRE1
and
NETO1
methylation was lower in HUVEC, HAEC and HASMC, but,
ALOX12
methylation was higher in HUVEC and HAEC, but, lower in HASMC than CEA plaques. Of inflammatory cells, methylation of the three genes was significantly lower in monocytes than T- and B-cells. On immunofluorescence statin for ALOX12, CD14(+)-monocytes was 3 times more frequent than CD4(+)-T-cell of total ALOX12-stained cells in plaques than non-plaque intima.
Conclusions:
The present study profiled and validated the promoter methylation changes of
AIRE1
,
ALOX12,
and
NETO1
as novel epigenetic markers related with atherosclerosis. In particular, epigenetic augmentation of the 3 genes occurred in monocytes of the cellular components composing atherosclerotic plaques.
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Affiliation(s)
- Jee Yeon Kim
- Chungnam Natl Univ Hosp, Daejeon, Korea, Republic of
| | - Bong-Gen Choi
- Chungnam Natl Univ Hosp, Daejeon, Korea, Republic of
| | | | | | | | | | | | | | | | - Junha Hwang
- Chungnam Natl Univ Hosp, Daejeon, Korea, Republic of
| | | | | | - Jei Kim
- Chungnam Natl Univ Hosp, Daejeon, Korea, Republic of
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16
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Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JPJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations. Genome Biol 2019; 20:249. [PMID: 31767039 PMCID: PMC6876109 DOI: 10.1186/s13059-019-1824-y] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Stephan Beck
- Medical Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Trey Ideker
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA.
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.
- The Wellcome Trust Sanger Institute, Cambridge, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany.
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau.
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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17
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Chung W, Kelly AD, Kropf P, Fung H, Jelinek J, Su XY, Roboz GJ, Kantarjian HM, Azab M, Issa JPJ. Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia. Clin Epigenetics 2019; 11:106. [PMID: 31331399 PMCID: PMC6647096 DOI: 10.1186/s13148-019-0704-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Background Guadecitabine is a novel DNA methyltransferase (DNMT) inhibitor with improved pharmacokinetics and clinical activity in a subset of patients with relapsed/refractory acute myeloid leukemia (r/r AML), but identification of this subset remains difficult. Methods To search for biomarkers of response, we measured genome-wide DNA methylation, mutations of 54 genes, and expression of a panel of 7 genes in pre-treatment samples from 128 patients treated at therapeutic doses in a phase I/II study. Results Response rate to guadecitabine was 17% (2 complete remission (CR), 3 CR with incomplete blood count recovery (CRi), or CR with incomplete platelets recovery (CRp)) in the phase I component and 23% (14 CR, 9 CRi/CRp) in phase II. There were no strong mutation or methylation predictors of response. Gene expression clustering defined a subset of patients (~ 20%) that had (i) high DNMT3B and low CDKN2B, CTCF, and CDA expression; (ii) enrichment for KRAS/NRAS mutations; (iii) frequent CpG island hypermethylation; (iv) low long interspersed nuclear element 1 (LINE-1) hypomethylation after treatment; and (v) resistance to guadecitabine in both phase I (response rate 0% vs. 33%, p = 0.07) and phase II components of the study (response rate 5% vs. 30%, p = 0.02). Multivariate analysis identified peripheral blood (PB) blasts and hemoglobin as predictors of response and cytogenetics, gene expression, RAS mutations, and hemoglobin as predictors of survival. Conclusions A subset of patients (~ 20%) with r/r AML is unlikely to benefit from guadecitabine as a single agent. In the remaining 80%, guadecitabine is a viable option with a median survival of 8 months and a 2-year survival rate of 21%. Trial registration NCT01261312. Electronic supplementary material The online version of this article (10.1186/s13148-019-0704-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA. .,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA.
| | - Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA
| | - Patricia Kropf
- Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA
| | - Henry Fung
- Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA.,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
| | | | - Gail J Roboz
- Weill Cornell Medicine, Division of Hematology and Oncology, The New York Presbyterian Hospital, New York, NY, USA
| | | | | | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA.,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
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18
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Park PH, Gharaibeh RZ, Cole L, Sun A, Chung W, Jelinek J, Pope JL, Jobin C, Issa JPJ. Abstract LB-141: CIMP is associated with altered microbiota composition in colorectal cancer patients. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
DNA methylation changes are important in cancer development and the etiology of the CpG Island Methylator Phenotype (CIMP), the most extreme form of aberrant promoter DNA methylation in cancer, can only partially be explained by genetic changes. An association between CIMP and the gut microbiota has been implicated in colorectal cancer (CRC) pathogenesis but the exact mechanisms underlying the observations are poorly understood. In order to clarify the link between CIMP and the microbiome in CRC, we studied human primary tumor and adjacent mucosal tissues (normal) from CRC patients (n=46). The patient samples were categorized by tumor sites (23 proximal and 23 distal), sex (28 males and 18 females), and age (69 yrs ±11). Bisulfite pyrosequencing and Digital Restriction Enzyme Analysis of Methylation (DREAM) were performed to determine the methylation of CpG sites in the CRC tumors. The tumor samples were selected based on their CIMP status (10 high, 10 low, and 26 negative) and the tumor sites. 16S rRNA gene sequencing using Illumina-Hi-Seq was performed on those samples. Principle Coordinate analysis of the 16S rRNA sequences showed that the microbiota of CIMP-positive (CIMP-high and -low combined) tumors was significantly different from the microbiota of the CIMP-negative tumors (PERMANOVA, P = 0.013). Linear discriminant analysis effect size (LEfSe) showed an enrichment of specific bacterial taxa in the CIMP-positive microbiota. Fusobacterium (LDA score = 4.71, p=0.033) and Erysipelotrichaceae (LDA score = 3.77, p=0.004) were most enriched in the CIMP-positive tumors along with Bacteroides. The microbiota of different tumor sites also showed significant difference with Fusobacterium (LDA score = 4.32, p=0.047) and Erysipelotrichaceae (LDA score = 3.45, p=0.039) being enriched in the proximal tumors compared to the distal tumors. All these bacterial taxa have previous been found to be associated with CRC and/or metabolic disorders. We validated the 16S rRNA data by qPCR analysis using genus-specific probes. In the same samples, Pan-Fusobacterium and Bacteroides fragilis were enriched in the CIMP-positive tumors. The median number of Pan-Fusobacterium per 100 human cells was 12-fold higher in the CIMP-positive tumors (p=0.0015) and 6-fold higher in the case of B. fragilis (p=0.0228). Thus, our data show broad difference in the microbiota of CIMP-positive CRCs compared to CIMP-negative CRCs. The significantly enriched bacterial taxa in CIMP-positive CRC suggest that these specific taxa could play an important role in aberrant DNA methylation modulation in colorectal cancer, and further studies should elucidate the mechanism underlying the CIMP/microbiota link in the context of CRC.
Citation Format: Pyoung Hwa Park, Raad Z. Gharaibeh, Lauren Cole, Ang Sun, Woonbok Chung, Jaroslav Jelinek, Jillian L. Pope, Christian Jobin, Jean-Pierre J. Issa. CIMP is associated with altered microbiota composition in colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-141.
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Affiliation(s)
| | | | | | - Ang Sun
- 1Temple University, Philadelphia, PA
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19
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Garcia-Manero G, Roboz G, Walsh K, Kantarjian H, Ritchie E, Kropf P, O'Connell C, Tibes R, Lunin S, Rosenblat T, Yee K, Stock W, Griffiths E, Mace J, Podoltsev N, Berdeja J, Jabbour E, Issa JPJ, Hao Y, Keer HN, Azab M, Savona MR. Guadecitabine (SGI-110) in patients with intermediate or high-risk myelodysplastic syndromes: phase 2 results from a multicentre, open-label, randomised, phase 1/2 trial. Lancet Haematol 2019; 6:e317-e327. [PMID: 31060979 DOI: 10.1016/s2352-3026(19)30029-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/13/2019] [Accepted: 02/13/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Guadecitabine is a next-generation hypomethylating agent whose active metabolite decitabine has a longer in-vivo exposure time than intravenous decitabine. More effective hypomethylating agents are needed for the treatment of myelodysplastic syndromes. In the present study, we aimed to compare the activity and safety of two doses of guadecitabine in hypomethylating agent treatment-naive or relapsed or refractory patients with intermediate-risk or high-risk myelodysplastic syndromes. METHODS This phase 2 part of the phase 1/2, randomised, open-label study enrolled patients aged 18 years or older from 14 North American medical centres with International Prognostic Scoring System intermediate-1-risk, intermediate-2-risk, or high-risk myelodysplastic syndromes, or chronic myelomonocytic leukaemia. They were either hypomethylating agent treatment-naive or had relapsed or refractory disease after previous hypomethylating agent treatment as determined by the investigators' judgment. Eligible patients had Eastern Cooperative Oncology Group performance status of 0-2. Patients were randomly assigned (1:1) using a computer algorithm for dynamic randomisation to subcutaneous guadecitabine 60 or 90 mg/m2 on days 1-5 of a 28-day treatment cycle. Treatment was stratified by previous treatment with hypomethylating agents and neither patients nor investigators were masked. The primary endpoint was overall response (a composite of complete response, partial response, marrow complete response, and haematological improvement) assessed in all patients who received at least one dose of study drug. This study is registered with ClinicalTrials.gov, number NCT01261312. FINDINGS Between July 9, 2012, and April 7, 2014, 105 patients were enrolled: 55 (52%) were allocated to guadecitabine 60 mg/m2 (28 patients were treatment-naive and 27 had relapsed or refractory disease after previous hypomethylating agent treatment) and 50 (48%) patients to 90 mg/m2 (23 patients were treatment-naive and 27 had relapsed or refractory disease). Three (3%) patients of 105 did not receive study treatment and were excluded from analyses. Median follow-up was 3·2 years (IQR 2·8-3·5). The proportion of patients achieving an overall response did not significantly differ between dose groups (21 of 53 [40%, 95% CI 27-54] with 60 mg/m2 and 27 of 49 [55%, 95% CI 40-69] with 90 mg/m2; p=0·16). 25 of 49 (51%, 95% CI 36-66) patients who were treatment-naive and 23 of 53 (43%, 30-58) patients with relapsed or refractory disease achieved an overall response. The most common grade 3 or worse adverse events in both groups, regardless of relationship to treatment, were thrombocytopenia (22 [41%] of 53 patients in the 60 mg/m2 group and 28 [57%] of 49 in the 90 mg/m2 group), neutropaenia (21 [40%] and 25 [51%]), anaemia (25 [47%] and 24 [49%]), febrile neutropaenia (17 [32%] and 21 [43%]), and pneumonia (13 [25%] and 15 [31%]). Seven (7%) of 102 patients died due to adverse events (three with 90 mg/m2 and four with 60 mg/m2), and all except one were in the relapsed or refractory cohort. Two deaths were deemed treatment related (septic shock with 60 mg/m2; pneumonia with 90 mg/m2). INTERPRETATION Guadecitabine was clinically active with acceptable tolerability in patients with intermediate-risk and high-risk myelodysplastic syndromes. Responses and overall survival in the relapsed or refractory cohort offer the potential of a new therapeutic option for patients for whom currently available hypomethylating agents are not successful. We therefore recommend guadecitabine at a dose of 60 mg/m2 on a 5-day schedule for these patients. FUNDING Astex Pharmaceuticals and Stand Up To Cancer.
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Affiliation(s)
| | - Gail Roboz
- New York-Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | | | - Hagop Kantarjian
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ellen Ritchie
- New York-Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | | | - Casey O'Connell
- Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | | | - Scott Lunin
- Fort Myers Cancer Center, Fort Myers, FL, USA
| | - Todd Rosenblat
- Columbia University Irving Medical Center, New York, NY, USA
| | - Karen Yee
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Wendy Stock
- The University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
| | | | - Joseph Mace
- Florida Cancer Specialists & Research Institute, St Petersburg, FL, USA
| | | | | | - Elias Jabbour
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research & Molecular Biology, Temple University, Philadelphia, PA, USA
| | - Yong Hao
- Astex Pharmaceuticals, Pleasanton, CA, USA
| | | | | | - Michael R Savona
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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20
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Shin JW, Kim JYK, Jelinek J, Hwang J, Jeong HS, Kim DH, Cho K, Rha SH, Lee YH, Kim GE, Kwon SU, Cha JK, Issa JPJ, Kim J. Abstract WP546: Changes in Promoter Methylation in AIRE1 and ALOX12: Novel Epigenetic Markers in Atherosclerotic Tissues. Stroke 2019. [DOI: 10.1161/str.50.suppl_1.wp546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective:
The present study aimed to identify and validate specific genes developing changes in promoter methylation in atherosclerotic plaques.
Approach and Results:
We initially comprehensively profiled DNA methylation signatures via Solexa sequencing, using amplicons prepared via methylated-CpG island amplification (MCA) in genomic DNA obtained from 5 plaques acquired through carotid endarterectomy (CEA) to identify genes with altered promoter methylation. The changes in promoter methylation of these genes were validated via bisulfite pyrosequencing from plaques and non-plaque intima of the common carotid artery (CCA) harvested from 20 cadavers as well as from 27 CEA plaques and 5 human umbilical vein endothelial cell (HUVEC) lines. Expression changes based on changes in promoter methylation in these genes were evaluated in 20 CEA plaques and in 2 HUVEC cell lines after demethylation with 5-aza-2'-deoxycytidine. Upon MCA-Solexa sequencing, five genes (
AIRE1
,
ALOX12
,
FANK1
,
NETO1
, and
SERHL2
) displayed changes in promoter methylation. Of these,
AIRE1
and
ALOX12
displayed significantly greater promoter methylation in plaques rather than in the non-plaque intima of the CCA. Furthermore, promoter methylation was greater in
AIRE1
in CEA plaques than in HUVECs, while that in
ALOX12
was greater in HUVEC cells than in CEA plaques. Concurrently, gene expression levels decreased with an increase in promoter methylation in these genes in CEA plaques. After DNA demethylation in HUVEC cells,
AIRE1
and
ALOX12
expression levels increased by 23 and 52 folds.
Conclusions:
Changes in promoter methylation in
AIRE1
and
ALOX12
were identified and validated in atherosclerotic plaques, thereby establishing novel epigenetic markers for atherosclerosis.
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Affiliation(s)
- Jong Wook Shin
- Neurology and Daejeon-Chungnam Regional Cerebrovascular Cntr, Chungnam Nat'l Univ. Hosp, Dae-jeon, Korea, Republic of
| | | | | | - Junha Hwang
- Neurology, Chungnam Nat'l Univ Hosp, Dae-jeon, Korea, Republic of
| | - Hye Seon Jeong
- Neurology and Daejeon-Chungnam Regional Cerebrovascular Cntr, Chungnam Nat'l Univ. Hosp, Dae-jeon, Korea, Republic of
| | - Dae Hyun Kim
- Neurology and Busan Regional Cerebrovascular Cntr, Dong-A Univ Hosp, Busan, Korea, Republic of
| | - Kwangjo Cho
- Thoracic and Cardiovascular Surgery, Dong-A Univ Hosp, Busan, Korea, Republic of
| | - Seo Hee Rha
- Pathology, Dong-A Univ Hosp, Busan, Korea, Republic of
| | - Young Ho Lee
- Anatomy, Chungnam National Univ, Dae-jeon, Korea, Republic of
| | - Geun-Eun Kim
- Vascular Surgery, Asan Med Cntr, Seoul, Korea, Republic of
| | - Sun U. Kwon
- Neurology, Asan Med Cntr, Seoul, Korea, Republic of
| | - Jae Kwan Cha
- Neurology and Busan Regional Cerebrovascular Cntr, Dong-A Univ Hosp, Busan, Korea, Republic of
| | | | - Jei Kim
- Neurology and Daejeon-Chungnam Regional Cerebrovascular Cntr, Chungnam Nat'l Univ, Dae-jeon, Korea, Republic of
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Zhang H, Pandey S, Travers M, Khowsathit J, Morton G, Sum H, Barrero CA, Merali C, Okamoto Y, Sato T, Garriga J, Bhanu NV, Simithy J, Patel B, Madzo J, Raynal N, Garcia BA, Jacobson MA, Merali S, Zhang Y, Childers W, Abou-Gharbia M, Karanicolas J, Baylin SB, Zahnow CA, Jelinek J, Graña X, Issa JPJ. Abstract 2952: Targeting CDK9 reactivates epigenetically silenced genes in cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In cancer, the epigenome is aberrantly reprogrammed leading to a wide range of heritable changes in gene expression, such as silencing of tumor suppressor genes (TSG). Altered epigenetic marks in cancer involve DNA methylation and histone post-translational modifications, and these come about as a result of aging and acquisition of genetic and epigenetic changes in readers/writers/editors of the epigenome. Given the reversible nature of epigenetic modifications, one goal of epigenetic therapy of cancer is to induce TSG reactivation, leading to cancer cell differentiation and cancer cell death.
To identify novel targets that can reactivate epigenetically silenced genes, we developed a phenotypic-based system, YB5. YB5 is a colon cancer cell line generated by stably transfecting SW48 cells with a vector containing GFP driven by a methylated and silenced CMV promoter. GFP re-expression can be achieved by known epigenetic drugs that lead to demethylation or induce active chromatin marks in the CMV promoter.
We screened a natural compound library for GFP activation in YB5 and identified a novel drug class that shares an aminothiazole core structure, and has epigenetic effects that are equivalent to DNA methyltransferase inhibitor (DNMTi). Target deconvolution identified CDK9 as the target of these drugs, which reactivate gene expression without affecting DNA methylation. It is well established that CDK9, the catalytic subunit of p-TEFb, is a transcriptional activator. CDK9 in complex with its regulatory subunit, Cyclin T1 or T2, is recruited by multiple mechanisms to promote RNAPII promoter-proximal pause release by phosphorylating negative elongation factors (DSIF and NELF). In addition, phosphorylation of the C-terminal domain (CTD) of RNAPII on Serine-2 allows recruitment of RNA processing factors, which work on the nascent RNA as it emerges from RNAPII. Our new data show that long-term CDK9 inhibition can reactivate epigenetically silenced genes with minimal downregulation effects, effects which are the opposite of the canonical role of CDK9-mediated transcriptional elongation. Mechanistically, we showed that CDK9 inhibition dephosphorylates the SWI/SNF protein SMARCA4 and represses HP1α expression, both of which contribute to gene reactivation. Based on gene activation, we developed the highly selective and potent CDK9 inhibitor MC180295 (IC50 =5nM) that has broad anti-cancer activity in-vitro and is effective in in-vivo cancer models. Additionally, CDK9 inhibition sensitizes with the immune checkpoint inhibitor α-PD-1 in vivo, making it an excellent target for epigenetic therapy of cancer. This is the first study that links CDK9 to maintaining gene silencing at epigenetically repressed loci in mammals. Excitingly, this is also the first example of kinase inhibitors as potential drugs that reverse epigenetic silencing.
Citation Format: Hanghang Zhang, Somnath Pandey, Meghan Travers, Jittasak Khowsathit, George Morton, Hongxing Sum, Carlos A. Barrero, Carmen Merali, Yasuyuki Okamoto, Takahiro Sato, Judit Garriga, Natarajan V. Bhanu, Johayra Simithy, Bela Patel, Jozef Madzo, Noël Raynal, Benjamin A. Garcia, Marlene A. Jacobson, Salim Merali, Yi Zhang, Wayne Childers, Magid Abou-Gharbia, John Karanicolas, Stephen B. Baylin, Cynthia A. Zahnow, Jaroslav Jelinek, Xavier Graña, Jean-Pierre J. Issa. Targeting CDK9 reactivates epigenetically silenced genes in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2952.
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Affiliation(s)
- Hanghang Zhang
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Somnath Pandey
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Meghan Travers
- 2The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - George Morton
- 4Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Hongxing Sum
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Carlos A. Barrero
- 4Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Carmen Merali
- 4Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Yasuyuki Okamoto
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Takahiro Sato
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Judit Garriga
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Natarajan V. Bhanu
- 5Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Johayra Simithy
- 5Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Bela Patel
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Jozef Madzo
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Noël Raynal
- 6Département de pharmacologie et physiologie, Université de Montréal, Quebec, Canada
| | - Benjamin A. Garcia
- 5Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Marlene A. Jacobson
- 4Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Salim Merali
- 4Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Yi Zhang
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Wayne Childers
- 4Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Magid Abou-Gharbia
- 4Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - John Karanicolas
- 3Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Stephen B. Baylin
- 2The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Cynthia A. Zahnow
- 2The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Jaroslav Jelinek
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Xavier Graña
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Jean-Pierre J. Issa
- 1Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA
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22
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Good CR, Panjarian S, Kelly AD, Madzo J, Patel B, Jelinek J, Issa JPJ. TET1-Mediated Hypomethylation Activates Oncogenic Signaling in Triple-Negative Breast Cancer. Cancer Res 2018; 78:4126-4137. [PMID: 29891505 DOI: 10.1158/0008-5472.can-17-2082] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 03/21/2018] [Accepted: 05/30/2018] [Indexed: 01/28/2023]
Abstract
Both gains and losses of DNA methylation are common in cancer, but the factors controlling this balance of methylation remain unclear. Triple-negative breast cancer (TNBC), a subtype that does not overexpress hormone receptors or HER2/NEU, is one of the most hypomethylated cancers observed. Here, we discovered that the TET1 DNA demethylase is specifically overexpressed in about 40% of patients with TNBC, where it is associated with hypomethylation of up to 10% of queried CpG sites and a worse overall survival. Through bioinformatic analyses in both breast and ovarian cancer cell line panels, we uncovered an intricate network connecting TET1 to hypomethylation and activation of cancer-specific oncogenic pathways, including PI3K, EGFR, and PDGF. TET1 expression correlated with sensitivity to drugs targeting the PI3K-mTOR pathway, and CRISPR-mediated deletion of TET1 in two independent TNBC cell lines resulted in reduced expression of PI3K pathway genes, upregulation of immune response genes, and substantially reduced cellular proliferation, suggesting dependence of oncogenic pathways on TET1 overexpression. Our work establishes TET1 as a potential oncogene that contributes to aberrant hypomethylation in cancer and suggests that TET1 could serve as a druggable target for therapeutic intervention.Significance: This study addresses a critical gap in knowledge of how and why methylation is prognostic in breast cancer and shows how this information can be used to stratify patients with TNBC for targeted therapy. Cancer Res; 78(15); 4126-37. ©2018 AACR.
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Affiliation(s)
- Charly Ryan Good
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Shoghag Panjarian
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Bela Patel
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania.
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Abstract
Epigenetic alterations such as DNA methylation defects and aberrant covalent histone modifications occur within all cancers and are selected for throughout the natural history of tumor formation, with changes being detectable in early onset, progression, and ultimately recurrence and metastasis. The ascertainment and use of these marks to identify at-risk patient populations, refine diagnostic criteria, and provide prognostic and predictive factors to guide treatment decisions are of growing clinical relevance. Furthermore, the targetable nature of epigenetic modifications provides a unique opportunity to alter treatment paradigms and provide new therapeutic options for patients whose malignancies possess these aberrant epigenetic modifications, paving the way for new and personalized medicine. DNA methylation has proven to be of significant clinical utility for its stability and relative ease of testing. The intent of this review is to elaborate upon well-supported examples of epigenetic precision medicine and how the field is moving forward, primarily in the context of aberrant DNA methylation.
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Affiliation(s)
- Rachael J Werner
- From the *Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
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Kelly AD, Madzo J, Madireddi P, Kropf P, Good CR, Jelinek J, Issa JPJ. Demethylator phenotypes in acute myeloid leukemia. Leukemia 2018; 32:2178-2188. [PMID: 29556023 PMCID: PMC6128790 DOI: 10.1038/s41375-018-0084-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/29/2018] [Accepted: 02/06/2018] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) often harbors mutations in epigenetic regulators, and also has frequent DNA hypermethylation, including the presence of CpG island methylator phenotypes (CIMPs). Although global hypomethylation is well known in cancer, the question of whether distinct demethylator phenotypes (DMPs) exist remains unanswered. Using Illumina 450k arrays for 194 patients from The Cancer Genome Atlas, we identified two distinct DMPs by hierarchical clustering: DMP.1 and DMP.2. DMP.1 cases harbored mutations in NPM1 (94%), FLT3 (71%) and DNMT3A (61%). Surprisingly, only 40% of patients with DNMT3A mutations were DMP.1, which has implications for mechanisms of transformation by this mutation. In contrast, DMP.2 AML was comprised of patients with t(8;21), inv(16) or t(15;17), suggesting common methylation defects connect these disparate rearrangements. RNA-seq revealed upregulated genes functioning in immune response (DMP.1) and development (DMP.2). We confirmed these findings by integrating independent 450k data sets (236 additional cases), and found prognostic effects by DMP status, independent of age and cytogenetics. The existence of DMPs has implications for AML pathogenesis and may augment existing tools in risk stratification.
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Affiliation(s)
- Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Priyanka Madireddi
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Patricia Kropf
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Charly R Good
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA. .,Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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Roboz GJ, Kantarjian HM, Yee KWL, Kropf PL, O'Connell CL, Griffiths EA, Stock W, Daver NG, Jabbour E, Ritchie EK, Walsh KJ, Rizzieri D, Lunin SD, Curio T, Chung W, Hao Y, Lowder JN, Azab M, Issa JPJ. Dose, schedule, safety, and efficacy of guadecitabine in relapsed or refractory acute myeloid leukemia. Cancer 2017; 124:325-334. [PMID: 29211308 PMCID: PMC5814873 DOI: 10.1002/cncr.31138] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/16/2017] [Accepted: 08/23/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND Outcomes for patients with relapsed or refractory acute myeloid leukemia (AML) are poor. Guadecitabine, a next‐generation hypomethylating agent, could be useful in treating such patients. METHODS In this multicenter, open‐label, phase 2 dose‐expansion study, AML patients from 10 North American medical centers were first randomized (1:1) to receive subcutaneous guadecitabine at 60 or 90 mg/m2 on 5 consecutive days in each 28‐day cycle (5‐day regimen). Subsequently, another cohort was treated for 10 days with 60 mg/m2 (10‐day regimen). RESULTS Between June 15, 2012, and August 19, 2013, 108 patients with previously treated AML consented to enroll in the study, and 103 of these patients were treated; 5 patients did not receive the study treatment. A total of 103 patients were included in the safety and efficacy analyses (24 and 26 patients who were randomly assigned to 60 and 90 mg/m2/d, respectively [5‐day regimen] and 53 patients who were assigned to 60 mg/m2/d [10‐day regimen]). The 90 mg/m2 dose showed no benefit in clinical outcomes in comparison with 60 mg/m2 in the randomized cohort. Composite complete response (CRc) and complete response (CR) rates were higher with the 10‐day regimen versus the 5‐day regimen (CRc, 30.2% vs 16.0%; P = .1061; CR, 18.9% vs 8%; P = .15). Adverse events (grade ≥ 3) were mainly hematologic, with a higher incidence on the 10‐day regimen. Early all‐cause mortality was low and similar between regimens. Twenty patients (8 on the 5‐day regimen and 12 on the 10‐day regimen) were bridged to hematopoietic cell transplantation. CONCLUSIONS Guadecitabine has promising clinical activity and an acceptable safety profile and thus warrants further development in this population. Cancer 2018;124:325‐34. © 2017 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. Outcomes for patients with relapsed or refractory acute myeloid leukemia are poor. Guadecitabine, a next‐generation hypomethylating agent, has promising clinical activity and an acceptable safety profile and warrants further development in this population. See also pages 242‐4.
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Affiliation(s)
- Gail J Roboz
- Weill Cornell Medicine, NewYork-Presbyterian Hospital, New York, New York
| | | | - Karen W L Yee
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Casey L O'Connell
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | | | - Naval G Daver
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elias Jabbour
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ellen K Ritchie
- Weill Cornell Medicine, NewYork-Presbyterian Hospital, New York, New York
| | | | | | - Scott D Lunin
- Florida Cancer Specialist and Research Institute, Fort Myers, Florida
| | - Tania Curio
- Weill Cornell Medicine, NewYork-Presbyterian Hospital, New York, New York
| | - Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Yong Hao
- Astex Pharmaceuticals, Pleasanton, California
| | | | | | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
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van der Ven LT, Jelinek J, Hodemaekers HM, Zwart EP, Ruiter S, van den Brandhof EJ, Issa JPJ, Pennings JL, Luijten M. An Adverse Outcome Pathway Analysis Employing DNA Methylation Effects in Arsenic-Exposed Zebrafish Embryos Supports a Role of Epigenetic Events in Arsenic-Induced Chronic Disease. ACTA ACUST UNITED AC 2017. [DOI: 10.1089/aivt.2017.0018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Leo T.M. van der Ven
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Hennie M. Hodemaekers
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Edwin P. Zwart
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sander Ruiter
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Evert-Jan van den Brandhof
- Center for Environmental Quality, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jean-Pierre J. Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeroen L.A. Pennings
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Mirjam Luijten
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Good CR, Madzo J, Patel B, Maegawa S, Engel N, Jelinek J, Issa JPJ. A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer. Nucleic Acids Res 2017; 45:8269-8281. [PMID: 28531272 PMCID: PMC5737541 DOI: 10.1093/nar/gkx435] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/14/2017] [Accepted: 05/03/2017] [Indexed: 02/07/2023] Open
Abstract
TET1 oxidizes methylated cytosine into 5-hydroxymethylcytosine (5hmC), resulting in regulation of DNA methylation and gene expression. Full length TET1 (TET1FL) has a CXXC domain that binds to unmethylated CpG islands (CGIs). This CXXC domain allows TET1 to protect CGIs from aberrant methylation, but it also limits its ability to regulate genes outside of CGIs. Here, we report a novel isoform of TET1 (TET1ALT) that has a unique transcription start site from an alternate promoter in intron 2, yielding a protein with a unique translation start site. Importantly, TET1ALT lacks the CXXC domain but retains the catalytic domain. TET1ALT is repressed in embryonic stem cells (ESCs) but becomes activated in embryonic and adult tissues while TET1FL is expressed in ESCs, but repressed in adult tissues. Overexpression of TET1ALT shows production of 5hmC with distinct (and weaker) effects on DNA methylation or gene expression when compared to TET1FL. TET1ALT is aberrantly activated in multiple cancer types including breast, uterine and glioblastoma, and TET1 activation is associated with a worse overall survival in breast, uterine and ovarian cancers. Our data suggest that the predominantly activated isoform of TET1 in cancer cells does not protect from CGI methylation and likely mediates dynamic site-specific demethylation outside of CGIs.
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Affiliation(s)
- Charly R. Good
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Bela Patel
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Shinji Maegawa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Nora Engel
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jean-Pierre J. Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
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Kelly AD, Madzo J, Madireddi P, Kropf P, Good CR, Jelinek J, Issa JPJ. Abstract 5382: A DNMT3A-independent hypomethylator phenotype is a unifying epigenetic signature of AML with good risk cytogenetics. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Acute myeloid leukemia (AML) causes the most leukemia-related deaths in the United States, and has frequent mutations in epigenetic regulators, including DNMT3A, IDH, and TET2. Such aberrations have been proposed to transform the epigenetic state in cancer, often involving DNA hypomethylation, however, the genomic specificity, causes, and clinical consequences of such methylation changes in AML remain unclear.
Methods: We queried genome-wide CpG methylation using The Cancer Genome Atlas (TCGA) AML samples (n=194) run on Illumina 450k arrays. We used RNA-seq data to study gene expression changes associated with hypomethylator phenotypes (HP). Analysis was done using R.
Results: Genome-wide analysis of CpG sites that are highly methylated in normal blood, and variably methylated in AML (β-value standard deviation in AML > 0.2; average β-value in normal blood > 0.8) revealed two distinct HPs by hierarchical clustering: Good-risk (GR) HP which included favorable cytogenetics, and DNMT-HP, which was enriched for DNMT3A mutations. We refined DNA methylation signatures of each HP cluster by differential methylation analysis and re-classified patients accordingly. Strikingly, all patients with t(8;21), inv(16), or t(15;17) belonged to the GR-HP+ group, suggesting that a common epigenetic thread connects these otherwise disparate genetic aberrations. From a clinical perspective GR-HP+ patients were younger than GR-HP- patients, and had significantly longer overall survival (median OS, years: GR-HP+ = Not reached; GR-HP- = 1.00; P < 0.001). In contrast, DNMT-HP+ cases were statistically equivalent to DNMT-HP- except for an enrichment for higher WBC counts, including no difference in survival (median OS, years: DNMT-HP+ = 0.92; DNMT-HP- = 1.34; P = 0.27). From an epigenetic perspective the two HP clusters harbored distinct DNA methylation changes; although both favored hypomethylation within non-CpG islands relative to CpG islands, the enrichment was more pronounced for DNMT-HP (Odds ratio: hypomethylated CpG islands/hypomethylated non-CpG islands, GR-HP = 0.64; DNMT-HP = 0.18). Genetic analysis revealed that GR-HP+ leukemia had wild-type IDH, DNMT3A, and NPM1 genes. In contrast, DNMT-HP+ AML had significantly more FLT3, NPM1, and DNMT3A mutations compared to DNMT-HP- patients. RNA-seq revealed significant up-regulation of genes in both HP phenotypes (216, and 150 genes for GR-HP and DNMT-HP, respectively at FDR < 0.01 and FC > 2). Pathway analysis of these genes revealed enrichments for ion channels and the complement pathway in DNMT-HP, and for nervous system and developmental genes in GR-HP.
Conclusions: Our data suggest that two HPs exist in AML with unique epigenetic and transcriptomic signatures. The striking association between GR-HP and different favorable cytogenetic changes suggests that a common set of epigenetic features may contribute to improved survival in these patients.
Citation Format: Andrew D. Kelly, Jozef Madzo, Priyanka Madireddi, Patricia Kropf, Charly R. Good, Jaroslav Jelinek, Jean-Pierre J. Issa. A DNMT3A-independent hypomethylator phenotype is a unifying epigenetic signature of AML with good risk cytogenetics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5382. doi:10.1158/1538-7445.AM2017-5382
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Affiliation(s)
- Andrew D. Kelly
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Jozef Madzo
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | | | - Patricia Kropf
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Charly R. Good
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Jaroslav Jelinek
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA
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Zhang H, Raynal NJM, Sato T, Okamoto Y, Garriga J, Garcia B, Morton G, Childers W, Jacobson MA, Baylin SB, Graña X, Abou-Gharbia M, Issa JPJ. Abstract 5064: Identifying novel potential epigenetic anti-cancer drugs from natural compounds using a phenotypic-based screening. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic aberrations such as DNA hypermethylation and repressive chromatin are validated targets for cancer chemotherapy. Since epigenetic modifications are reversible, the goal of epigenetic therapy is to reverse the abnormal alternations in cancer cells and induce tumor suppressor gene reactivation, leading to cancer cell differentiation and cell death. Many known anti-cancer drugs are derived from natural compounds and there have been reports of natural compounds modulating epigenetic activity. To explore this idea, our lab developed a phenotypic-based system (YB5) by stably transfecting SW48 cells with a vector containing GFP driven by a methylated and silenced CMV promoter. GFP re-expression can be achieved by known epigenetic drugs that lead to demethylation or induce active chromatin marks in the CMV promoter. By screening an NDL-3040 natural compounds library and grouping the compounds based on chemical structures, we identified two main drug classes. We then synthesized 77 new analogs based on class #1’s lead’s structure and 23 were positive in the YB5 system. The most potent analog (HH2) can induce ~60% GFP+ cells upon 500nM treatment after 96hr. All the positive hits can also be validated in two other cancer cell lines (MCF7 and HCT116). Consistent with GFP reactivation, endogenous hypermethylated genes (MGMT, RARβ, etc) can also be re-expressed upon drug treatment. We then performed RNA-seq analysis to identify global gene expression changes following drug treatment. We observed that most genes (2964 genes) were upregulated upon HH1 treatment (10uM) and that many of the upregulated genes were expressed in normal tissues but repressed in cancer, indicating that they might be potential tumor suppressor genes (TSGs). Consistent with this, 94 TSGs could be reactivated upon 10uM drug treatment. These drug target upregulated genes were also enriched for hypermethylation. By performing connectivity mapping using RNA-seq, we identified X as the class #1 drug target. The on-target effect could be further validated by using other selective X inhibitors as well as a dominant negative X construct. Consistent with drug inhibition, dominant-negative X can also reactivate drug targeted hypermethylated genes. Additionally, when we overexpressed wild-type X, we saw that GFP induction as well as endogenous gene reactivations can be inhibited. Strikingly, by using GFP induction as readout to optimize drugs, we found that the in vitro IC50 against X for our top lead compound (HH2) is only 5nM and it is at least 22-fold selective for X over other X family members. Thus, a novel epigenetic drug class derived from natural compounds was identified and can be developed by targeting silenced gene expression.
Citation Format: Hanghang Zhang, Noël J.-M Raynal, Takahiro Sato, Yasuyuki Okamoto, Judith Garriga, Benjamin Garcia, George Morton, Wayne Childers, Marlene A. Jacobson, Stephen B. Baylin, Xavier Graña, Magid Abou-Gharbia, Jean-Pierre J. Issa. Identifying novel potential epigenetic anti-cancer drugs from natural compounds using a phenotypic-based screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5064. doi:10.1158/1538-7445.AM2017-5064
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Affiliation(s)
| | | | - Takahiro Sato
- 1Fels Institute for Cancer Research, Philadelphia, PA
| | | | | | - Benjamin Garcia
- 2Perelman School of Medicine, University of Pennsylvania Philadelphia, Philadelphia, PA
| | - George Morton
- 3Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Wayne Childers
- 3Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Marlene A. Jacobson
- 3Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Stephen B. Baylin
- 4The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Xavier Graña
- 1Fels Institute for Cancer Research, Philadelphia, PA
| | - Magid Abou-Gharbia
- 3Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
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Toth R, Scherer D, Kelemen LE, Risch A, Hazra A, Balavarca Y, Issa JPJ, Moreno V, Eeles RA, Ogino S, Wu X, Ye Y, Hung RJ, Goode EL, Ulrich CM. Genetic Variants in Epigenetic Pathways and Risks of Multiple Cancers in the GAME-ON Consortium. Cancer Epidemiol Biomarkers Prev 2017; 26:816-825. [PMID: 28115406 PMCID: PMC6054308 DOI: 10.1158/1055-9965.epi-16-0728] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 11/16/2022] Open
Abstract
Background: Epigenetic disturbances are crucial in cancer initiation, potentially with pleiotropic effects, and may be influenced by the genetic background.Methods: In a subsets (ASSET) meta-analytic approach, we investigated associations of genetic variants related to epigenetic mechanisms with risks of breast, lung, colorectal, ovarian and prostate carcinomas using 51,724 cases and 52,001 controls. False discovery rate-corrected P values (q values < 0.05) were considered statistically significant.Results: Among 162,887 imputed or genotyped variants in 555 candidate genes, SNPs in eight genes were associated with risk of more than one cancer type. For example, variants in BABAM1 were confirmed as a susceptibility locus for squamous cell lung, overall breast, estrogen receptor (ER)-negative breast, and overall prostate, and overall serous ovarian cancer; the most significant variant was rs4808076 [OR = 1.14; 95% confidence interval (CI) = 1.10-1.19; q = 6.87 × 10-5]. DPF1 rs12611084 was inversely associated with ER-negative breast, endometrioid ovarian, and overall and aggressive prostate cancer risk (OR = 0.93; 95% CI = 0.91-0.96; q = 0.005). Variants in L3MBTL3 were associated with colorectal, overall breast, ER-negative breast, clear cell ovarian, and overall and aggressive prostate cancer risk (e.g., rs9388766: OR = 1.06; 95% CI = 1.03-1.08; q = 0.02). Variants in TET2 were significantly associated with overall breast, overall prostate, overall ovarian, and endometrioid ovarian cancer risk, with rs62331150 showing bidirectional effects. Analyses of subpathways did not reveal gene subsets that contributed disproportionately to susceptibility.Conclusions: Functional and correlative studies are now needed to elucidate the potential links between germline genotype, epigenetic function, and cancer etiology.Impact: This approach provides novel insight into possible pleiotropic effects of genes involved in epigenetic processes. Cancer Epidemiol Biomarkers Prev; 26(6); 816-25. ©2017 AACR.
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Affiliation(s)
- Reka Toth
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Scherer
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Linda E Kelemen
- Medical University of South Carolina and Hollings Cancer Center, Charleston, South Carolina
| | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Cancer Research and Epigenetics, Department of Molecular Biology, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Aditi Hazra
- Brigham and Women's Hospital, Harvard Medical School, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yesilda Balavarca
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Victor Moreno
- Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | | | - Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- University of Toronto, Toronto, Canada
| | - Ellen L Goode
- Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Cornelia M Ulrich
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Huntsman Cancer Institute, Salt Lake City, Utah
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Abstract
Next-generation sequencing has revealed that more than 50% of human cancers harbour mutations in enzymes that are involved in chromatin organization. Tumour cells not only are activated by genetic and epigenetic alterations, but also routinely use epigenetic processes to ensure their escape from chemotherapy and host immune surveillance. Hence, a growing emphasis of recent drug discovery efforts has been on targeting the epigenome, including DNA methylation and histone modifications, with several new drugs being tested and some already approved by the US Food and Drug Administration (FDA). The future will see the increasing success of combining epigenetic drugs with other therapies. As epigenetic drugs target the epigenome as a whole, these true 'genomic medicines' lessen the need for precision approaches to individualized therapies.
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Affiliation(s)
- Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Stephen Baylin
- Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21287, USA
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Abstract
Aberrant DNA methylation is a critically important modification in cancer cells, which, through promoter and enhancer DNA methylation changes, use this mechanism to activate oncogenes and silence of tumor-suppressor genes. Targeting DNA methylation in cancer using DNA hypomethylating drugs reprograms tumor cells to a more normal-like state by affecting multiple pathways, and also sensitizes these cells to chemotherapy and immunotherapy. The first generation hypomethylating drugs azacitidine and decitabine are routinely used for the treatment of myeloid leukemias and a next-generation drug (guadecitabine) is currently in clinical trials. This review will summarize preclinical and clinical data on DNA hypomethylating drugs as a cancer therapy.
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Affiliation(s)
- Takahiro Sato
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140.,Fox Chase Cancer Center, Temple Health, Philadelphia, Pennsylvania 19111
| | - Patricia Kropf
- Fox Chase Cancer Center, Temple Health, Philadelphia, Pennsylvania 19111
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Kelly AD, Issa JPJ. The promise of epigenetic therapy: reprogramming the cancer epigenome. Curr Opin Genet Dev 2017; 42:68-77. [PMID: 28412585 DOI: 10.1016/j.gde.2017.03.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 02/07/2023]
Abstract
Epigenetics refers to heritable molecular determinants of phenotype independent of DNA sequence. Epigenetic features include DNA methylation, histone modifications, non-coding RNAs, and chromatin structure. The epigenetic status of cells plays a crucial role in determining their differentiation state and proper function within multicellular organisms. Disruption of these processes is now understood to be a major contributor to cancer development and progression, and recent efforts have attempted to pharmacologically reverse such altered epigenetics. In this mini-review we introduce the concept of epigenetic drivers of cancer and discuss how aberrant DNA methylation, histone modifications, and chromatin states are being targeted using drugs either in preclinical, or clinical development, and how they fit in the context of existing therapies.
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Affiliation(s)
- Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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Raynal NJM, Da Costa EM, Lee JT, Gharibyan V, Ahmed S, Zhang H, Sato T, Malouf GG, Issa JPJ. Repositioning FDA-Approved Drugs in Combination with Epigenetic Drugs to Reprogram Colon Cancer Epigenome. Mol Cancer Ther 2016; 16:397-407. [PMID: 27980103 DOI: 10.1158/1535-7163.mct-16-0588] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/28/2016] [Accepted: 11/17/2016] [Indexed: 11/16/2022]
Abstract
Epigenetic drugs, such as DNA methylation inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi), are approved in monotherapy for cancer treatment. These drugs reprogram gene expression profiles, reactivate tumor suppressor genes (TSG) producing cancer cell differentiation and apoptosis. Epigenetic drugs have been shown to synergize with other epigenetic drugs or various anticancer drugs. To discover new molecular entities that enhance epigenetic therapy, we performed a high-throughput screening using FDA-approved libraries in combination with DNMTi or HDACi. As a screening model, we used YB5 system, a human colon cancer cell line, which contains an epigenetically silenced CMV-GFP locus, mimicking TSG silencing in cancer. CMV-GFP reactivation is triggered by DNMTi or HDACi and responds synergistically to DNMTi/HDACi combination, which phenocopies TSG reactivation upon epigenetic therapy. GFP fluorescence was used as a quantitative readout for epigenetic activity. We discovered that 45 FDA-approved drugs (4% of all drugs tested) in our FDA-approved libraries enhanced DNMTi and HDACi activity, mainly belonging to anticancer and antiarrhythmic drug classes. Transcriptome analysis revealed that combination of decitabine (DNMTi) with the antiarrhythmic proscillaridin A produced profound gene expression reprogramming, which was associated with downregulation of 153 epigenetic regulators, including two known oncogenes in colon cancer (SYMD3 and KDM8). Also, we identified about 85 FDA-approved drugs that antagonized DNMTi and HDACi activity through cytotoxic mechanisms, suggesting detrimental drug interactions for patients undergoing epigenetic therapy. Overall, our drug screening identified new combinations of epigenetic and FDA-approved drugs, which can be rapidly implemented into clinical trials. Mol Cancer Ther; 16(2); 397-407. ©2016 AACR.
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Affiliation(s)
- Noël J-M Raynal
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania. .,Département de pharmacologie et physiologie, Université de Montréal and Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada
| | - Elodie M Da Costa
- Département de pharmacologie et physiologie, Université de Montréal and Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada
| | - Justin T Lee
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Vazganush Gharibyan
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Saira Ahmed
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hanghang Zhang
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Takahiro Sato
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Gabriel G Malouf
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, University Pierre and Marie Curie (Paris VI), Institut Universitaire de Cancérologie, AP-HP, Paris, France
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
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Sato T, Cesaroni M, Chung W, Panjarian S, Tran A, Madzo J, Okamoto Y, Zhang H, Chen X, Jelinek J, Issa JPJ. Transcriptional Selectivity of Epigenetic Therapy in Cancer. Cancer Res 2016; 77:470-481. [PMID: 27879268 DOI: 10.1158/0008-5472.can-16-0834] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 09/26/2016] [Accepted: 10/21/2016] [Indexed: 12/22/2022]
Abstract
A central challenge in the development of epigenetic cancer therapy is the ability to direct selectivity in modulating gene expression for disease-selective efficacy. To address this issue, we characterized by RNA-seq, DNA methylation, and ChIP-seq analyses the epigenetic response of a set of colon, breast, and leukemia cancer cell lines to small-molecule inhibitors against DNA methyltransferases (DAC), histone deacetylases (Depsi), histone demethylases (KDM1A inhibitor S2101), and histone methylases (EHMT2 inhibitor UNC0638 and EZH2 inhibitor GSK343). We also characterized the effects of DAC as combined with the other compounds. Averaged over the cancer cell models used, we found that DAC affected 8.6% of the transcriptome and that 95.4% of the genes affected were upregulated. DAC preferentially regulated genes that were silenced in cancer and that were methylated at their promoters. In contrast, Depsi affected the expression of 30.4% of the transcriptome but showed little selectivity for gene upregulation or silenced genes. S2101, UNC0638, and GSK343 affected only 2% of the transcriptome, with UNC0638 and GSK343 preferentially targeting genes marked with H3K9me2 or H3K27me3, respectively. When combined with histone methylase inhibitors, the extent of gene upregulation by DAC was extended while still maintaining selectivity for DNA-methylated genes and silenced genes. However, the genes upregulated by combination treatment exhibited limited overlap, indicating the possibility of targeting distinct sets of genes based on different epigenetic therapy combinations. Overall, our results demonstrated that DNA methyltransferase inhibitors preferentially target cancer-relevant genes and can be combined with inhibitors targeting histone methylation for synergistic effects while still maintaining selectivity. Cancer Res; 77(2); 470-81. ©2016 AACR.
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Affiliation(s)
- Takahiro Sato
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania.
| | - Matteo Cesaroni
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Shoghag Panjarian
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Anthony Tran
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Yasuyuki Okamoto
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Hanghang Zhang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Xiaowei Chen
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
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Abstract
Oxidation of 5-methylcytosine by TET family proteins can induce DNA replication-dependent (passive) DNA demethylation and base excision repair (BER)-based (active) DNA demethylation. The balance of active vs. passive TET-induced demethylation remains incompletely determined. In the context of large scale DNA demethylation, active demethylation may require massive induction of the DNA repair machinery and thus compromise genome stability. To study this issue, we constructed a tetracycline-controlled TET-induced global DNA demethylation system in HEK293T cells. Upon TET overexpression, we observed induction of DNA damage and activation of a DNA damage response; however, BER genes are not upregulated to promote DNA repair. Depletion of TDG (thymine DNA glycosylase) or APEX1 (apurinic/apyrimidinic endonuclease 1), two key BER enzymes, enhances rather than impairs global DNA demethylation, which can be explained by stimulated proliferation. By contrast, growth arrest dramatically blocks TET-induced global DNA demethylation. Thus, in the context of TET-induction in HEK293T cells, the DNA replication-dependent passive mechanism functions as the predominant pathway for global DNA demethylation. In the same context, BER-based active demethylation is markedly restricted by limited BER upregulation, thus potentially preventing a disastrous DNA damage response to extensive active DNA demethylation.
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Affiliation(s)
- Chunlei Jin
- a Fels Institute for Cancer Research and Molecular Biology; Temple University ; Philadelphia , PA USA.,b Department of Epigenetics and Molecular Carcinogenesis ; The University of Texas MD Anderson Cancer Center ; Houston , TX USA
| | - Taichun Qin
- c Department of Cancer Biology ; The University of Texas MD Anderson Cancer Center ; Houston , TX USA
| | - Michelle Craig Barton
- b Department of Epigenetics and Molecular Carcinogenesis ; The University of Texas MD Anderson Cancer Center ; Houston , TX USA
| | - Jaroslav Jelinek
- a Fels Institute for Cancer Research and Molecular Biology; Temple University ; Philadelphia , PA USA
| | - Jean-Pierre J Issa
- a Fels Institute for Cancer Research and Molecular Biology; Temple University ; Philadelphia , PA USA
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Zhang H, Raynal NJM, Sato T, Okamoto Y, Garriga J, Morton G, Childers W, Jacobson MA, Baylin SB, Graña X, Abou-Gharbia M, Issa JPJ. Abstract 4701: A phenotypic cell-based screen to identify novel potential epigenetic anti-cancer drugs from natural compounds. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic aberrations such as DNA hypermethylation and repressive chromatin are validated targets for cancer chemotherapy. Since epigenetic modifications are reversible, the goal of epigenetic therapy is to reverse the abnormal alternations in cancer cells and induce tumor suppressor genes reactivation, leading to cancer cell differentiation and cell death. Thus, epigenetic enzymes are attractive drug targets in the field of drug discovery. Many known anti-cancer drugs are derived from natural compounds and there have been reports of natural compounds modulating epigenetic activity. Therefore, it would be of interest to screen natural compounds as potential epigenetic drugs. In an effort to identify novel targets that can reactivate hypermethylated silenced genes, our lab developed a phenotypic-based system, YB5. YB5 is a colon cancer cell line generated by stably transfecting SW48 cells with a vector containing GFP driven by a methylated and silenced CMV promoter. GFP re-expression can be achieved by known epigenetic drugs that lead to demethylation or induce active chromatin marks in the CMV promoter. By screening an NDL-3040 library and grouping the molecules based on chemical structures, we were able to identify three main drug classes. The Moulder Center then synthesized 60 new analogs based on class #1's lead's structure and 15 are positive in the YB5 system. The most potent analog can induce 10% GFP+ cells upon 500nM treatment. All the positive hits can also be validated in two other cancer cells (MCF7 and HCT116). Consistent with GFP reactivation, endogenous hypermethylated genes can be reactivated upon drug treatment. Also, GFP positive cells show higher endogenous gene reactivation than unsorted and GFP negative cells. By performing RNA-seq analysis upon class #1 top lead treatment followed by connectivity mapping, we identified X as the class #1 drug target. The on-target effect can be validated by using other selective X inhibitors as well as a dominant negative X construct. Consistent with drug inhibition, dominant-negative X can also reactivate drug targeted hypermethylated genes. Proliferation assays showed differential sensitivities of a panel of colon cancer cell lines compared to normal cells. These drugs can also lead to G2/M arrest and GFP positive cells are more likely to be arrested than GFP negative cells. Besides class #1 drugs, a novel class of LSD1 inhibitors was identified and the most active drug can induce 15% GFP at 5uM. Consistent with LSD1 inhibition, many known LSD1 target genes can also be upregulated. Like known LSD1 inhibitors, these compounds significantly inhibited proliferation of AML cells. We also identified some known natural compounds that have epigenetic activities, including arsenic trioxide, cardiac glycosides, and toyocamycin. Thus, many novel epigenetic drug classes derived from natural compounds were identified and can be developed by targeting silenced gene expression.
Citation Format: Hanghang Zhang, Noël J.-M Raynal, Takahiro Sato, Yasuyuki Okamoto, Judit Garriga, George Morton, Wayne Childers, Marlene A. Jacobson, Stephen B. Baylin, Xavier Graña, Magid Abou-Gharbia, Jean-Pierre J. Issa. A phenotypic cell-based screen to identify novel potential epigenetic anti-cancer drugs from natural compounds. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4701.
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Affiliation(s)
| | | | - Takahiro Sato
- 1Fels Institute for Cancer Research, Philadelphia, PA
| | | | - Judit Garriga
- 1Fels Institute for Cancer Research, Philadelphia, PA
| | - George Morton
- 2Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Wayne Childers
- 2Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Marlene A. Jacobson
- 2Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
| | - Stephen B. Baylin
- 3The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Xavier Graña
- 1Fels Institute for Cancer Research, Philadelphia, PA
| | - Magid Abou-Gharbia
- 2Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA
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Kelly AD, Kroeger H, Yamazaki J, Taby R, Neumann F, Yu S, Lee JT, He R, Liang S, Lu Y, Cesaroni M, Pierce SA, Kornblau SM, Bueso-Ramos CE, Ravandi F, Kantarjain HM, Jelinek J, Issa JPJ. Abstract 2779: A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Acute myeloid leukemia (AML) causes the most leukemia-related deaths in the United States, and has frequent epigenetic aberrations, including a CpG island methylator phenotype (CIMP). CIMP defines unique molecular subtypes of other cancers and has been linked to mutations in IDH1/2, however the clinical consequences of CIMP and the role of IDH1/2 mutations in AML remain unclear.
Methods: To measure genome-wide CpG methylation we used Digital Restriction Enzyme Analysis of Methylation (DREAM) on AML bone marrow samples and normal peripheral blood controls. For validation we used methylation data from patient samples from The Cancer Genome Atlas (TCGA) on the Illumina Infinium HumanMethylation450 platform. We also used RNA-seq data from TCGA, and microarray data from GEO (GSE6891). Statistical analysis was done using R.
Results: Genome-wide analysis of variably methylated CpG sites in 96 AML bone marrow samples using DREAM revealed two distinct CpG island methylator phenotypes by hierarchical clustering: IDH-CIMP (I-CIMP) in which 7/10 cases had oncogenic IDH1/2 mutations, and AML-CIMP (A-CIMP), which lacked any mutations in IDH1/2. At median follow-up of 6.16 years, A-CIMP cases, but not I-CIMP cases were associated with longer overall survival (median OS, years: A-CIMP = Not reached, P = 0.08; I-CIMP = 3.35, P = 0.50; CIMP-negative = 1.17). We validated and extended these findings using TCGA data. In this cohort A-CIMP cases also had significantly longer OS compared to CIMP-negative (median OS, years: A-CIMP = 2.34, P = 0.01; I-CIMP = 1.25, P = 0.89; CIMP-negative = 1.00). Aberrant hypermethylation in A-CIMP occurred preferentially at CpG islands by a factor greater than 3, while I-CIMP cases demonstrated a slight preference for hypermethylation at sites outside CpG islands. Interestingly, A-CIMP was enriched in CEBPA (19%) and WT1 mutations (14%), but inversely correlated with IDH, TET2, and NPM1 mutations. Functional pathway analysis revealed that genes hypermethylated in A-CIMP are associated with pluripotency maintenance - including PAX6, GBX2, and HOXA9 - and RNA-seq data largely, but not entirely, recapitulated methylation-based patterns. There was a strong correlation between promoter CpG island methylation and gene expression for many A-CIMP genes. Finally, the transcriptional program associated with A-CIMP was found to correlate with outcome and genetic backgrounds in both TCGA and additional independent datasets.
Conclusions: Taken together, our data suggest that CIMP in AML is complex, multifactorial and cannot be explained solely by coding gene mutations (e.g. IDH1/2, TET2). There is an association between A-CIMP and curability in multiple AML datasets that cannot be recapitulated by mutational data alone and that may be worth validating in prospective studies.
Citation Format: Andrew D. Kelly, Heike Kroeger, Jumpei Yamazaki, Rodolphe Taby, Frank Neumann, Sijia Yu, Justin T. Lee, Rong He, Shoudan Liang, Yue Lu, Matteo Cesaroni, Sherry A. Pierce, Steven M. Kornblau, Carlos E. Bueso-Ramos, Farhad Ravandi, Hagop M. Kantarjain, Jaroslav Jelinek, Jean-Pierre J. Issa. A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2779.
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Affiliation(s)
| | - Heike Kroeger
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Rodolphe Taby
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Frank Neumann
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sijia Yu
- 1Temple University School of Medicine, Philadelphia, PA
| | - Justin T. Lee
- 1Temple University School of Medicine, Philadelphia, PA
| | - Rong He
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shoudan Liang
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yue Lu
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Farhad Ravandi
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
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Sato T, Cesaroni M, Panjarian S, Tran A, Madzo J, Okamoto Y, Zhang H, Chen X, Jelinek J, Issa JPJ. Abstract 2657: Target specificity of epigenetic therapy in cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A major question facing the use of epigenetic therapies in cancer is specificity in modulating gene expression. In addition, combined targeting of DNA and histone methylation remains largely unexplored despite the promising synergistic effects observed from combining DNA methyltransferase inhibitors with HDAC inhibitors. To address these questions, we performed RNA-seq, DNA methylation analysis and ChIP-seq (H3K4me2, H3K9me2, and H3K27me3) to study the effects of inhibitors of DNA methyltransferases (DAC), histone deacetylases (Depsi), histone demethylases (KDM1A inhibitor S2101), and histone methylases (EHMT2 inhibitor UNC0638 and EZH2 inhibitor GSK343) in three different cancer models (colon cancer, breast cancer, and leukemia). In colon cancer cells (YB5), DAC affected 3% of the transcriptome and 93% of the effect was gene upregulation. DAC had a greater effect on genes expressed in normal tissues and silenced in cancer (443 genes) compared to genes that do not change in cancer (194 genes). 90% of DAC targets genes showed no promoter DNA methylation in normal colon but gained methylation in cancer. Depsi changed the expression of 35% of the transcriptome and showed little specificity for gene upregulation or silenced genes. S2101, UNC0638, and GSK343 had limited effects on their own (<1.5% of the transcriptome), but UNC0638 and GSK343 preferentially targeted genes with H3K9me2 or H3K27me3, respectively. DAC combined with histone methylation inhibitors led to synergistic gene upregulation while still maintaining specificity for DNA methylated and silenced genes. These synergistic genes had limited overlap, indicating the possibility to target distinct sets of genes based on different epigenetic therapy combinations. IPA analysis demonstrated that these genes are enriched in cancer pathways, and consistent with this analysis, the combination therapies were able to decrease cancer cell proliferation more effectively than monotherapy. Broadly similar results were seen with genome wide studies in both breast cancer (MCF7) and leukemia (HL-60) cells. These results demonstrate that DNA methyltransferase inhibitors preferentially target cancer relevant genes, and can be combined with inhibitors targeting histone methylation for synergistic effects while still maintaining specificity.
Citation Format: Takahiro Sato, Matteo Cesaroni, Shoghag Panjarian, Anthony Tran, Jozef Madzo, Yasuyuki Okamoto, Hanghang Zhang, Xiaowei Chen, Jaroslav Jelinek, Jean-Pierre J. Issa. Target specificity of epigenetic therapy in cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2657.
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Malouf GG, Tahara T, Paradis V, Fabre M, Guettier C, Yamazaki J, Long H, Lu Y, Raynal NJM, Jelinek J, Mouawad R, Khayat D, Brugières L, Raymond E, Issa JPJ. Methylome sequencing for fibrolamellar hepatocellular carcinoma depicts distinctive features. Epigenetics 2016. [PMID: 26224146 DOI: 10.1080/15592294.2015.1076955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
With the goal of studying epigenetic alterations in fibrolamellar hepatocellular carcinoma (FLC) and establish an associated DNA methylation signature, we analyzed LINE-1 methylation in a cohort of FLC and performed next-generation sequencing of DNA methylation in a training set of pure-FLCs and non-cirrhotic hepatocellular carcinomas (nc-HCC). DNA methylation was correlated with gene expression. Furthermore, we established and validated an epigenetic signature differentiating pure-FLC from other HCCs. LINE-1 methylation correlated with shorter recurrence-free survival and overall survival in resected pure-FLC patients. Unsupervised clustering using CG sites located in islands distinguished pure-FLC from nc-HCC. Major DNA methylation changes occurred outside promoters, mainly in gene bodies and intergenic regions located in the vicinity of liver developmental genes (i.e., SMARCA4 and RXRA). Partially methylated domains were more prone to DNA methylation changes. Furthermore, we identified several putative tumor suppressor genes (e.g., DLEU7) and oncogenes (e.g., DUSP4). While ∼ 70% of identified gene promoters gaining methylation were marked by bivalent histone marks (H3K4me3/H3K27me3) in embryonic stem cells, ∼ 70% of those losing methylation were marked by H3K4me3. Finally, we established a pure FLC DNA methylation signature and validated it in an independent dataset. Our analysis reveals a distinct epigenetic signature of pure FLC as compared to nc-HCC, with DNA methylation changes occurring in the vicinity of liver developmental genes. These data suggest new options for targeting FLC based on cancer epigenome aberrations.
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Affiliation(s)
- Gabriel G Malouf
- a Department of Leukemia ; the University of Texas MD Anderson Cancer Center ; Houston , TX USA
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Issa JPJ. Abstract IA23: Multiple targetable pathways for epigenetic therapy. Cancer Res 2016. [DOI: 10.1158/1538-7445.chromepi15-ia23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic reprogramming erases the malignant potential of some transformed cells. The aim of epigenetic therapy is to achieve some degree of reprogramming in-vivo through reversing epigenetic changes and reactivating important genes including tumor-suppressor genes. It is hoped that this strategy will modify the malignant phenotype and induce clearance of the malignant clone by various mechanisms, including apoptosis, senescence and an immune response. Epigenetic modifying agents may also have mechanisms of anticancer action unrelated to gene reactivation. The DNA methyltransferase inhibitors azacitidine, decitabine and guadecitabine induce clinically meaningful remissions or improvements in 30-60% of patients with myeloid leukemias and prolong survival compared to standard approaches including chemotherapy. This therapy is accompanied by (i) global and gene specific demethylation, (ii) reactivation of silenced gene expression, (iii) delayed responses that correlate with early epigenetic reactivation and result in clonal elimination and (iv) eventual relapses and resistance the mechanisms of which appear to involve genetic evolution in some cases.
Two strategies have been proposed to enhance the efficacy of DNMT inhibitors - targeting other epigenetic pathways and unbiased screens for epigenetic activity. Using gene expression as an endpoint, we compared inhibitors of DNMTs (decitabine, DAC), HDACs, G9A, EZH2 and LSD1 in-vitro. We find that DNMT inhibition is the most specific approach to reactivation of genes silenced in cancer and, while HDAC inhibition is also very effective, it also has the highest rate of non-specific effects, which may explain why adding HDAC inhibitors to DNMT inhibitors has been disappointing clinically to date. Drugs that inhibit G9A, EZH2 or LSD1 had modest effects on their own but showed significant, non-overlapping synergy with DAC, while preserving specificity. To perform unbiased screens for epigenetic activity, we used a live cell assay based on DNA methylation mediated silencing of a CMV transgene driving GFP expression. In a screen of FDA approved drugs, we found three classical epigenetic targeted drugs (DNA methylation and histone deacetylase inhibitors) and 11 other drugs that reactivate GFP as well as endogenous TSGs in multiple cancer cell lines. These newly identified drugs, most prominently cardiac glycosides and arsenic trioxide, did not change DNA methylation locally or histone modifications globally. Instead, all 11 drugs altered calcium signaling and triggered calcium-calmodulin kinase (CamK) activity leading to MeCP2 phosphorylation and its nuclear exclusion. Blocking CamK activity abolished gene reactivation and cancer cell killing by these drugs, showing that triggering calcium fluxes is an essential component of their epigenetic mechanism of action. In a separate screen for synergy with DNMT inhibition, we found that platinum compounds showed striking synergy in activating GFP. This was dose dependent, observed both in concurrent and sequential combinations, seen with other alkylating agents, and linked mechanistically to significantly inhibited HP1α expression.
Our data uncover multiple distinct mechanisms that can be targeted for epigenetic therapy in cancer.
Citation Format: Jean-Pierre J. Issa. Multiple targetable pathways for epigenetic therapy. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA23.
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Affiliation(s)
- Jean-Pierre J. Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA
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Bouwmeester MC, Ruiter S, Lommelaars T, Sippel J, Hodemaekers HM, van den Brandhof EJ, Pennings JL, Kamstra JH, Jelinek J, Issa JPJ, Legler J, van der Ven LT. Zebrafish embryos as a screen for DNA methylation modifications after compound exposure. Toxicol Appl Pharmacol 2016; 291:84-96. [DOI: 10.1016/j.taap.2015.12.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 12/19/2022]
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Raynal NJM, Lee JT, Wang Y, Beaudry A, Madireddi P, Garriga J, Malouf GG, Dumont S, Dettman EJ, Gharibyan V, Ahmed S, Chung W, Childers WE, Abou-Gharbia M, Henry RA, Andrews AJ, Jelinek J, Cui Y, Baylin SB, Gill DL, Issa JPJ. Targeting Calcium Signaling Induces Epigenetic Reactivation of Tumor Suppressor Genes in Cancer. Cancer Res 2015; 76:1494-505. [PMID: 26719529 DOI: 10.1158/0008-5472.can-14-2391] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/18/2015] [Indexed: 01/09/2023]
Abstract
Targeting epigenetic pathways is a promising approach for cancer therapy. Here, we report on the unexpected finding that targeting calcium signaling can reverse epigenetic silencing of tumor suppressor genes (TSG). In a screen for drugs that reactivate silenced gene expression in colon cancer cells, we found three classical epigenetic targeted drugs (DNA methylation and histone deacetylase inhibitors) and 11 other drugs that induced methylated and silenced CpG island promoters driving a reporter gene (GFP) as well as endogenous TSGs in multiple cancer cell lines. These newly identified drugs, most prominently cardiac glycosides, did not change DNA methylation locally or histone modifications globally. Instead, all 11 drugs altered calcium signaling and triggered calcium-calmodulin kinase (CamK) activity, leading to MeCP2 nuclear exclusion. Blocking CamK activity abolished gene reactivation and cancer cell killing by these drugs, showing that triggering calcium fluxes is an essential component of their epigenetic mechanism of action. Our data identify calcium signaling as a new pathway that can be targeted to reactivate TSGs in cancer.
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Affiliation(s)
- Noël J-M Raynal
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania. Département de pharmacologie, Université de Montréal and Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada
| | - Justin T Lee
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Youjun Wang
- Beijing Key Laboratory of Gene Resources and Molecular Development College of Life Sciences, Beijing Normal University, Beijing, P.R. China
| | - Annie Beaudry
- Département de pharmacologie, Université de Montréal and Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada
| | - Priyanka Madireddi
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Judith Garriga
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Gabriel G Malouf
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah Dumont
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elisha J Dettman
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vazganush Gharibyan
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Saira Ahmed
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Wayne E Childers
- Moulder Center for Drug Discovery Research, Philadelphia, Pennsylvania
| | | | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Ying Cui
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Donald L Gill
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, The Milton S. Hershey Medical Center, Hershey, Pennsylvania
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania.
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Kropf P, Barnes G, Tang B, Pathak A, Issa JPJ. Healthcare utilization and costs associated with tyrosine kinase inhibitor switching in patients with chronic myeloid leukemia. Leuk Lymphoma 2015; 57:935-41. [DOI: 10.3109/10428194.2015.1088654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Yamazaki J, Taby R, Jelinek J, Raynal NJM, Cesaroni M, Pierce SA, Kornblau SM, Bueso-Ramos CE, Ravandi F, Kantarjian HM, Issa JPJ. Hypomethylation of TET2 Target Genes Identifies a Curable Subset of Acute Myeloid Leukemia. J Natl Cancer Inst 2015; 108:djv323. [PMID: 26568194 DOI: 10.1093/jnci/djv323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 10/08/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is curable in a subset of cases. The DNA methylation regulator TET2 is frequently mutated in AML, and we hypothesized that studying TET2-specific differentially methylated CpGs (tet2-DMCs) improves AML classification. METHODS We used bisulfite pyrosequencing to analyze the methylation status of four tet2-DMCs (SP140, MCCC1, EHMT1, and MTSS1) in a test group of 94 consecutive patients and a validation group of 92 consecutive patients treated with cytarabine-based chemotherapy. Data were analyzed with hierarchical clustering, Cox proportional hazards regression, and Kaplan-Meier analyses. All statistical tests were two-sided. RESULTS In the test cohort, hierarchical clustering analysis identified low levels of tet2-DMC methylation in 31 of 94 (33%) cases, and these had markedly longer overall survival (median survival 72+ vs 14 months, P = .002). Similar results were seen in the validation cohort. tet2-DMC-low status was shown to be an independent predictor of overall survival (hazard ratio = 0.29, P = .0002). In The Cancer Genome Atlas (TCGA) dataset where DNA methylation was analyzed by a different platform, tet2-DMC-low methylation was also associated with improved outcome (median survival = 55 vs 15 months, P = .0003) and was a better predictor of survival than mutations in TET2, IDH1, or IDH2, individually or combined. CONCLUSIONS Low levels of tet2-DMC methylation define a subgroup of AML that is highly curable and cannot be identified solely by genetic and cytogenetic analyses.
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Affiliation(s)
- Jumpei Yamazaki
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rodolphe Taby
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Noel J M Raynal
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Matteo Cesaroni
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sherry A Pierce
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Steven M Kornblau
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carlos E Bueso-Ramos
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Farhad Ravandi
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hagop M Kantarjian
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX.
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Affiliation(s)
- James N Lowder
- Astex Pharmaceuticals, 4420 Rosewood Drive, Suite 200, Pleasanton, CA 92488, USA
| | - Pietro Taverna
- Astex Pharmaceuticals, 4420 Rosewood Drive, Suite 200, Pleasanton, CA 92488, USA
| | - Jean-Pierre J Issa
- Fels Institute, Temple University School of Medicine & Cancer Epigenetics Program, Fox Chase Cancer Center, Temple Health, 3307 North Broad Street, Room 154, Philadelphia, PA 19140, USA
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Kopetz S, Desai J, Chan E, Hecht JR, O'Dwyer PJ, Maru D, Morris V, Janku F, Dasari A, Chung W, Issa JPJ, Gibbs P, James B, Powis G, Nolop KB, Bhattacharya S, Saltz L. Phase II Pilot Study of Vemurafenib in Patients With Metastatic BRAF-Mutated Colorectal Cancer. J Clin Oncol 2015; 33:4032-8. [PMID: 26460303 PMCID: PMC4669589 DOI: 10.1200/jco.2015.63.2497] [Citation(s) in RCA: 494] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Purpose BRAF V600E mutation is seen in 5% to 8% of patients with metastatic colorectal cancer (CRC) and is associated with poor prognosis. Vemurafenib, an oral BRAF V600 inhibitor, has pronounced activity in patients with metastatic melanoma, but its activity in patients with BRAF V600E–positive metastatic CRC was unknown. Patients and Methods In this multi-institutional, open-label study, patients with metastatic CRC with BRAF V600 mutations were recruited to an expansion cohort at the previously determined maximum-tolerated dose of 960 mg orally twice a day. Results Twenty-one patients were enrolled, of whom 20 had received at least one prior metastatic chemotherapy regimen. Grade 3 toxicities included keratoacanthomas, rash, fatigue, and arthralgia. Of the 21 patients treated, one patient had a confirmed partial response (5%; 95% CI, 1% to 24%) and seven other patients had stable disease by RECIST criteria. Median progression-free survival was 2.1 months. Patterns of concurrent mutations, microsatellite instability status, CpG island methylation status, PTEN loss, EGFR expression, and copy number alterations were not associated with clinical benefit. In contrast to prior expectations, concurrent KRAS and NRAS mutations were detected at low allele frequency in a subset of the patients' tumors (median, 0.21% allele frequency) and were apparent mechanisms of acquired resistance in vemurafenib-sensitive patient-derived xenograft models. Conclusion In marked contrast to the results seen in patients with BRAF V600E–mutant melanoma, single-agent vemurafenib did not show meaningful clinical activity in patients with BRAF V600E mutant CRC. Combination strategies are now under development and may be informed by the presence of intratumor heterogeneity of KRAS and NRAS mutations.
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Affiliation(s)
- Scott Kopetz
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia.
| | - Jayesh Desai
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Emily Chan
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Joel Randolph Hecht
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Peter J O'Dwyer
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Dipen Maru
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Van Morris
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Filip Janku
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Arvind Dasari
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Woonbook Chung
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Jean-Pierre J Issa
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Peter Gibbs
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Brian James
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Garth Powis
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Keith B Nolop
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Suman Bhattacharya
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Leonard Saltz
- Scott Kopetz, Dipen Maru, Van Morris, Filip Janku, and Arvind Dasari, The University of Texas MD Anderson Cancer Center, Houston, TX; Emily Chan, Vanderbilt-Ingram Cancer Center, Nashville, TN; Joel Randolph Hecht, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles; Brian James and Garth Powis, Sanford Burnham Institute, La Jolla; Keith B. Nolop, Plexxikon, Berkeley; Suman Bhattacharya, Genentech, South San Francisco, CA; Peter J. O'Dwyer, Abramson Cancer Center at University of Pennsylvania, Philadelphia, PA; Woonbook Chung and Jean-Pierre J. Issa, Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA; Leonard Saltz, Memorial Sloan-Kettering Cancer Center, New York, NY; and Jayesh Desai and Peter Gibbs, Royal Melbourne Hospital, Parkville, Victoria, Australia
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Qin T, Si J, Raynal NJM, Wang X, Gharibyan V, Ahmed S, Hu X, Jin C, Lu Y, Shu J, Estecio MR, Jelinek J, Issa JPJ. Epigenetic synergy between decitabine and platinum derivatives. Clin Epigenetics 2015; 7:97. [PMID: 26366234 PMCID: PMC4567801 DOI: 10.1186/s13148-015-0131-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/01/2015] [Indexed: 01/25/2023] Open
Abstract
Background Aberrant epigenetic silencing of tumor suppressor genes has been recognized as a driving force in cancer. Epigenetic drugs such as the DNA methylation inhibitor decitabine reactivate genes and are effective in myeloid leukemia, but resistance often develops and efficacy in solid tumors is limited. To improve their clinical efficacy, we searched among approved anti-cancer drugs for an epigenetic synergistic combination with decitabine. Results We used the YB5 cell line, a clonal derivative of the SW48 colon cancer cell line that contains a single copy of a hypermethylated cytomegalovirus (CMV) promoter driving green fluorescent protein (GFP) to screen for drug-induced gene reactivation and synergy with decitabine. None of the 16 anti-cancer drugs tested had effects on their own. However, in combination with decitabine, platinum compounds showed striking synergy in activating GFP. This was dose dependent, observed both in concurrent and sequential combinations, and also seen with other alkylating agents. Clinically achievable concentrations of carboplatin at (25 μM) and decitabine reactivated GFP in 28 % of the YB5 cells as compared to 15 % with decitabine alone. Epigenetic synergy was also seen at endogenously hypermethylated tumor suppressor genes such as MLH1 and PDLIM4. Genome-wide studies showed that reactivation of hypermethylated genes by the combination was significantly better than that induced by decitabine alone or carboplatin alone. Platinum compounds did not enhance decitabine-induced hypomethylation. Rather, we found significantly inhibited HP1α expression by carboplatin and the combination. This was accompanied by increased histone H3 lysine 4 (H3K4) trimethylation and histone H3 lysine 9 (H3K9) acetylation at reactivated genes (P < 0.0001) and reduced occupancy by methyl-binding proteins including MeCP2 and methyl-CpG-binding domain protein 2 (MBD2) (P < 0.0001). Conclusions Our results suggest that the combination of decitabine with platinum analogs shows epigenetic synergy that might be exploited in the treatment of different cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0131-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taichun Qin
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jiali Si
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Noël J-M Raynal
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Fels Institute for Cancer Research and Molecular Biology, Temple University, 3307 North Broad Street, Rm 154, PAHB, Philadelphia, PA 19140 USA
| | - Xiaodan Wang
- Harbin Institute of Hematology & Oncology, Harbin, 150010 China
| | - Vazganush Gharibyan
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Saira Ahmed
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Xin Hu
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Chunlei Jin
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Yue Lu
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jingmin Shu
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Marcos Rh Estecio
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jaroslav Jelinek
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Fels Institute for Cancer Research and Molecular Biology, Temple University, 3307 North Broad Street, Rm 154, PAHB, Philadelphia, PA 19140 USA
| | - Jean-Pierre J Issa
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Fels Institute for Cancer Research and Molecular Biology, Temple University, 3307 North Broad Street, Rm 154, PAHB, Philadelphia, PA 19140 USA
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Issa JPJ, Roboz G, Rizzieri D, Jabbour E, Stock W, O'Connell C, Yee K, Tibes R, Griffiths EA, Walsh K, Daver N, Chung W, Naim S, Taverna P, Oganesian A, Hao Y, Lowder JN, Azab M, Kantarjian H. Safety and tolerability of guadecitabine (SGI-110) in patients with myelodysplastic syndrome and acute myeloid leukaemia: a multicentre, randomised, dose-escalation phase 1 study. Lancet Oncol 2015; 16:1099-1110. [PMID: 26296954 DOI: 10.1016/s1470-2045(15)00038-8] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND Hypomethylating agents are used to treat cancers driven by aberrant DNA methylation, but their short half-life might limit their activity, particularly in patients with less proliferative diseases. Guadecitabine (SGI-110) is a novel hypomethylating dinucleotide of decitabine and deoxyguanosine resistant to degradation by cytidine deaminase. We aimed to assess the safety and clinical activity of subcutaneously given guadecitabine in patients with acute myeloid leukaemia or myelodysplastic syndrome. METHODS In this multicentre, open-label, phase 1 study, patients from nine North American medical centres with myelodysplastic syndrome or acute myeloid leukaemia that was refractory to or had relapsed after standard treatment were randomly assigned (1:1) to receive subcutaneous guadecitabine, either once-daily for 5 consecutive days (daily × 5), or once-weekly for 3 weeks, in a 28-day treatment cycle. Patients were stratified by disease. A 3 + 3 dose-escalation design was used in which we treated patients with guadecitabine doses of 3-125 mg/m(2) in separate dose-escalation cohorts. A twice-weekly treatment schedule was added to the study after a protocol amendment. The primary objective was to assess safety and tolerability of guadecitabine, determine the maximum tolerated and biologically effective dose, and identify the recommended phase 2 dose of guadecitabine. Safety analyses included all patients who received at least one dose of guadecitabine. Pharmacokinetic and pharmacodynamic analyses to determine the biologically effective dose included all patients for whom samples were available. This study is registered with ClinicalTrials.gov, number NCT01261312. FINDINGS Between Jan 4, 2011, and April 11, 2014, we enrolled and treated 93 patients: 35 patients with acute myeloid leukaemia and nine patients with myelodysplastic syndrome in the daily × 5 dose-escalation cohorts, 28 patients with acute myeloid leukaemia and six patients with myelodysplastic syndrome in the once-weekly dose-escalation cohorts, and 11 patients with acute myeloid leukaemia and four patients with myelodysplastic syndrome in the twice-weekly dose-escalation cohorts. The most common grade 3 or higher adverse events were febrile neutropenia (38 [41%] of 93 patients), pneumonia (27 [29%] of 93 patients), thrombocytopenia (23 [25%] of 93 patients), anaemia (23 [25%] of 93 patients), and sepsis (16 [17%] of 93 patients). The most common serious adverse events were febrile neutropenia (29 [31%] of 93 patients), pneumonia (26 [28%] of 93 patients), and sepsis (16 [17%] of 93 patients). Six of the 74 patients with acute myeloid leukaemia and six of the 19 patients with myelodysplastic syndrome had a clinical response to treatment. Two dose-limiting toxicities were noted in patients with myelodysplastic syndrome at 125 mg/m(2) daily × 5, thus the maximum tolerated dose in patients with myelodysplastic syndrome was 90 mg/m(2) daily × 5. The maximum tolerated dose was not reached in patients with acute myeloid leukaemia. Potent dose-related DNA demethylation occurred on the daily × 5 regimen, reaching a plateau at 60 mg/m(2) (designated as the biologically effective dose). INTERPRETATION Guadecitabine given subcutaneously at 60 mg/m(2) daily × 5 is well tolerated and is clinically and biologically active in patients with myelodysplastic syndrome and acute myeloid leukaemia. Guadecitabine 60 mg/m(2) daily × 5 is the recommended phase 2 dose, and these findings warrant further phase 2 studies. FUNDING Astex Pharmaceuticals, Stand Up To Cancer.
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Affiliation(s)
- Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA; Cancer Epigenetics Program, Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA.
| | - Gail Roboz
- Weill Cornell Medical College and New York Presbyterian Hospital, Division of Hematology and Oncology, New York, NY, USA
| | | | - Elias Jabbour
- University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, TX, USA
| | | | - Casey O'Connell
- Jane Anne Nohl Division of Hematology Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Karen Yee
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Raoul Tibes
- Mayo Clinic Arizona, Division of Hematology and Medical Oncology, Scottsdale, AZ, USA
| | | | - Katherine Walsh
- Ohio State University, James Cancer Hospital, Wexner Medical Center, Columbus, OH, USA
| | - Naval Daver
- University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, TX, USA
| | - Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA
| | - Sue Naim
- Astex Pharmaceuticals, Pleasanton, CA, USA
| | | | | | - Yong Hao
- Astex Pharmaceuticals, Pleasanton, CA, USA
| | | | | | - Hagop Kantarjian
- University of Texas MD Anderson Cancer Center, Department of Leukemia, Houston, TX, USA
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Kelly AD, Kroeger H, Yamazaki J, Taby R, Neumann F, Lee JT, He R, Liang S, Lu Y, Cesaroni M, Pierce SA, Kornblau SM, Bueso-Ramos CE, Ravandi F, Kantarjian HM, Issa JPJ, Jelinek J. Abstract B22: Genome-wide methylation analysis reveals an independently validated CpG island methylator phenotype associated with favorable prognosis in acute myeloid leukemia. Epigenetics 2015. [DOI: 10.1158/1557-3265.hemmal14-b22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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