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Yang X, Wang Z, Samovich SN, Kapralov AA, Amoscato AA, Tyurin VA, Dar HH, Li Z, Duan S, Kon N, Chen D, Tycko B, Zhang Z, Jiang X, Bayir H, Stockwell BR, Kagan VE, Gu W. PHLDA2-mediated phosphatidic acid peroxidation triggers a distinct ferroptotic response during tumor suppression. Cell Metab 2024; 36:762-777.e9. [PMID: 38309267 DOI: 10.1016/j.cmet.2024.01.006] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/14/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
Although the role of ferroptosis in killing tumor cells is well established, recent studies indicate that ferroptosis inducers also sabotage anti-tumor immunity by killing neutrophils and thus unexpectedly stimulate tumor growth, raising a serious issue about whether ferroptosis effectively suppresses tumor development in vivo. Through genome-wide CRISPR-Cas9 screenings, we discover a pleckstrin homology-like domain family A member 2 (PHLDA2)-mediated ferroptosis pathway that is neither ACSL4-dependent nor requires common ferroptosis inducers. PHLDA2-mediated ferroptosis acts through the peroxidation of phosphatidic acid (PA) upon high levels of reactive oxygen species (ROS). ROS-induced ferroptosis is critical for tumor growth in the absence of common ferroptosis inducers; strikingly, loss of PHLDA2 abrogates ROS-induced ferroptosis and promotes tumor growth but has no obvious effect in normal tissues in both immunodeficient and immunocompetent mouse tumor models. These data demonstrate that PHLDA2-mediated PA peroxidation triggers a distinct ferroptosis response critical for tumor suppression and reveal that PHLDA2-mediated ferroptosis occurs naturally in vivo without any treatment from ferroptosis inducers.
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Affiliation(s)
- Xin Yang
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Zhe Wang
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Svetlana N Samovich
- Center for Free Radical and Antioxidant Health and Departments of Environmental Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Pediatrics, Division of Critical Care and Hospital Medicine, Redox Health Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander A Kapralov
- Center for Free Radical and Antioxidant Health and Departments of Environmental Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Andrew A Amoscato
- Center for Free Radical and Antioxidant Health and Departments of Environmental Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Vladimir A Tyurin
- Center for Free Radical and Antioxidant Health and Departments of Environmental Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Haider H Dar
- Center for Free Radical and Antioxidant Health and Departments of Environmental Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Zhiming Li
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Shoufu Duan
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Ning Kon
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Delin Chen
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Benjamin Tycko
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Department of Pediatrics and Department of Genetics and Development, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Hülya Bayir
- Center for Free Radical and Antioxidant Health and Departments of Environmental Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Pediatrics, Division of Critical Care and Hospital Medicine, Redox Health Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Critical Care Medicine, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Valerian E Kagan
- Center for Free Radical and Antioxidant Health and Departments of Environmental Health, Chemistry, Pharmacology and Chemical Biology, Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wei Gu
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA.
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Listwan TA, Krinsky‐McHale SJ, Kovacs CM, Lee JH, Pang DI, Schupf N, Tycko B, Zigman WB, Silverman W. Prodromal Alzheimer's disease can affect activities of daily living for adults with Down syndrome. Alzheimers Dement (Amst) 2024; 16:e12562. [PMID: 38476636 PMCID: PMC10927922 DOI: 10.1002/dad2.12562] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 03/14/2024]
Abstract
INTRODUCTION Alzheimer's disease (AD) affecting adults with Down syndrome (DS-AD), like late-onset AD (LOAD) in the neurotypical population, has preclinical, prodromal, and more advanced stages. Only tasks placing high demands on cognition are expected to be affected during the prodromal stage, with activities of daily living (ADLs) typically being spared. However, cognitive demands of ADLs could be high for adults with DS and may be affected during prodromal DS-AD. METHODS Cognitively stable cases that subsequently developed prodromal DS-AD were identified within a set of archived data from a previous longitudinal study. Measures of ADLs and multiple cognitive domains were examined over time. RESULTS Clear declines in ADLs accompanied cognitive declines with prodromal DS-AD while stability in all measures was verified during preclinical DS-AD. DISCUSSION Operationally defining prodromal DS-AD is essential to disease staging in this high-risk population and for informing treatment options and timing as new disease-modifying drugs become available. Highlights Cognitive and functional stability were demonstrated prior to the onset of prodromal DS-AD.ADL declines accompanied cognitive declines as adults with DS transitioned to prodromal AD.Declines in ADLs should be a defining feature of prodromal AD for adults with DS.Better characterization of prodromal DS-AD can improve AD diagnosis and disease staging.Improvements in DS-AD diagnosis and staging could also inform the timing of interventions.
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Affiliation(s)
- Tracy A. Listwan
- Department of PsychologyNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew YorkUSA
| | - Sharon J. Krinsky‐McHale
- Department of PsychologyNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew YorkUSA
| | - Cynthia M. Kovacs
- Department of PsychologyNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew YorkUSA
| | - Joseph H. Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainG. H. Sergievsky CenterDepartments of Epidemiology and NeurologyCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Deborah I. Pang
- Department of PsychologyNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew YorkUSA
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainG. H. Sergievsky CenterDepartments of Epidemiology and NeurologyCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Benjamin Tycko
- Hackensack Meridian HealthCenter for Discovery and InnovationNutleyNew JerseyUSA
| | - Warren B. Zigman
- Department of PsychologyNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew YorkUSA
| | - Wayne Silverman
- Department of PediatricsUniversity of CaliforniaIrvineCaliforniaUSA
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Barcelona V, Abuaish S, Lee S, Harkins S, Butler A, Tycko B, Baccarelli AA, Walsh K, Monk CE. Stress and DNA Methylation of Blood Leukocytes among Pregnant Latina Women. Epigenomes 2023; 7:27. [PMID: 37987302 PMCID: PMC10660842 DOI: 10.3390/epigenomes7040027] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Latinas experience physical and psychological stressors in pregnancy leading to increased morbidity and higher risk for adverse birth outcomes. Epigenetic changes, including DNA methylation (DNAm), have been proposed as markers to create more refined risk stratification, yet few of these studies have examined these changes in Latinas. We conducted a secondary analysis of stored blood leukocytes of Latina women (n = 58) enrolled in a larger National Institutes of Health funded R01 project (2011-2016). We examined DNAm on eight candidate stress genes to compare physically and psychologically stressed participants to healthy (low stress) participants. We found unique CpGs that were differentially methylated in stressed women early- and mid-pregnancy compared to the healthy group, though none remained significant after FDR correction. Both physical and psychological stress were associated with hypomethylation at two consecutive CpG sites on NR3C1 in early pregnancy and one CpG site on NR3C1 in mid-pregnancy before adjustment. Stress was also associated with hypomethylation at two CpG sites on FKBP5 in early and mid-pregnancy but were no longer significant after FDR adjustment. Though we did not find statistically significant differences in DNAm during pregnancy between stressed and healthy women in this sample, signals were consistent with previous findings. Future work in larger samples should further examine the associations between stress and DNAm in pregnancy as this mechanism may explain underlying perinatal health inequities.
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Affiliation(s)
| | - Sameera Abuaish
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Seonjoo Lee
- Mental Health Data Science, New York State Psychiatric Institute, New York, NY 10032, USA;
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY 10032, USA
- Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
| | - Sarah Harkins
- Columbia University School of Nursing, New York, NY 10032, USA;
| | - Ashlie Butler
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
| | - Benjamin Tycko
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA;
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA;
| | - Kate Walsh
- Department of Psychology, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Catherine E. Monk
- Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
- New York State Psychiatric Institute, New York, NY 10032, USA
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4
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LaMarca EA, Saito A, Plaza-Jennings A, Espeso-Gil S, Hellmich A, Fernando MB, Javidfar B, Liao W, Estill M, Townsley K, Florio A, Ethridge JE, Do C, Tycko B, Shen L, Kamiya A, Tsankova NM, Brennand KJ, Akbarian S. R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription. bioRxiv 2023:2023.07.18.549494. [PMID: 37503149 PMCID: PMC10370098 DOI: 10.1101/2023.07.18.549494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
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Affiliation(s)
- Elizabeth A LaMarca
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Amara Plaza-Jennings
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio Espeso-Gil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allyse Hellmich
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla Townsley
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Florio
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - James E Ethridge
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine Do
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Nadejda M Tsankova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Current affiliation: Department of Psychiatry, Yale University, New Haven, CT 06511, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Xing Z, Li Y, Cortes-Gomez E, Jiang X, Gao S, Pao A, Shan J, Song Y, Perez A, Yu T, Highsmith MR, Boadu F, Conroy JM, Singh PK, Bakin AV, Cheng J, Duan Z, Wang J, Liu S, Tycko B, Yu YE. Dissection of a Down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome. Hum Mol Genet 2023; 32:2205-2218. [PMID: 37014740 PMCID: PMC10281752 DOI: 10.1093/hmg/ddad056] [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: 10/15/2022] [Revised: 02/13/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
As an aneuploidy, trisomy is associated with mammalian embryonic and postnatal abnormalities. Understanding the underlying mechanisms involved in mutant phenotypes is broadly important and may lead to new strategies to treat clinical manifestations in individuals with trisomies, such as trisomy 21 [Down syndrome (DS)]. Although increased gene dosage effects because of a trisomy may account for the mutant phenotypes, there is also the possibility that phenotypic consequences of a trisomy can arise because of the presence of a freely segregating extra chromosome with its own centromere, i.e. a 'free trisomy' independent of gene dosage effects. Presently, there are no reports of attempts to functionally separate these two types of effects in mammals. To fill this gap, here we describe a strategy that employed two new mouse models of DS, Ts65Dn;Df(17)2Yey/+ and Dp(16)1Yey/Df(16)8Yey. Both models carry triplications of the same 103 human chromosome 21 gene orthologs; however, only Ts65Dn;Df(17)2Yey/+ mice carry a free trisomy. Comparison of these models revealed the gene dosage-independent impacts of an extra chromosome at the phenotypic and molecular levels for the first time. They are reflected by impairments of Ts65Dn;Df(17)2Yey/+ males in T-maze tests when compared with Dp(16)1Yey/Df(16)8Yey males. Results from the transcriptomic analysis suggest the extra chromosome plays a major role in trisomy-associated expression alterations of disomic genes beyond gene dosage effects. This model system can now be used to deepen our mechanistic understanding of this common human aneuploidy and obtain new insights into the effects of free trisomies in other human diseases such as cancers.
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Affiliation(s)
- Zhuo Xing
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Yichen Li
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Eduardo Cortes-Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiaoling Jiang
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Shuang Gao
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Bioinformatics, OmniSeq Inc., Buffalo, NY, USA
| | - Annie Pao
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jidong Shan
- Molecular Cytogenetics Core, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yinghui Song
- Molecular Cytogenetics Core, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Amanda Perez
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tao Yu
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Max R Highsmith
- Department of Electric Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Frimpong Boadu
- Department of Electric Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Jeffrey M Conroy
- Research and Development, OmniSeq Inc., Buffalo, NY, USA
- Research Support Services, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Prashant K Singh
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Andrei V Bakin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jianlin Cheng
- Department of Electric Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Y Eugene Yu
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, USA
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6
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Wu H, Castano A, Liao Y, Santella R, Brenner D, Terry MB, Tycko B. Abstract P4-03-26: Blood DNA Methylation and Breast Cancer: a Prospective Case-Control Analysis in the Breast Cancer Prospective Family Study Cohort. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p4-03-26] [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: 03/06/2023]
Abstract
Abstract
Breast cancer has increased dramatically in young women < 50 years in the US over the past decade. DNA methylation is a type of epigenetic change that plays an important role in cancer etiology by silencing tumor suppressor genes or DNA repair-related genes through hypermethylation or activating oncogenes through hypomethylation. Previous genome-wide association studies have suggested DNA methylation in blood is a potential epigenetic markers of breast cancer risk. In this study, we applied targeted methyl-seq to examine the DNA methylation profile in regulatory sequences of 57 known DNA repair pathway genes, together with 123 other genes, located in immune-related loci and genome-wide association peaks for breast cancer. We used a nested case-control design within the Breast Cancer Prospective Family Study Cohort (FroF-SC) and examined DNA methylation profile in DNA from the blood of breast cancer cases (N=293) and age-matched controls (N=327). In the preliminary data analysis, we observed that the methylation levels in 5 genes were statistically significantly different between cases and controls using Wilcoxon Rank Sum Test (Table 1). Some candidate loci show methylation values spanning a wide range (Std Dev) in both cases and controls, suggesting the presence of genotype-dependent allele-specific methylation (ASM). We then conducted generalized estimating equations (GEE model) adjusting for age at blood draw and calculated the odds ratios (ORs) and 95%CI for the association between methylation levels in the 90th and 10th percentiles of differentially methylated genes (90% vs 10% methylation) and breast cancer risk. The ORs (95% CI) from the GEE models were 1.26 (0.97, 1.63, p=0.08) for CD6, 1.27 (0.85, 1.91, p=0.24) for SDCCAG3, 1.12 (0.85, 1.48, p=0.40) for DCLRE1B, 1.29 (0.88, 1.90, p=0.20) for IP09, and 1.63 (1.08, 2.45, p=0.02) for GNPDA1 (Table 2). The associations were not different by age group. Our preliminary results suggest that DNA methylation measured in blood may be a biomarker of breast cancer susceptibility.
Citation Format: HuiChen Wu, Angelica Castano, Yuyan Liao, Regina Santella, David Brenner, Mary Beth Terry, Benjamin Tycko. Blood DNA Methylation and Breast Cancer: a Prospective Case-Control Analysis in the Breast Cancer Prospective Family Study Cohort [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-03-26.
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Affiliation(s)
| | | | | | | | | | | | - Benjamin Tycko
- 7Hackensack Meridian Health Center for Discovery and Innovation
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7
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Orlacchio A, Weissinger D, Do C, Tycko B, Simeone DM, Gonda T. Abstract C041: Hypomethylating therapy induces a potential immuno-suppressive myeloid phenotype by altering cancer cell cytokine secretion in PDAC. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-c041] [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: 11/17/2022]
Abstract
Abstract
Introduction: We have previously shown using the KPC (KrasLSL G12D/+; p53 r172H/+; Pdx1-Cre) mouse model of PDAC that sequential treatment with the DNA hypomethylating agents (HMA) followed by anti-PD-1 led to increased tumor necrosis, slowed tumor growth, increased tumor-infiltrating CD8+ cells, and significantly increased mean survival. However, acquired treatment resistance occurred, with emergence of a specific subtype of M2-polarized putatively immunosuppressive Chi3l3+ macrophages. In this study, we characterize the mechanism of polarization of these cells, define their function, and identify a potential therapeutic strategy to combine with epigentic therapy to prevent unfavourable macrophage polarization and improve the efficacy of epigenetic priming of immunotherapy against PDAC. Methods: Studies were conducted with primary macrophages (PM)e isolated from bone marrow (BMDM) or the peritoneum of 6-8 weeks mice and RAW264.7 cells were also used and exposed to conditioned media from primary KPC cell lines with and without previous treatment with the HMAs decitabine or azacytidine. The effect was compared with polarization by direct HMA, IFN-γ and IL-4. Gene set enrichment analysis was done on RNASeq data from myeloid cells and validated by RT-PCR. We used cytokine arrays and Western blot validation to identify secreted cytokines from KPC cells. Results: We profiled expression of RAW264.7 cells, BMDM and PMs following exposure to IL-4 or IFN-γ and identified a signature associated with each treatment (CD206, Fizz1, Tlr8, IGF1, Mgl2 associated with IL-4 and TNFα, CD86, CD64, CD40, NOS2 associated with IFN-γ). Direct exposure of myeloid cells to hypomethylating agents did not result in a significant polarization. We next used conditioned media of KPC cells to identify a hypomethylation specific effect and found a significant IL-4 like enrichment (Chi3l3, Arg1, Il4i1, Raet1a, Lgals4) and a HMA-specific myeloid signature (CD137, IL1a, Ccl2, Ccl7, Spp1) with treatment. To assess which cytokines might trigger this polarization, we employed cytokine arrays and identified a small number of candidate cytokines that are specific to hypomethylation induced polarization of myeloid cells, including CXCL1/2, CCL2, GM-CSF, FGF-21, IGFBP-6 and ICAM-1. Conclusions: Our results show that paracrine secretion of cytokines from cancer cells treated with HMA drugs, rather than direct effect of hypomethylating therapy on macrophages, is responsible for polarizing macrophages into an immunosuppressive subtype. We further identified several candidate cytokines secreted by cancer cells following hypomethylating therapy that may be relevant for this immunosuppressive polarization of macrophages and might be specific therapeutic targets in combination with hypomethylating therapy.
Citation Format: Arturo Orlacchio, Daniel Weissinger, Catherine Do, Benjamin Tycko, Diane M. Simeone, Tamas Gonda. Hypomethylating therapy induces a potential immuno-suppressive myeloid phenotype by altering cancer cell cytokine secretion in PDAC [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C041.
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Affiliation(s)
- Arturo Orlacchio
- 1Department of Medicine, NYU Grossman School of Medicine, New York, NY,
| | - Daniel Weissinger
- 2Pancreatic Cancer Center, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY,
| | - Catherine Do
- 3Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ,
| | - Benjamin Tycko
- 4Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Diane M. Simeone
- 2Pancreatic Cancer Center, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY,
| | - Tamas Gonda
- 1Department of Medicine, NYU Grossman School of Medicine, New York, NY,
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Oczkowicz M, Tycko B, Demars J. Editorial: Genomic imprinting and monoallelic gene expression mechanisms and applications. Front Genet 2022; 13:1067443. [DOI: 10.3389/fgene.2022.1067443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
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Lyu C, Huang M, Liu N, Chen Z, Lupo PJ, Tycko B, Witte JS, Hobbs CA, Li M. Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci. Bioinformatics 2022; 38:3853-3862. [PMID: 35781319 PMCID: PMC9364381 DOI: 10.1093/bioinformatics/btac443] [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] [Received: 09/07/2021] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION CpG sites within the same genomic region often share similar methylation patterns and tend to be co-regulated by multiple genetic variants that may interact with one another. RESULTS We propose a multi-trait methylation random field (multi-MRF) method to evaluate the joint association between a set of CpG sites and a set of genetic variants. The proposed method has several advantages. First, it is a multi-trait method that allows flexible correlation structures between neighboring CpG sites (e.g. distance-based correlation). Second, it is also a multi-locus method that integrates the effect of multiple common and rare genetic variants. Third, it models the methylation traits with a beta distribution to characterize their bimodal and interval properties. Through simulations, we demonstrated that the proposed method had improved power over some existing methods under various disease scenarios. We further illustrated the proposed method via an application to a study of congenital heart defects (CHDs) with 83 cardiac tissue samples. Our results suggested that gene BACE2, a methylation quantitative trait locus (QTL) candidate, colocalized with expression QTLs in artery tibial and harbored genetic variants with nominal significant associations in two genome-wide association studies of CHD. AVAILABILITY AND IMPLEMENTATION https://github.com/chenlyu2656/Multi-MRF. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chen Lyu
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN 47405, USA,Department of Population Health, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manyan Huang
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Nianjun Liu
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Zhongxue Chen
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Philip J Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA,Department of Biomedical Data Sciences, Stanford University, Stanford, CA 94305, USA
| | - Charlotte A Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ming Li
- To whom correspondence should be addressed.
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10
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Queder N, Phelan MJ, Taylor L, Tustison N, Doran E, Hom C, Nguyen D, Lai F, Pulsifer M, Price J, Kreisl WC, Rosas HD, Krinsky‐McHale S, Brickman AM, Yassa MA, Schupf N, Silverman W, Lott IT, Head E, Mapstone M, Keator DB, Ances BM, Andrews HF, Bell K, Birn RM, Brickman AM, Bulova P, Cheema A, Chen K, Christian BT, Clare I, Clark L, Cohen AD, Constantino JN, Doran EW, Fagan A, Feingold E, Foroud TM, Handen BL, Hartley SL, Head E, Henson R, Hom C, Honig L, Ikonomovic MD, Johnson SC, Jordan C, Kamboh MI, Keator D, Klunk WE, Kofler JK, Kreisl WC, Krinsky‐McHale SJ, Lai F, Lao P, Laymon C, Lee JH, Lott IT, Lupson V, Mapstone M, Mathis CA, Minhas DS, Nadkarni N, O'Bryant S, Pang D, Petersen M, Price JC, Pulsifer M, Reiman E, Rizvi B, Rosas HD, Schupf N, Silverman WP, Tudorascu DL, Tumuluru R, Tycko B, Varadarajan B, White DA, Yassa MA, Zaman S, Zhang F. Joint-label fusion brain atlases for dementia research in Down syndrome. Alzheimers Dement (Amst) 2022; 14:e12324. [PMID: 35634535 PMCID: PMC9131930 DOI: 10.1002/dad2.12324] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/28/2022] [Accepted: 04/25/2022] [Indexed: 01/07/2023]
Abstract
Research suggests a link between Alzheimer's Disease in Down Syndrome (DS) and the overproduction of amyloid plaques. Using Positron Emission Tomography (PET) we can assess the in-vivo regional amyloid load using several available ligands. To measure amyloid distributions in specific brain regions, a brain atlas is used. A popular method of creating a brain atlas is to segment a participant's structural Magnetic Resonance Imaging (MRI) scan. Acquiring an MRI is often challenging in intellectually-imparied populations because of contraindications or data exclusion due to significant motion artifacts or incomplete sequences related to general discomfort. When an MRI cannot be acquired, it is typically replaced with a standardized brain atlas derived from neurotypical populations (i.e. healthy individuals without DS) which may be inappropriate for use in DS. In this project, we create a series of disease and diagnosis-specific (cognitively stable (CS-DS), mild cognitive impairment (MCI-DS), and dementia (DEM-DS)) probabilistic group atlases of participants with DS and evaluate their accuracy of quantifying regional amyloid load compared to the individually-based MRI segmentations. Further, we compare the diagnostic-specific atlases with a probabilistic atlas constructed from similar-aged cognitively-stable neurotypical participants. We hypothesized that regional PET signals will best match the individually-based MRI segmentations by using DS group atlases that aligns with a participant's disorder and disease status (e.g. DS and MCI-DS). Our results vary by brain region but generally show that using a disorder-specific atlas in DS better matches the individually-based MRI segmentations than using an atlas constructed from cognitively-stable neurotypical participants. We found no additional benefit of using diagnose-specific atlases matching disease status. All atlases are made publicly available for the research community. Highlight Down syndrome (DS) joint-label-fusion atlases provide accurate positron emission tomography (PET) amyloid measurements.A disorder-specific DS atlas is better than a neurotypical atlas for PET quantification.It is not necessary to use a disease-state-specific atlas for quantification in aged DS.Dorsal striatum results vary, possibly due to this region and dementia progression.
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Affiliation(s)
- Nazek Queder
- Department of Psychiatry and Human BehaviorUniversity of California IrvineIrvineCaliforniaUSA,Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and MemoryUniversity of California IrvineIrvineCaliforniaUSA
| | - Michael J. Phelan
- Institute for Memory Impairments and Neurological DisordersUniversity of California IrvineIrvineCaliforniaUSA
| | - Lisa Taylor
- Department of Psychiatry and Human BehaviorUniversity of California IrvineIrvineCaliforniaUSA
| | - Nicholas Tustison
- Department of RadiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Eric Doran
- Department of PediatricsUniversity of CaliforniaIrvine Medical CenterOrangeCaliforniaUSA
| | - Christy Hom
- Department of Psychiatry and Human BehaviorUniversity of California IrvineIrvineCaliforniaUSA
| | - Dana Nguyen
- Department of Psychiatry and Human BehaviorUniversity of California IrvineIrvineCaliforniaUSA
| | - Florence Lai
- Massachusetts General HospitalHarvard UniversityBostonMassachusettsUSA
| | - Margaret Pulsifer
- Massachusetts General HospitalHarvard UniversityBostonMassachusettsUSA
| | - Julie Price
- Massachusetts General HospitalHarvard UniversityBostonMassachusettsUSA
| | | | - Herminia D. Rosas
- Massachusetts General HospitalHarvard UniversityBostonMassachusettsUSA
| | - Sharon Krinsky‐McHale
- New York State Institute for Basic Research in Developmental DisabilitiesNew YorkNew YorkUSA
| | - Adam M. Brickman
- Department of NeurologyColumbia UniversityNew YorkNew YorkUSA,Taub Institute for Research on Alzheimer's Disease and the Aging BrainDepartment of NeurologyVagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Michael A. Yassa
- Department of Psychiatry and Human BehaviorUniversity of California IrvineIrvineCaliforniaUSA,Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and MemoryUniversity of California IrvineIrvineCaliforniaUSA,Department of NeurologyUniversity of California IrvineIrvineCaliforniaUSA
| | - Nicole Schupf
- Department of NeurologyColumbia UniversityNew YorkNew YorkUSA,Taub Institute for Research on Alzheimer's Disease and the Aging BrainDepartment of NeurologyVagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Wayne Silverman
- Department of PediatricsUniversity of CaliforniaIrvine Medical CenterOrangeCaliforniaUSA
| | - Ira T. Lott
- Department of PediatricsUniversity of CaliforniaIrvine Medical CenterOrangeCaliforniaUSA
| | - Elizabeth Head
- Department of Pathology & Laboratory MedicineUniversity of California IrvineIrvineCaliforniaUSA
| | - Mark Mapstone
- Department of NeurologyUniversity of California IrvineIrvineCaliforniaUSA
| | - David B. Keator
- Department of Psychiatry and Human BehaviorUniversity of California IrvineIrvineCaliforniaUSA
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Min D, Byun J, Lee EJ, Khan AA, Liu C, Loudig O, Hu W, Zhao Y, Herlyn M, Tycko B, Cole PA, Ryu B. Epigenetic Silencing of BMP6 by the SIN3A-HDAC1/2 Repressor Complex Drives Melanoma Metastasis via FAM83G/PAWS1. Mol Cancer Res 2022; 20:217-230. [PMID: 34610961 PMCID: PMC9744461 DOI: 10.1158/1541-7786.mcr-21-0289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/21/2021] [Revised: 08/24/2021] [Accepted: 09/30/2021] [Indexed: 12/14/2022]
Abstract
Aberrant epigenetic transcriptional regulation is linked to metastasis, a primary cause of cancer-related death. Dissecting the epigenetic mechanisms controlling metastatic progression may uncover important insights to tumor biology and potential therapeutic targets. Here, we investigated the role of the SIN3A histone deacetylase 1 and 2 (SIN3A-HDAC1/2) complex in cancer metastasis. Using a mouse model of melanoma metastasis, we found that the SIN3A-HDAC1/2 transcription repressor complex silences BMP6 expression, causing increased metastatic dissemination and tumor growth via suppression of BMP6-activated SMAD5 signaling. We further discovered that FAM83G/PAWS1, a downstream effector of BMP6-SMAD5 signaling, contributes critically to metastatic progression by promoting actin-dependent cytoskeletal dynamics and cell migration. Pharmacologic inhibition of the SIN3A-HDAC1/2 complex reduced the numbers of melanoma cells in the circulation and inhibited metastatic tumor growth by inducing disseminated cell dormancy, highlighting the SIN3A-HDAC1/2 repressor complex as a potential therapeutic target for blocking cancer metastasis. IMPLICATIONS: This study identifies the novel molecular links in the metastatic progression to target cytoskeletal dynamics in melanoma and identifies the SIN3A-HDAC1/2 complex and FAM83G/PAWS1 as potential targets for melanoma adjuvant therapy.
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Affiliation(s)
- Dongkook Min
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA
| | - Jaemin Byun
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA
| | - Eun-Joon Lee
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA
| | - Abdul A Khan
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA
| | - Christina Liu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA
| | - Oliver Loudig
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA,John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ 07601, USA,Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, 20057, USA
| | - Wei Hu
- Department of Chemistry and Chemistry Biology, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Yong Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA,John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program. Wistar Institute, Philadelphia, PA 19104, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA,John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ 07601, USA,Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, 20057, USA
| | - Phillip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Byungwoo Ryu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110, USA,John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ 07601, USA,Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, 20057, USA
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12
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Lyu C, Huang M, Liu N, Chen Z, Lupo PJ, Tycko B, Witte JS, Hobbs CA, Li M. Detecting methylation quantitative trait loci using a methylation random field method. Brief Bioinform 2021; 22:bbab323. [PMID: 34414410 PMCID: PMC8575051 DOI: 10.1093/bib/bbab323] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/09/2021] [Accepted: 07/24/2021] [Indexed: 11/13/2022] Open
Abstract
DNA methylation may be regulated by genetic variants within a genomic region, referred to as methylation quantitative trait loci (mQTLs). The changes of methylation levels can further lead to alterations of gene expression, and influence the risk of various complex human diseases. Detecting mQTLs may provide insights into the underlying mechanism of how genotypic variations may influence the disease risk. In this article, we propose a methylation random field (MRF) method to detect mQTLs by testing the association between the methylation level of a CpG site and a set of genetic variants within a genomic region. The proposed MRF has two major advantages over existing approaches. First, it uses a beta distribution to characterize the bimodal and interval properties of the methylation trait at a CpG site. Second, it considers multiple common and rare genetic variants within a genomic region to identify mQTLs. Through simulations, we demonstrated that the MRF had improved power over other existing methods in detecting rare variants of relatively large effect, especially when the sample size is small. We further applied our method to a study of congenital heart defects with 83 cardiac tissue samples and identified two mQTL regions, MRPS10 and PSORS1C1, which were colocalized with expression QTL in cardiac tissue. In conclusion, the proposed MRF is a useful tool to identify novel mQTLs, especially for studies with limited sample sizes.
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Affiliation(s)
- Chen Lyu
- Department of Epidemiology and Biostatistics, Indiana University, Bloomington, IN, USA
| | - Manyan Huang
- Department of Epidemiology and Biostatistics, Indiana University, Bloomington, IN, USA
| | - Nianjun Liu
- Department of Epidemiology and Biostatistics, Indiana University, Bloomington, IN, USA
| | - Zhongxue Chen
- Department of Epidemiology and Biostatistics, Indiana University, Bloomington, IN, USA
| | - Philip J Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | | | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University, Bloomington, IN, USA
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Chen XQ, Xing Z, Chen QD, Salvi RJ, Zhang X, Tycko B, Mobley WC, Yu YE. Mechanistic Analysis of Age-Related Clinical Manifestations in Down Syndrome. Front Aging Neurosci 2021; 13:700280. [PMID: 34276349 PMCID: PMC8281234 DOI: 10.3389/fnagi.2021.700280] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/09/2021] [Indexed: 12/15/2022] Open
Abstract
Down syndrome (DS) is the most common genetic cause of Alzheimer's disease (AD) due to trisomy for all or part of human chromosome 21 (Hsa21). It is also associated with other phenotypes including distinctive facial features, cardiac defects, growth delay, intellectual disability, immune system abnormalities, and hearing loss. All adults with DS demonstrate AD-like brain pathology, including amyloid plaques and neurofibrillary tangles, by age 40 and dementia typically by age 60. There is compelling evidence that increased APP gene dose is necessary for AD in DS, and the mechanism for this effect has begun to emerge, implicating the C-terminal APP fragment of 99 amino acid (β-CTF). The products of other triplicated genes on Hsa21 might act to modify the impact of APP triplication by altering the overall rate of biological aging. Another important age-related DS phenotype is hearing loss, and while its mechanism is unknown, we describe its characteristics here. Moreover, immune system abnormalities in DS, involving interferon pathway genes and aging, predispose to diverse infections and might modify the severity of COVID-19. All these considerations suggest human trisomy 21 impacts several diseases in an age-dependent manner. Thus, understanding the possible aging-related mechanisms associated with these clinical manifestations of DS will facilitate therapeutic interventions in mid-to-late adulthood, while at the same time shedding light on basic mechanisms of aging.
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Affiliation(s)
- Xu-Qiao Chen
- Department of Neurosciences, University of California San Diego, La Jolla, CA, United States
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Quang-Di Chen
- Department of Communicative Disorders and Sciences and Center for Hearing and Deafness, University at Buffalo, Buffalo, NY, United States
| | - Richard J Salvi
- Department of Communicative Disorders and Sciences and Center for Hearing and Deafness, University at Buffalo, Buffalo, NY, United States
| | - Xuming Zhang
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, United States.,Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, United States
| | - William C Mobley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, United States
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States.,Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, United States
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Li M, Lyu C, Huang M, Do C, Tycko B, Lupo PJ, MacLeod SL, Randolph CE, Liu N, Witte JS, Hobbs CA. Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease. BMC Genom Data 2021; 22:20. [PMID: 34112112 PMCID: PMC8194170 DOI: 10.1186/s12863-021-00975-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/18/2020] [Accepted: 06/02/2021] [Indexed: 12/27/2022] Open
Abstract
Background Most congenital heart defects (CHDs) result from complex interactions among genetic susceptibilities, epigenetic modifications, and maternal environmental exposures. Characterizing the complex relationship between genetic, epigenetic, and transcriptomic variation will enhance our understanding of pathogenesis in this important type of congenital disorder. We investigated cis-acting effects of genetic single nucleotide polymorphisms (SNPs) on local DNA methylation patterns within 83 cardiac tissue samples and prioritized their contributions to CHD risk by leveraging results of CHD genome-wide association studies (GWAS) and their effects on cardiac gene expression. Results We identified 13,901 potential methylation quantitative trait loci (mQTLs) with a false discovery threshold of 5%. Further co-localization analyses and Mendelian randomization indicated that genetic variants near the HLA-DRB6 gene on chromosome 6 may contribute to CHD risk by regulating the methylation status of nearby CpG sites. Additional SNPs in genomic regions on chromosome 10 (TNKS2-AS1 gene) and chromosome 14 (LINC01629 gene) may simultaneously influence epigenetic and transcriptomic variations within cardiac tissues. Conclusions Our results support the hypothesis that genetic variants may influence the risk of CHDs through regulating the changes of DNA methylation and gene expression. Our results can serve as an important source of information that can be integrated with other genetic studies of heart diseases, especially CHDs. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00975-2.
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Affiliation(s)
- Ming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA.
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - Manyan Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | | | | | | | - Nianjun Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - John S Witte
- University of California at San Francisco, San Francisco, CA, 94158, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
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15
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Petersen ME, Rafii MS, Zhang F, Hall J, Julovich D, Ances BM, Schupf N, Krinsky-McHale SJ, Mapstone M, Silverman W, Lott I, Klunk W, Head E, Christian B, Foroud T, Lai F, Diana Rosas H, Zaman S, Wang MC, Tycko B, Lee JH, Handen B, Hartley S, Fortea J, O'Bryant S. Plasma Total-Tau and Neurofilament Light Chain as Diagnostic Biomarkers of Alzheimer's Disease Dementia and Mild Cognitive Impairment in Adults with Down Syndrome. J Alzheimers Dis 2021; 79:671-681. [PMID: 33337378 DOI: 10.3233/jad-201167] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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]
Abstract
BACKGROUND The need for diagnostic biomarkers of cognitive decline is particularly important among aging adults with Down syndrome (DS). Growing empirical support has identified the utility of plasma derived biomarkers among neurotypical adults with mild cognitive impairment (MCI) and Alzheimer's disease (AD); however, the application of such biomarkers has been limited among the DS population. OBJECTIVE This study aimed to investigate the cross-sectional diagnostic performance of plasma neurofilament light chain (Nf-L) and total-tau, individually and in combination among a cohort of DS adults. METHODS Plasma samples were analyzed from n = 305 (n = 225 cognitively stable (CS); n = 44 MCI-DS; n = 36 DS-AD) participants enrolled in the Alzheimer's Biomarker Consortium -Down Syndrome. RESULTS In distinguishing DS-AD participants from CS, Nf-L alone produced an AUC of 90%, total-tau alone reached 74%, and combined reached an AUC of 86%. When age and gender were included, AUC increased to 93%. Higher values of Nf-L, total-tau, and age were all shown to be associated with increased risk for DS-AD. When distinguishing MCI-DS participants from CS, Nf-L alone produced an AUC of 65%, while total-tau alone reached 56%. A combined model with Nf-L, total-tau, age, and gender produced an AUC of 87%. Both higher values in age and total-tau were found to increase risk for MCI-DS; Nf-L levels were not associated with increased risk for MCI-DS. CONCLUSION Advanced assay techniques make total-tau and particularly Nf-L useful biomarkers of both AD pathology and clinical status in DS and have the potential to serve as outcome measures in clinical trials for future disease-modifying drugs.
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Affiliation(s)
- Melissa E Petersen
- University of North Texas Health Science Center, Department of Family Medicine and Institute for Translational Research, Fort Worth, TX, USA
| | - Michael S Rafii
- Alzheimer's Therapeutic Research Institute (ATRI), Keck School of Medicine, University of Southern California, San Diego, CA, USA
| | - Fan Zhang
- University of North Texas Health Science Center, Department of Family Medicine and Institute for Translational Research, Fort Worth, TX, USA
| | - James Hall
- University of North Texas Health Science Center, Institute for Translational Research and Department of Pharmacology and Neuroscience, Fort Worth, TX, USA
| | - David Julovich
- University of North Texas Health Science Center, Institute for Translational Research and Department of Pharmacology and Neuroscience, Fort Worth, TX, USA
| | - Beau M Ances
- Washington University School of Medicine in St. Louis, Center for Advanced Medicine Neuroscience, St. Louis, MO, USA
| | - Nicole Schupf
- Columbia University Irving Medical Center, Taub Institute for Research on Alzheimer's Disease and the Aging Brain/G.H. Sergievsky Center, New York, NY, USA.,Columbia University, Mailman School of Public Health, Department of Epidemiology, New York, NY, USA.,Columbia University Irving Medical Center, Department of Neurology, Neurological Institute, New York, NY, USA.,Columbia University Medical Center, Department of Psychiatry, New York, NY, USA
| | - Sharon J Krinsky-McHale
- NYS Institute for Basic Research in Developmental Disabilities, Department of Psychology, Staten Island, NY, USA
| | - Mark Mapstone
- University of California, Irvine, Department of Neurology, Irvine, CA, USA
| | - Wayne Silverman
- University of California, Irvine, School of Medicine, Department of Pediatrics, Orange, CA, USA
| | - Ira Lott
- University of California, Irvine, School of Medicine, Department of Pediatrics, Orange, CA, USA
| | - William Klunk
- University of Pittsburgh, Department of Psychiatry, Pittsburgh, PA, USA
| | - Elizabeth Head
- University of California, Irvine, Department of Pathology, Irvine, CA, USA
| | - Brad Christian
- University of Wisconsin Madison, Department of Medical Physics and Psychiatry, Madison, WI, USA
| | - Tatiana Foroud
- Indiana University School of Medicine, Department of Medical & Molecular Genetics, Indianapolis, IN, USA
| | - Florence Lai
- Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Charlestown, MA, USA
| | - H Diana Rosas
- Massachusetts General Hospital, Departments of Neurology and Radiology, Harvard Medical School, Charlestown, MA, USA
| | - Shahid Zaman
- University of Cambridge, School of Clinical Medicine, Department of Psychiatry, Cambridge, UK.,Cambridgeshire and Peterborough NHS Foundation Trust, Fulbourn Hospital, Cambridge, UK
| | - Mei-Cheng Wang
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Benjamin Tycko
- Columbia University Irving Medical Center, Department of Pathology and Cell Biology, New York, NY, USA
| | - Joseph H Lee
- Columbia University Irving Medical Center, Taub Institute for Research on Alzheimer's Disease and the Aging Brain/G.H. Sergievsky Center, New York, NY, USA
| | - Benjamin Handen
- University of Pittsburgh, Department of Psychiatry, Pittsburgh, PA, USA
| | - Sigan Hartley
- University of Wisconsin, School of Human Ecology and Waisman Center, Madison, WI, USA
| | - Juan Fortea
- Barcelona Down Medical Center, Fundació Catalana de Síndrome de Down, Barcelona, Spain.,Sant Pau Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau, Universitat Aut`onoma de Barcelona, Barcelona, Spain
| | - Sid O'Bryant
- University of North Texas Health Science Center, Institute for Translational Research and Department of Pharmacology and Neuroscience, Fort Worth, TX, USA
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Gonda TA, Fang J, Salas M, Do C, Hsu E, Zhukovskaya A, Siegel A, Takahashi R, Lopez-Bujanda ZA, Drake CG, Manji GA, Wang TC, Olive KP, Tycko B. A DNA Hypomethylating Drug Alters the Tumor Microenvironment and Improves the Effectiveness of Immune Checkpoint Inhibitors in a Mouse Model of Pancreatic Cancer. Cancer Res 2020; 80:4754-4767. [PMID: 32816859 DOI: 10.1158/0008-5472.can-20-0285] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/26/2020] [Accepted: 07/30/2020] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer that has proven refractory to immunotherapy. Previously, treatment with the DNA hypomethylating drug decitabine (5-aza-dC; DAC) extended survival in the KPC-Brca1 mouse model of PDAC. Here we investigated the effects of DAC in the original KPC model and tested combination therapy with DAC followed by immune checkpoint inhibitors (ICI). Four protocols were tested: PBS vehicle, DAC, ICI (anti-PD-1 or anti-VISTA), and DAC followed by ICI. For each single-agent and combination treatment, tumor growth was measured by serial ultrasound, tumor-infiltrating lymphoid and myeloid cells were characterized, and overall survival was assessed. Single-agent DAC led to increased CD4+ and CD8+ tumor-infiltrating lymphocytes (TIL), PD1 expression, and tumor necrosis while slowing tumor growth and modestly increasing mouse survival without systemic toxicity. RNA-sequencing of DAC-treated tumors revealed increased expression of Chi3l3 (Ym1), reflecting an increase in a subset of tumor-infiltrating M2-polarized macrophages. While ICI alone had modest effects, DAC followed by either of ICI therapies additively inhibited tumor growth and prolonged mouse survival. The best results were obtained using DAC followed by anti-PD-1, which extended mean survival from 26 to 54 days (P < 0.0001). In summary, low-dose DAC inhibits tumor growth and increases both TILs and a subset of tumor-infiltrating M2-polarized macrophages in the KPC model of PDAC, and DAC followed by anti-PD-1 substantially prolongs survival. Because M2-polarized macrophages are predicted to antagonize antitumor effects, targeting these cells may be important to enhance the efficacy of combination therapy with DAC plus ICI. SIGNIFICANCE: In a pancreatic cancer model, a DNA hypomethylating drug increases tumor-infiltrating effector T cells, increases a subset of M2 macrophages, and significantly prolongs survival in combination with immune checkpoint inhibitors.See related commentary by Nephew, p. 4610.
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Affiliation(s)
- Tamas A Gonda
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York. .,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Division of Gastroenterology and Hepatology, Department of Medicine, New York University, New York, New York
| | - Jarwei Fang
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York
| | - Martha Salas
- Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, New Jersey
| | - Catherine Do
- Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, New Jersey
| | - Emily Hsu
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Anna Zhukovskaya
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York
| | - Ariel Siegel
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York
| | - Ryota Takahashi
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Zoila A Lopez-Bujanda
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Graduate Program in Pathobiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Charles G Drake
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Gulam A Manji
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Timothy C Wang
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Kenneth P Olive
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Benjamin Tycko
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University, New York, New York. .,John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, New Jersey.,Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C
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17
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Petersen ME, Zhang F, Schupf N, Krinsky‐McHale SJ, Hall J, Mapstone M, Cheema A, Silverman W, Lott I, Rafii MS, Handen B, Klunk W, Head E, Christian B, Foroud T, Lai F, Rosas HD, Zaman S, Ances BM, Wang M, Tycko B, Lee JH, O'Bryant S. Proteomic profiles for Alzheimer's disease and mild cognitive impairment among adults with Down syndrome spanning serum and plasma: An Alzheimer's Biomarker Consortium-Down Syndrome (ABC-DS) study. Alzheimers Dement (Amst) 2020; 12:e12039. [PMID: 32626817 PMCID: PMC7327223 DOI: 10.1002/dad2.12039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Previously generated serum and plasma proteomic profiles were examined among adults with Down syndrome (DS) to determine whether these profiles could discriminate those with mild cognitive impairment (MCI-DS) and Alzheimer's disease (DS-AD) from those cognitively stable (CS). METHODS Data were analyzed on n = 305 (n = 225 CS; n = 44 MCI-DS; n = 36 DS-AD) enrolled in the Alzheimer's Biomarker Consortium-Down Syndrome (ABC-DS). RESULTS Distinguishing MCI-DS from CS, the serum profile produced an area under the curve (AUC) = 0.95 (sensitivity [SN] = 0.91; specificity [SP] = 0.99) and an AUC = 0.98 (SN = 0.96; SP = 0.97) for plasma when using an optimized cut-off score. Distinguishing DS-AD from CS, the serum profile produced an AUC = 0.93 (SN = 0.81; SP = 0.99) and an AUC = 0.95 (SN = 0.86; SP = 1.0) for plasma when using an optimized cut-off score. AUC remained unchanged to slightly improved when age and sex were included. Eotaxin3, interleukin (IL)-10, C-reactive protein, IL-18, serum amyloid A , and FABP3 correlated fractions at r2 > = 0.90. DISCUSSION Proteomic profiles showed excellent detection accuracy for MCI-DS and DS-AD.
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Affiliation(s)
- Melissa E. Petersen
- Department of Family Medicine Institute for Translational ResearchUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Fan Zhang
- Vermont Genetics NetworkUniversity of VermontBurlingtonVermontUSA
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia University Irving Medical CenterNew YorkNew YorkUSA
- G.H. Sergievsky CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of Epidemiology, Mailman School of Public HealthColumbia UniversityNew YorkNew YorkUSA
- Department of NeurologyNeurological InstituteColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of PsychiatryColumbia University Medical CenterNew YorkNew YorkUSA
| | - Sharon J. Krinsky‐McHale
- Department of PsychologyNYS Institute for Basic Research in Developmental DisabilitiesStaten IslandNew YorkUSA
| | - James Hall
- Department of Pharmacology and Neuroscience Institute for Translational ResearchUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Mark Mapstone
- Department of NeurologyUniversity of CaliforniaIrvineCaliforniaUSA
| | - Amrita Cheema
- Georgetown University Medical CenterWashingtonDistrict of ColumbiaUSA
| | - Wayne Silverman
- Department of Pediatrics, School of MedicineUniversity of CaliforniaIrvineCaliforniaUSA
| | - Ira Lott
- Department of Pediatrics, School of MedicineUniversity of CaliforniaIrvineCaliforniaUSA
| | - Michael S. Rafii
- Department of Neurology, Keck School of MedicineUniversity of Southern CaliforniaSan DiegoCaliforniaUSA
| | - Benjamin Handen
- Department of PsychiatryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - William Klunk
- Department of PsychiatryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Elizabeth Head
- Department of PathologyUniversity of CaliforniaIrvineCaliforniaUSA
| | - Brad Christian
- Department of Medical Physics and PsychiatryUniversity of Wisconsin MadisonMadisonWisconsinUSA
| | - Tatiana Foroud
- Department of Medical & Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Florence Lai
- Department of Neurology, Massachusetts General HospitalHarvard Medical SchoolCharlestownMassachusettsUSA
| | - H. Diana Rosas
- Departments of Neurology and Radiology, Massachusetts General HospitalHarvard Medical SchoolCharlestownMassachusettsUSA
| | - Shahid Zaman
- Department of Psychiatry, School of Clinical MedicineUniversity of CambridgeCambridgeUK
- Cambridgeshire and Peterborough NHS Foundation TrustFulbourn HospitalCambridgeUK
| | - Beau M. Ances
- Washingston University School of Medicine in St. LouisSt. LouisMissouriUSA
| | - Mei‐Cheng Wang
- Johns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Benjamin Tycko
- Department of Pathology and Cell BiologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Joseph H. Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia University Irving Medical CenterNew YorkNew YorkUSA
- G.H. Sergievsky CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
- Department of Epidemiology, Mailman School of Public HealthColumbia UniversityNew YorkNew YorkUSA
- Department of NeurologyNeurological InstituteColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Sid O'Bryant
- Department of Pharmacology and Neuroscience Institute for Translational ResearchUniversity of North Texas Health Science CenterFort WorthTexasUSA
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18
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Do C, Dumont ELP, Salas M, Castano A, Mujahed H, Maldonado L, Singh A, DaSilva-Arnold SC, Bhagat G, Lehman S, Christiano AM, Madhavan S, Nagy PL, Green PHR, Feinman R, Trimble C, Illsley NP, Marder K, Honig L, Monk C, Goy A, Chow K, Goldlust S, Kaptain G, Siegel D, Tycko B. Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs. Genome Biol 2020; 21:153. [PMID: 32594908 PMCID: PMC7322865 DOI: 10.1186/s13059-020-02059-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 09/16/2019] [Accepted: 05/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in normal and neoplastic cells, remain to be clarified. RESULTS We perform whole genome methyl-seq on diverse normal cells and tissues and three cancer types. After excluding imprinting, the data pinpoint 15,112 high-confidence ASM differentially methylated regions, of which 1838 contain SNPs in strong linkage disequilibrium or coinciding with GWAS peaks. ASM frequencies are increased in cancers versus matched normal tissues, due to widespread allele-specific hypomethylation and focal allele-specific hypermethylation in poised chromatin. Cancer cells show increased allele switching at ASM loci, but disruptive SNPs in specific classes of CTCF and transcription factor binding motifs are similarly correlated with ASM in cancer and non-cancer. Rare somatic mutations affecting these same motif classes track with de novo ASM. Allele-specific transcription factor binding from ChIP-seq is enriched among ASM loci, but most ASM differentially methylated regions lack such annotations, and some are found in otherwise uninformative "chromatin deserts." CONCLUSIONS ASM is increased in cancers but occurs by a shared mechanism involving disruptive SNPs in CTCF and transcription factor binding sites in both normal and neoplastic cells. Dense ASM mapping in normal plus cancer samples reveals candidate rSNPs that are difficult to find by other approaches. Together with GWAS data, these rSNPs can nominate specific transcriptional pathways in susceptibility to autoimmune, cardiometabolic, neuropsychiatric, and neoplastic diseases.
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Affiliation(s)
- Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA.
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA.
| | - Emmanuel L P Dumont
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Martha Salas
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Angelica Castano
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Huthayfa Mujahed
- Department of Medicine, Huddinge, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Leonel Maldonado
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21287, USA
| | - Arunjot Singh
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sonia C DaSilva-Arnold
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Govind Bhagat
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
- Division of Gastroenterology and Celiac Center, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Soren Lehman
- Department of Medicine, Huddinge, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Angela M Christiano
- Departments of Dermatology and Genetics and Development, Columbia University Medical Center, New York, NY, 10032, USA
| | - Subha Madhavan
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | | | - Peter H R Green
- Division of Gastroenterology and Celiac Center, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Rena Feinman
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Cornelia Trimble
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21287, USA
| | - Nicholas P Illsley
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Karen Marder
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Lawrence Honig
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Catherine Monk
- Departments of Psychiatry and Behavioral Medicine and Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Andre Goy
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Kar Chow
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Samuel Goldlust
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - George Kaptain
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - David Siegel
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA.
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA.
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA.
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19
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Dumont ELP, Tycko B, Do C. CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation. Bioinformatics 2020; 36:3558-3560. [PMID: 32119067 PMCID: PMC7267820 DOI: 10.1093/bioinformatics/btaa149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/19/2019] [Revised: 01/28/2020] [Accepted: 02/25/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Methods for quantifying the imbalance in CpG methylation between alleles genome-wide have been described but their algorithmic time complexity is quadratic and their practical use requires painstaking attention to infrastructure choice, implementation and execution. To solve this problem, we developed CloudASM, a scalable, ultra-efficient, turn-key, portable pipeline on Google Cloud Platform (GCP) that uses a novel pipeline manager and GCP's serverless enterprise data warehouse. AVAILABILITY AND IMPLEMENTATION CloudASM is freely available in the GitHub repository https://github.com/TyckoLab/CloudASM and a sample dataset and its results are also freely available at https://console.cloud.google.com/storage/browser/cloudasm. CONTACT emmanuel.dumont@hmh-cdi.org.
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Affiliation(s)
- Emmanuel L P Dumont
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
- Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ 07110, USA
- Lombardi Comprehensive Cancer, Center Georgetown University, Washington, DC 20007, USA
| | - Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
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20
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Robakis TK, Lee S, Werner E, Liu G, Miller M, Wylie D, Champagne FA, Salas M, Do C, Tycko B, Monk C. DNA methylation patterns in T lymphocytes are generally stable in human pregnancies but CD3 methylation is associated with perinatal psychiatric symptoms. Brain Behav Immun Health 2020; 3:100044. [PMID: 34589835 PMCID: PMC8474679 DOI: 10.1016/j.bbih.2020.100044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Objectives To determine whether DNA methylation patterns in genes coding for selected T-lymphocyte proteins are associated with perinatal psychiatric distress or with complications of pregnancy. Methods T lymphocyte DNA was obtained from pregnant women across three time points in pregnancy and the postpartum period and epigenetic patterns were assessed using Illumina 450 K Methylation Beadchips. Seven selected genes critical for T cell function were analyzed for methylation changes during pregnancy and for associations of methylation patterns with psychiatric distress or with pregnancy complications, with particular attention paid to spatial aggregations of methyl groups, termed ‘hotspots,’ within the selected genes. Results In the candidate gene approach, DNA methylation density within a single cluster of 9 contiguous CpG loci within the CD3 gene was found to be strongly associated with anxiety and depression in mid- and late pregnancy, and weakly associated with the presence of complications of pregnancy. Average DNA methylation density across each of the seven genes examined, and assay-wide, was found to be relatively stable across pregnancy and postpartum, but methylation within the CD3 hotspot was more malleable and changes over time were coordinated across the nine cytosines in the hotspot. CD3 CpGs did not pass array-wide tests for significance, but CpG clusters in two other genes, DTNBP1 and OXSR1, showed array-wide significant associations with anxiety. Conclusions Despite the need for tolerating the fetal hemi-allograft, overall DNA methylation patterns in T lymphocytes are generally stable over the mid to late course of human pregnancies and postpartum. However, site-specific changes in DNA methylation density in CD3 appear linked to both symptoms of depression and anxiety in pregnancy and, less strongly, to adverse pregnancy outcomes. Associations exist between DNA methylation density in T cells and measures of stress and mental health in pregnant women. Global DNA methylation density is generally stable over the course of pregnancy. A subregion within the CD3 gene has unusually variable DNA methylation density and is associated with anxiety and depression. Spatial and gene specificity may be important elements of epigenetic regulation of immune function in pregnancy.
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Affiliation(s)
- Thalia K Robakis
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seonjoo Lee
- Columbia University Department of Psychiatry, New York, NY, 10032, USA
| | - Elizabeth Werner
- Columbia University Department of Psychiatry, New York, NY, 10032, USA
| | - Grace Liu
- Columbia University Department of Psychiatry, New York, NY, 10032, USA
| | - Melissa Miller
- University of Texas at Austin Department of Psychology, Austin, TX, 78712, USA
| | - Dennis Wylie
- University of Texas at Austin Department of Psychology, Austin, TX, 78712, USA
| | - Frances A Champagne
- University of Texas at Austin Department of Psychology, Austin, TX, 78712, USA
| | - Martha Salas
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Catherine Do
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Benjamin Tycko
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Catherine Monk
- Columbia University Department of Psychiatry, New York, NY, 10032, USA
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21
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Walsh K, McCormack CA, Webster R, Pinto A, Lee S, Feng T, Krakovsky HS, O'Grady SM, Tycko B, Champagne FA, Werner EA, Liu G, Monk C. Maternal prenatal stress phenotypes associate with fetal neurodevelopment and birth outcomes. Proc Natl Acad Sci U S A 2019; 116:23996-24005. [PMID: 31611411 PMCID: PMC6883837 DOI: 10.1073/pnas.1905890116] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [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] [Indexed: 11/18/2022] Open
Abstract
Maternal prenatal stress influences offspring neurodevelopment and birth outcomes including the ratio of males to females born; however, there is limited understanding of what types of stress matter, and for whom. Using a data-driven approach with 27 variables from questionnaires, ambulatory diaries, and physical assessments collected early in the singleton pregnancies of 187 women, 3 latent profiles of maternal prenatal stress emerged that were differentially associated with sex at birth, birth outcomes, and fetal neurodevelopment. Most women (66.8%) were in the healthy group (HG); 17.1% were in the psychologically stressed group (PSYG), evidencing clinically meaningful elevations in perceived stress, depression, and anxiety; and 16% were in the physically stressed group (PHSG) with relatively higher ambulatory blood pressure and increased caloric intake. The population normative male:female secondary sex ratio (105:100) was lower in the PSYG (2:3) and PHSG (4:9), and higher in the HG (23:18), consistent with research showing diminished male births in maternal stress contexts. PHSG versus HG infants were born 1.5 wk earlier (P < 0.05) with 22% compared to 5% born preterm. PHSG versus HG fetuses had decreased fetal heart rate-movement coupling (P < 0.05), which may indicate slower central nervous system development, and PSYG versus PHSG fetuses had more birth complications, consistent with previous findings among offspring of women with psychiatric illness. Social support most strongly differentiated the HG, PSYG, and PHSG groups, and higher social support was associated with increased odds of male versus female births. Stress phenotypes in pregnant women are associated with male vulnerability and poor fetal outcomes.
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Affiliation(s)
- Kate Walsh
- Ferkauf Graduate School of Psychology, Yeshiva University, The Bronx, NY 10461
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032
| | - Clare A McCormack
- Center for Science and Society, Columbia University, New York, NY 10027
| | - Rachel Webster
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032
| | - Anita Pinto
- Data Science, Columbia University, New York, NY 10027
| | - Seonjoo Lee
- Division of Behavioral Medicine, New York State Psychiatric Institute, New York, NY 10032
- Department of Biostatistics (in Psychiatry), Mailman School of Public Health, Columbia University, New York, NY 10032
| | - Tianshu Feng
- Department of Biostatistics (in Psychiatry), Mailman School of Public Health, Columbia University, New York, NY 10032
| | - H Sloan Krakovsky
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032
| | - Sinclaire M O'Grady
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110
| | - Frances A Champagne
- Department of Psychiatry, Columbia University, New York, NY 10032
- Department of Psychology, University of Texas at Austin, Austin, TX 78712
| | - Elizabeth A Werner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032
- Department of Psychiatry, Columbia University, New York, NY 10032
| | - Grace Liu
- Department of Psychiatry, Columbia University, New York, NY 10032
| | - Catherine Monk
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032;
- Division of Behavioral Medicine, New York State Psychiatric Institute, New York, NY 10032
- Department of Psychiatry, Columbia University, New York, NY 10032
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22
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Tekola-Ayele F, Workalemahu T, Gorfu G, Shrestha D, Tycko B, Wapner R, Zhang C, Louis GMB. Sex differences in the associations of placental epigenetic aging with fetal growth. Aging (Albany NY) 2019; 11:5412-5432. [PMID: 31395791 PMCID: PMC6710059 DOI: 10.18632/aging.102124] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 03/28/2019] [Accepted: 07/21/2019] [Indexed: 12/15/2022]
Abstract
Identifying factors that influence fetal growth in a sex-specific manner can help unravel mechanisms that explain sex differences in adverse neonatal outcomes and in-utero origins of cardiovascular disease disparities. Premature aging of the placenta, a tissue that supports fetal growth and exhibits sex-specific epigenetic changes, is associated with pregnancy complications. Using DNA methylation-based age estimator, we investigated the sex-specific relationship of placental epigenetic aging with fetal growth across 13-40 weeks gestation, neonatal size, and risk of low birth weight. Placental epigenetic age acceleration (PAA), the difference between DNA methylation age and gestational age, was associated with reduced fetal weight among males but with increased fetal weight among females. PAA was inversely associated with fetal weight, abdominal circumference, and biparietal diameter at 32-40 weeks among males but was positively associated with all growth measures among females across 13-40 weeks. A 1-week increase in PAA was associated with 2-fold (95% CI 1.2, 3.2) increased odds for low birth weight and 1.5-fold (95% CI 1.1, 2.0) increased odds for small-for-gestational age among males. In all, fetal growth was significantly reduced in males but not females exposed to a rapidly aging placenta. Epigenetic aging of the placenta may underlie sex differences in neonatal outcomes.
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Affiliation(s)
- Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tsegaselassie Workalemahu
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gezahegn Gorfu
- Department of Clinical Laboratory Science, College of Nursing and Allied Health Sciences, Howard University, Washington, DC 20059, USA
| | - Deepika Shrestha
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation and the Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ 07110, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Cuilin Zhang
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Germaine M. Buck Louis
- Dean’s Office, College of Health and Human Services, George Mason University, Fairfax, VA 22030, USA
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23
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Ambrosini G, Do C, Tycko B, Realubit RB, Karan C, Musi E, Carvajal RD, Chua V, Aplin AE, Schwartz GK. Inhibition of NF-κB-Dependent Signaling Enhances Sensitivity and Overcomes Resistance to BET Inhibition in Uveal Melanoma. Cancer Res 2019; 79:2415-2425. [PMID: 30885979 DOI: 10.1158/0008-5472.can-18-3177] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/29/2019] [Accepted: 03/13/2019] [Indexed: 01/08/2023]
Abstract
Bromodomain and extraterminal protein inhibitors (BETi) are epigenetic therapies aimed to target dysregulated gene expression in cancer cells. Despite early successes of BETi in a range of malignancies, the development of drug resistance may limit their clinical application. Here, we evaluated the mechanisms of BETi resistance in uveal melanoma, a disease with little treatment options, using two approaches: a high-throughput combinatorial drug screen with the clinical BET inhibitor PLX51107 and RNA sequencing of BETi-resistant cells. NF-κB inhibitors synergistically sensitized uveal melanoma cells to PLX51107 treatment. Furthermore, genes involved in NF-κB signaling were upregulated in BETi-resistant cells, and the transcription factor CEBPD contributed to the mechanism of resistance. These findings suggest that inhibitors of NF-κB signaling may improve the efficacy of BET inhibition in patients with advanced uveal melanoma. SIGNIFICANCE: These findings provide evidence that inhibitors of NF-κB signaling synergize with BET inhibition in in vitro and in vivo models, suggesting a clinical utility of these targeted therapies in patients with uveal melanoma.
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Affiliation(s)
- Grazia Ambrosini
- The Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.
| | - Catherine Do
- Division of Genetics & Epigenetics, Department of Biomedical Research, Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, New Jersey
| | - Benjamin Tycko
- Division of Genetics & Epigenetics, Department of Biomedical Research, Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, New Jersey
| | - Ronald B Realubit
- The Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Charles Karan
- The Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Elgilda Musi
- The Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Richard D Carvajal
- The Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Division of Hematology/Oncology, Columbia University Medical Center, New York, New York
| | - Vivian Chua
- Cancer Biology and Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Andrew E Aplin
- Cancer Biology and Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Gary K Schwartz
- The Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Division of Hematology/Oncology, Columbia University Medical Center, New York, New York
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24
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Youn A, Kim KI, Rabadan R, Tycko B, Shen Y, Wang S. A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes. BMC Med Genomics 2018; 11:98. [PMID: 30400878 PMCID: PMC6218985 DOI: 10.1186/s12920-018-0425-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 03/27/2018] [Accepted: 10/19/2018] [Indexed: 01/08/2023] Open
Abstract
Background Recent large-scale cancer sequencing studies have discovered many novel cancer driver genes (CDGs) in human cancers. Some studies also suggest that CDG mutations contribute to cancer-associated epigenomic and transcriptomic alterations across many cancer types. Here we aim to improve our understanding of the connections between CDG mutations and altered cancer cell epigenomes and transcriptomes on pan-cancer level and how these connections contribute to the known association between epigenome and transcriptome. Method Using multi-omics data including somatic mutation, DNA methylation, and gene expression data of 20 cancer types from The Cancer Genome Atlas (TCGA) project, we conducted a pan-cancer analysis to identify CDGs, when mutated, have strong associations with genome-wide methylation or expression changes across cancer types, which we refer as methylation driver genes (MDGs) or expression driver genes (EDGs), respectively. Results We identified 32 MDGs, among which, eight are known chromatin modification or remodeling genes. Many of the remaining 24 MDGs are connected to chromatin regulators through either regulating their transcription or physically interacting with them as potential co-factors. We identified 29 EDGs, 26 of which are also MDGs. Further investigation on target genes’ promoters methylation and expression alteration patterns of these 26 overlapping driver genes shows that hyper-methylation of target genes’ promoters are significantly associated with down-regulation of the same target genes and hypo-methylation of target genes’ promoters are significantly associated with up-regulation of the same target genes. Conclusion This finding suggests a pivotal role for genetically driven changes in chromatin remodeling in shaping DNA methylation and gene expression patterns during tumor development. Electronic supplementary material The online version of this article (10.1186/s12920-018-0425-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahrim Youn
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA.,The Jackson Laboratory For Genomic Medicine, Farmington, Connecticut, USA
| | - Kyung In Kim
- The Jackson Laboratory For Genomic Medicine, Farmington, Connecticut, USA
| | - Raul Rabadan
- Department of System Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Benjamin Tycko
- Division of Genetics & Epigenetics, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Yufeng Shen
- Department of System Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA.,Columbia Genome Center, Columbia University, New York, New York, USA
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA.
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25
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Wu HC, Do C, Andrulis IL, John EM, Daly MB, Buys SS, Chung WK, Knight JA, Bradbury AR, Keegan THM, Schwartz L, Krupska I, Miller RL, Santella RM, Tycko B, Terry MB. Breast cancer family history and allele-specific DNA methylation in the legacy girls study. Epigenetics 2018; 13:240-250. [PMID: 29436922 DOI: 10.1080/15592294.2018.1435243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 02/02/2023] Open
Abstract
Family history, a well-established risk factor for breast cancer, can have both genetic and environmental contributions. Shared environment in families as well as epigenetic changes that also may be influenced by shared genetics and environment may also explain familial clustering of cancers. Epigenetic regulation, such as DNA methylation, can change the activity of a DNA segment without a change in the sequence; environmental exposures experienced across the life course can induce such changes. However, genetic-epigenetic interactions, detected as methylation quantitative trait loci (mQTLs; a.k.a. meQTLs) and haplotype-dependent allele-specific methylation (hap-ASM), can also contribute to inter-individual differences in DNA methylation patterns. To identify differentially methylated regions (DMRs) associated with breast cancer susceptibility, we examined differences in white blood cell DNA methylation in 29 candidate genes in 426 girls (ages 6-13 years) from the LEGACY Girls Study, 239 with and 187 without a breast cancer family history (BCFH). We measured methylation by targeted massively parallel bisulfite sequencing (bis-seq) and observed BCFH DMRs in two genes: ESR1 (Δ4.9%, P = 0.003) and SEC16B (Δ3.6%, P = 0.026), each of which has been previously implicated in breast cancer susceptibility and pubertal development. These DMRs showed high inter-individual variability in methylation, suggesting the presence of mQTLs/hap-ASM. Using single nucleotide polymorphisms data in the bis-seq amplicon, we found strong hap-ASM in SEC16B (with allele specific-differences ranging from 42% to 74%). These findings suggest that differential methylation in genes relevant to breast cancer susceptibility may be present early in life, and that inherited genetic factors underlie some of these epigenetic differences.
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Affiliation(s)
- Hui-Chen Wu
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY
| | - Catherine Do
- c John Theurer Cancer Center , Hackensack University Medical Center , Hackensack NJ
| | - Irene L Andrulis
- d Lunenfeld-Tanenbaum Research Institute , Sinai Health System , Toronto , Ontario.,e Departments of Molecular Genetics and Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
| | - Esther M John
- f Cancer Prevention Institute of California , Fremont CA.,g Department of Health Research & Policy (Epidemiology) , and Stanford Cancer Institute, Stanford University School of Medicine , Stanford , CA
| | - Mary B Daly
- h Department of Clinical Genetics , Fox Chase Cancer Center , Philadelphia , PA
| | - Saundra S Buys
- i Department of Medicine and , Huntsman Cancer Institute, University of Utah Health Sciences Center , UT
| | - Wendy K Chung
- j Departments of Pediatrics ; Department of Medicine , Columbia University College of Physicians and Surgeons , New York , NY
| | - Julia A Knight
- d Lunenfeld-Tanenbaum Research Institute , Sinai Health System , Toronto , Ontario.,k Dalla Lana School of Public Health , University of Toronto , Toronto
| | - Angela R Bradbury
- l Departments of Medicine, Division of Hematology/Oncology, Department of Medical Ethics and Health Policy, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA
| | - Theresa H M Keegan
- m Center for Oncology Hematology Outcomes Research and Training (COHORT).,n Division of Hematology and Oncology , University of California Davis School of Medicine , Sacramento , CA
| | - Lisa Schwartz
- o Department of Pediatrics, Division of Oncology, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA.,p The Children's Hospital of Philadelphia , Philadelphia , PA
| | - Izabela Krupska
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY
| | - Rachel L Miller
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,j Departments of Pediatrics ; Department of Medicine , Columbia University College of Physicians and Surgeons , New York , NY
| | - Regina M Santella
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY
| | - Benjamin Tycko
- c John Theurer Cancer Center , Hackensack University Medical Center , Hackensack NJ.,q Lombardi Comprehensive Cancer Center , Georgetown University , Washington , DC
| | - Mary Beth Terry
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY.,r Imprints Center , Columbia University Medical Center , New York , NY.,s Department of Epidemiology , Mailman School of Public Health of Columbia University , New York , NY
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26
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Safyan RA, Gonda T, Tycko B, Chabot JA, Manji GA, Schwartz GK, Oberstein PE. Phase II open-label, single-center study evaluating safety and efficacy of pembrolizumab following induction with the hypomethylating agent azacitidine in patients with advanced pancreatic cancer after failure of first-line therapy. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.4_suppl.tps534] [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: 11/20/2022] Open
Abstract
TPS534 Background: First-line cytotoxic chemotherapy improves survival for patients with metastatic pancreatic adenocarcinoma (PDA) but the majority will progress after a median of 5-7 months. CD8 T-cells are thought to be the major anti-tumor effector cells and their density in resected pancreatic tumors correlates with survival. Our published pre-clinical data in the KPC-Brca1 mouse model shows that treatment with a hypomethylating agent inhibits tumor growth (Shakya, Gonda et al., Cancer Res, 2013) and, in recent data (B.T. and T.G. in preparation), combining a hypomethylating agent with an immune checkpoint inhibitor leads to slowing of tumor growth and increased survival in KPC mice. We propose a novel approach to improve response rates with immune checkpoint blockade in pancreatic cancer by utilizing a hypomethylating agent to prime the tumor and its microenvironment, thereby increasing the number of intratumoral effector T cells, decreasing the immunosuppressive cell population, and influencing stromal-tumor cell interactions. Methods: Thirty-one evaluable subjects with advanced pancreatic cancer will be enrolled in this phase II study to evaluate the efficacy and safety of pembrolizumab following induction with azacitidine in the second-line setting. All subjects will have received a single line of chemotherapy for locally advanced or metastatic PDA prior to study enrollment. Subjects must have available baseline biopsy or archival tissue for analysis. Low-dose azacitidine (50 mg/m2 subcutaneous) will be given daily for 5 days every 4 weeks, and pembrolizumab 200 mg IV will be administered starting on day 15 and then continued every 3 weeks. Subjects will undergo an on-treatment biopsy during week 8. The primary efficacy endpoint will be PFS according to RECIST v1.1 criteria. There will be an accelerated phase Ib dose determination component with an initial 6 subjects. Secondary endpoints will include safety/tolerability, ORR, DOR, and OS. Multiple correlative analyses utilizing tissue and serum samples will be performed. Clinical trial information: NCT03264404.
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Affiliation(s)
| | - Tamas Gonda
- Columbia University College of Physicians and Surgeons, New York, NY
| | | | - John A. Chabot
- Columbia University College of Physicians and Surgeons/ New York-Presbyterian Hospital, New York, NY
| | - Gulam Abbas Manji
- Columbia University Medical Center/ New York-Presbyterian Hospital, New York, NY
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27
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Schupf N, Lee JH, Pang D, Zigman WB, Tycko B, Krinsky-McHale S, Silverman W. Epidemiology of estrogen and dementia in women with Down syndrome. Free Radic Biol Med 2018; 114:62-68. [PMID: 28843780 PMCID: PMC5748249 DOI: 10.1016/j.freeradbiomed.2017.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 10/19/2022]
Abstract
Several lines of investigation have shown a protective role for estrogen in Alzheimer's disease through a number of biological actions. This review examines studies of the role of estrogen-related factors in age at onset and risk for Alzheimer's disease in women with Down syndrome, a population at high risk for early onset of dementia. The studies are consistent in showing that early age at menopause and that low levels of endogenous bioavailable estradiol in postmenopausal women with Down syndrome are associated with earlier age at onset and overall risk for dementia. Polymorphisms in genes associated with estrogen receptor activity and in genes for estrogen biosynthesis affecting endogenous estrogen are related to age at onset and cumulative incidence of dementia, and may serve as biomarkers of risk. To date, no clinical trials of estrogen or hormone replacement therapy (ERT/HRT) have been published for women with Down syndrome. While findings from clinical trials of ERT or HRT for dementia have generally been negative among women in the neurotypical population, the short interval between menopause and onset of cognitive decline, together with a more positive balance between potential benefits and risks, suggests an opportunity to evaluate the efficacy of ERT/HRT for delaying or preventing dementia in this high risk population, although questions concerning the optimal formulation and timing of the hormone therapy are not yet resolved.
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Affiliation(s)
- Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, United States; G.H. Sergievsky Center, Columbia University, New York, NY, United States; Departments of Neurology and Psychiatry, Columbia University Medical Center, New York, NY, United States; Department of Epidemiology, Mailman School of Public Health Columbia University, New York, NY, United States.
| | - Joseph H Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, United States; G.H. Sergievsky Center, Columbia University, New York, NY, United States; Department of Epidemiology, Mailman School of Public Health Columbia University, New York, NY, United States
| | - Deborah Pang
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York, NY, United States
| | - Warren B Zigman
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York, NY, United States
| | - Benjamin Tycko
- Department of Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Sharon Krinsky-McHale
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York, NY, United States
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, United States
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28
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Jiang Y, Loh YHE, Rajarajan P, Hirayama T, Liao W, Kassim BS, Javidfar B, Hartley BJ, Kleofas L, Park RB, Labonte B, Ho SM, Chandrasekaran S, Do C, Ramirez BR, Peter CJ, C W JT, Safaie BM, Morishita H, Roussos P, Nestler EJ, Schaefer A, Tycko B, Brennand KJ, Yagi T, Shen L, Akbarian S. The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain. Nat Genet 2017; 49:1239-1250. [PMID: 28671686 PMCID: PMC5560095 DOI: 10.1038/ng.3906] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [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: 02/03/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022]
Abstract
We report locus-specific disintegration of megabase-scale chromosomal conformations in brain after neuronal ablation of Kmt1e/Setdb1 histone H3-lysine 9 methyltransferase, including a large topologically associated 1.2Mb domain conserved in human and mouse and encompassing >70 genes at the clustered Protocadherin (cPcdh) locus. TADcPcdh in mutant neurons showed abnormal accumulations of CTCF transcriptional regulator and 3D genome organizer at cryptic binding sites, converted into permissive state with DNA cytosine hypomethylation and histone hyperacetylation. Broadly upregulated expression across cPcdh included defective S-type Protocadherin single-cell stochastic constraint. Setdb1-dependent loop formations, bypassing 0.2–1Mb of linear genome, radiated from TADPcdh fringes towards cPcdh cis-regulatory sequences, counterbalanced shorter-range facilitative promoter-enhancer contacts and carried loop-bound polymorphisms associated with genetic risk for schizophrenia. We show that KRAB-zinc finger Setdb1 repressor complex, shielding neuronal 3D genomes from excess CTCF binding, is critically required for structural maintenance of TADcPcdh.
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Affiliation(s)
- Yan Jiang
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yong-Hwee Eddie Loh
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Prashanth Rajarajan
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Teruyoshi Hirayama
- Kokoro-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Will Liao
- New York Genome Center, New York, New York, USA
| | - Bibi S Kassim
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Behnam Javidfar
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brigham J Hartley
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Kleofas
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Royce B Park
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benoit Labonte
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Seok-Man Ho
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sandhya Chandrasekaran
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Catherine Do
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Brianna R Ramirez
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Cyril J Peter
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Julia T C W
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brian M Safaie
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hirofumi Morishita
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Panos Roussos
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Mental Illness Research, Education and Clinical Center, James J. Peters Virginia Medical Center, New York, New York, USA
| | - Eric J Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anne Schaefer
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Kristen J Brennand
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Takeshi Yagi
- Kokoro-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Li Shen
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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29
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Ambrosini G, Tycko B, Do C, Schwartz GK. Abstract 4154: Resistance to BET inhibitors involves the β-catenin pathway in uveal melanoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4154] [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
Uveal melanoma (UM) is an aggressive intraocular malignancy with high tendency to metastasize to the liver. Currently available drugs have shown limited clinical activity in patients with UM and there is an urgent need for new effective therapies. Recent findings from our laboratory demonstrated that UM cells are sensitive to BET inhibitors (BETi) through the induction of cell cycle arrest and apoptosis. However, despite the initial inhibitory effects, UM cells acquire resistance to this class of drugs following chronic drug exposure. In order to understand the mechanistic basis for BETi resistance in UM, we assessed genome-wide CpG methylation patterns in UM cell lines that had been rendered resistant to the clinical BET inhibitor PLX51107 (Plexxikon, Berkeley, CA) following chronic drug exposure. The comparison between BET inhibitor-resistant versus sensitive cell lines revealed differential methylation of 1700 genes, including several involved in Wnt/β-catenin signaling, as well as other signaling pathways. Immunoblotting analysis confirmed that β-catenin protein was induced and activated in the resistant cells, while depletion of β-catenin by siRNA re-sensitized the resistant cells to the BET inhibitor. We then explored several combinations of PLX51107 with drugs that block β-catenin transcriptional activity through inhibition of its phosphorylation by PAK4 or through the inhibition of binding partners like Cdk8 and CBP. All these combinations increased the activity of the BET inhibitor in both sensitive and resistant cells, and these effects were synergistic, with combination indexes (CI) <1. These observations support the evidence that acquired resistant to BET inhibitors is mediated, at least in part, by activation of the Wnt/β-catenin pathway, and inhibitors of this pathway may provide a means to overcome acquired BET inhibitor resistance in UM patients treated with this class of drugs.
Citation Format: Grazia Ambrosini, Benjamin Tycko, Chaterine Do, Gary K. Schwartz. Resistance to BET inhibitors involves the β-catenin pathway in uveal melanoma [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 4154. doi:10.1158/1538-7445.AM2017-4154
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Abstract
Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS). Sequence variants in CCCTC-binding factor (CTCF) and transcription factor binding sites have been mechanistically linked to mQTLs and hap-ASM. Identifying these sites can point to disease-associated transcriptional pathways, with implications for targeted treatment and prevention.
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Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Alyssa Shearer
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Joel Gelernter
- Departments of Psychiatry, Genetics, and Neurobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Taub Institute for Research on Alzheimer's disease and the Aging Brain, New York, NY, 10032, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
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Lee JH, Lee AJ, Dang LH, Pang D, Kisselev S, Krinsky-McHale SJ, Zigman WB, Luchsinger JA, Silverman W, Tycko B, Clark LN, Schupf N. Candidate gene analysis for Alzheimer's disease in adults with Down syndrome. Neurobiol Aging 2017; 56:150-158. [PMID: 28554490 DOI: 10.1016/j.neurobiolaging.2017.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 07/14/2015] [Revised: 03/17/2017] [Accepted: 04/21/2017] [Indexed: 11/16/2022]
Abstract
Individuals with Down syndrome (DS) overexpress many genes on chromosome 21 due to trisomy and have high risk of dementia due to the Alzheimer's disease (AD) neuropathology. However, there is a wide range of phenotypic differences (e.g., age at onset of AD, amyloid β levels) among adults with DS, suggesting the importance of factors that modify risk within this particularly vulnerable population, including genotypic variability. Previous genetic studies in the general population have identified multiple genes that are associated with AD. This study examined the contribution of polymorphisms in these genes to the risk of AD in adults with DS ranging from 30 to 78 years of age at study entry (N = 320). We used multiple logistic regressions to estimate the likelihood of AD using single-nucleotide polymorphisms (SNPs) in candidate genes, adjusting for age, sex, race/ethnicity, level of intellectual disability and APOE genotype. This study identified multiple SNPs in APP and CST3 that were associated with AD at a gene-wise level empirical p-value of 0.05, with odds ratios in the range of 1.5-2. SNPs in MARK4 were marginally associated with AD. CST3 and MARK4 may contribute to our understanding of potential mechanisms where CST3 may contribute to the amyloid pathway by inhibiting plaque formation, and MARK4 may contribute to the regulation of the transition between stable and dynamic microtubules.
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Affiliation(s)
- Joseph H Lee
- Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Taub Institute, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA.
| | - Annie J Lee
- Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lam-Ha Dang
- Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA
| | - Deborah Pang
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Sergey Kisselev
- Department of Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Sharon J Krinsky-McHale
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Warren B Zigman
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - José A Luchsinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Tycko
- Department of Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lorraine N Clark
- Taub Institute, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Nicole Schupf
- Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Taub Institute, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA
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32
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Xiao MF, Xu D, Craig MT, Pelkey KA, Chien CC, Shi Y, Zhang J, Resnick S, Pletnikova O, Salmon D, Brewer J, Edland S, Wegiel J, Tycko B, Savonenko A, Reeves RH, Troncoso JC, McBain CJ, Galasko D, Worley PF. NPTX2 and cognitive dysfunction in Alzheimer's Disease. eLife 2017; 6. [PMID: 28440221 PMCID: PMC5404919 DOI: 10.7554/elife.23798] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [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: 12/01/2016] [Accepted: 03/15/2017] [Indexed: 12/14/2022] Open
Abstract
Memory loss in Alzheimer’s disease (AD) is attributed to pervasive weakening and loss of synapses. Here, we present findings supporting a special role for excitatory synapses connecting pyramidal neurons of the hippocampus and cortex with fast-spiking parvalbumin (PV) interneurons that control network excitability and rhythmicity. Excitatory synapses on PV interneurons are dependent on the AMPA receptor subunit GluA4, which is regulated by presynaptic expression of the synaptogenic immediate early gene NPTX2 by pyramidal neurons. In a mouse model of AD amyloidosis, Nptx2-/- results in reduced GluA4 expression, disrupted rhythmicity, and increased pyramidal neuron excitability. Postmortem human AD cortex shows profound reductions of NPTX2 and coordinate reductions of GluA4. NPTX2 in human CSF is reduced in subjects with AD and shows robust correlations with cognitive performance and hippocampal volume. These findings implicate failure of adaptive control of pyramidal neuron-PV circuits as a pathophysiological mechanism contributing to cognitive failure in AD. DOI:http://dx.doi.org/10.7554/eLife.23798.001
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Affiliation(s)
- Mei-Fang Xiao
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States.,Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Desheng Xu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Michael T Craig
- Program in Developmental Neurobiology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Kenneth A Pelkey
- Program in Developmental Neurobiology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Chun-Che Chien
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Yang Shi
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Juhong Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Susan Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, United States
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - David Salmon
- Department of Neurosciences, University of California San Diego Medical Center, San Diego, United States.,Shiley-Marcos Alzheimer's Disease Research Center, University of California San Diego Medical Center, San Diego, United States
| | - James Brewer
- Department of Neurosciences, University of California San Diego Medical Center, San Diego, United States.,Shiley-Marcos Alzheimer's Disease Research Center, University of California San Diego Medical Center, San Diego, United States
| | - Steven Edland
- Shiley-Marcos Alzheimer's Disease Research Center, University of California San Diego Medical Center, San Diego, United States.,Division of Biostatistics and Bioinformatics, University of California San Diego, San Diego, United States
| | - Jerzy Wegiel
- Institute for Basic Research, New York City, United States
| | - Benjamin Tycko
- Taub Institute for Research on Alzheimer's disease and the Aging Brain, Columbia University, New York City, United States
| | - Alena Savonenko
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Roger H Reeves
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States.,Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Chris J McBain
- Program in Developmental Neurobiology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego Medical Center, San Diego, United States.,Shiley-Marcos Alzheimer's Disease Research Center, University of California San Diego Medical Center, San Diego, United States
| | - Paul F Worley
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, United States
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Yotova I, Hsu E, Do C, Gaba A, Sczabolcs M, Dekan S, Kenner L, Wenzl R, Tycko B. Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis. PLoS One 2017; 12:e0170859. [PMID: 28125717 PMCID: PMC5268815 DOI: 10.1371/journal.pone.0170859] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 10/14/2016] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Since its pathogenesis may involve epigenetic changes, we used Illumina 450K Methylation Beadchips to profile CpG methylation in endometriosis stromal cells compared to stromal cells from normal endometrium. We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains. Genes found to have DM included examples encoding transporters (SLC22A23), signaling components (BDNF, DAPK1, ROR1, and WNT5A) and transcription factors (GATA family, HAND2, HOXA cluster, NR5A1, OSR2, TBX3). Intriguingly, among the TF genes with DM we also found JAZF1, a proto-oncogene affected by chromosomal translocations in endometrial stromal tumors. Using RNA-Seq we identified a subset of the DM genes showing differential expression (DE), with the likelihood of DE increasing with the extent of the DM and its location in enhancer elements. Supporting functional relevance, treatment of stromal cells with the hypomethylating drug 5aza-dC led to activation of DAPK1 and SLC22A23 and repression of HAND2, JAZF1, OSR2, and ROR1 mRNA expression. We found that global 5hmC is decreased in endometriotic versus normal epithelial but not stroma cells, and for JAZF1 and BDNF examined by oxidative bis-seq, found that when 5hmC is detected, patterns of 5hmC paralleled those of 5mC. Together with prior studies, these results define a consistent epigenetic signature in endometriosis stromal cells and nominate specific transcriptional and signaling pathways as therapeutic targets.
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Affiliation(s)
- Iveta Yotova
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
- * E-mail:
| | - Emily Hsu
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Catherine Do
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Aulona Gaba
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Matthias Sczabolcs
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Sabine Dekan
- Department of Experimental Pathology, Clinical Institute of Pathology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Lukas Kenner
- Department of Experimental Pathology, Clinical Institute of Pathology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
- Pathology Laboratory Animal Pathology University of Veterinary Medicine Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Rene Wenzl
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
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Abstract
An important line of postgenomic research seeks to understand how genetic factors can influence epigenetic patterning. Here we review epigenetic effects of chromosomal aneuploidies, focusing on findings in Down syndrome (DS, trisomy 21). Recent work in human DS and mouse models has shown that the extra chromosome 21 acts in trans to produce epigenetic changes, including differential CpG methylation (DS-DM), in specific sets of downstream target genes, mostly on other chromosomes. Mechanistic hypotheses emerging from these data include roles of chromosome 21-linked methylation pathway genes (DNMT3L and others) and transcription factor genes (RUNX1, OLIG2, GABPA, ERG and ETS2) in shaping the patterns of DS-DM. The findings may have broader implications for trans-acting epigenetic effects of chromosomal and subchromosomal aneuploidies in other human developmental and neuropsychiatric disorders, and in cancers.
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Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Taub Institute for Research on Alzheimer's disease & the Aging Brain, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
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Xing Z, Li Y, Pao A, Bennett AS, Tycko B, Mobley WC, Yu YE. Mouse-based genetic modeling and analysis of Down syndrome. Br Med Bull 2016; 120:111-122. [PMID: 27789459 PMCID: PMC5146682 DOI: 10.1093/bmb/ldw040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/07/2016] [Accepted: 10/03/2016] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Down syndrome (DS), caused by human trisomy 21 (Ts21), can be considered as a prototypical model for understanding the effects of chromosomal aneuploidies in other diseases. Human chromosome 21 (Hsa21) is syntenically conserved with three regions in the mouse genome. SOURCES OF DATA A review of recent advances in genetic modeling and analysis of DS. Using Cre/loxP-mediated chromosome engineering, a substantial number of new mouse models of DS have recently been generated, which facilitates better understanding of disease mechanisms in DS. AREAS OF AGREEMENT Based on evolutionary conservation, Ts21 can be modeled by engineered triplication of Hsa21 syntenic regions in mice. The validity of the models is supported by the exhibition of DS-related phenotypes. AREAS OF CONTROVERSY Although substantial progress has been made, it remains a challenge to unravel the relative importance of specific candidate genes and molecular mechanisms underlying the various clinical phenotypes. GROWING POINTS Further understanding of mechanisms based on data from mouse models, in parallel with human studies, may lead to novel therapies for clinical manifestations of Ts21 and insights to the roles of aneuploidies in other developmental disorders and cancers.
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Affiliation(s)
- Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Yichen Li
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Abigail S Bennett
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - William C Mobley
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA .,Cellular and Molecular Biology Program, Roswell Park Division of Graduate School, Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY 14263, USA
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Gonda T, Fang J, Do C, Zhukovskaya A, Salas M, Tycko B. Abstract 3213: Hypomethylation therapy leads to immune polarization and improved efficacy of immunotherapy in transgenic model of pancreatic cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3213] [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
Despite significant activity of immunotherapies in several malignancies, their efficacy in pancreatic cancer has been limited. One possible explanation may be the absence of a tumor microenvironment and immune cells that are necessary. We have demonstrated that 5-aza-2-deoxycitidine (DAC) had a profound effect on pancreatic cancer associated stroma and up-regulated many immune pathways. Therefore we proposed that hypomethylating therapy may alter the microenvironment to allow immue checkpoint inhibitors greater therapeutic efficacy.
METHODS
Transgenic mice that spontaneously develop pancreatic cancer (Kras, Trp53, Pdx-1 Cre [KPC]) underwent weekly transabdominal ultrasound to detect mice initially with larger (6-8 mm) and subsequently with smaller (3-5 mm) tumors. PBS or DAC (5 mg/kg) and anti -PD1H or isotype control antibody were administered every 72 hours intraperitoneally for 3 doses. Tumor size was monitored biweekly and 3D tumor volume reconstruction was used to estimate size. The immune cell infiltrate was characterized by quantitative immunohistochemistry or by FACS.
RESULTS
Mice treated with DAC with 6-8 mm tumors demonstrated a significantly increased survival and tumor necrosis as well as polarization of the infiltrating macrophages towards an M1 (CD86, CD163) phenotype and a trend towards an increase in infiltrating CD8 cells compared with controls. The shift in the T cell population and the macrophage phenotypes was not seen in the spleen or peripheral blood of either wild type or tumor bearing animals treated with DAC compared with controls. We subsequently treated mice with 3 doses of DAC followed by 3 doses of anti -PD1H and compared them to anti-PD1H alone in KPC mice with smaller (3-5 mm) tumors. In DAC + anti-PD1H we noted a decrease in the growth rate of tumors, an increased survival and a significant increase in necrosis and CD8 infiltrates, as well as a significant decrease in Ki67 and increase in Tunel staining compared with anti-PD1H alone.
CONCLUSIONS
Our results suggest that DAC pre-treatment prior to checkpoint inhibitors may favorably polarize the tumor infiltrating immune cell population, lead to increased recruitment of CD8 positive T cells, result in marked tumor necrosis and slow tumor growth. These effects ultimately contribute to increased therapeutic efficacy of checkpoint inhibitors in pancreatic cancer. We plan to optimize the efficacy of epigenetic therapy and checkpoint inhibitors by using other monoclonal antibodies (anti-PD1, PD1L)and different dosing regimens.
Citation Format: Tamas Gonda, Jarwei Fang, Catheine Do, Anna Zhukovskaya, Martha Salas, Benjamin Tycko. Hypomethylation therapy leads to immune polarization and improved efficacy of immunotherapy in transgenic model of pancreatic 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 3213.
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Monk C, Feng T, Lee S, Krupska I, Champagne FA, Tycko B. Distress During Pregnancy: Epigenetic Regulation of Placenta Glucocorticoid-Related Genes and Fetal Neurobehavior. Am J Psychiatry 2016; 173:705-13. [PMID: 27013342 PMCID: PMC5026410 DOI: 10.1176/appi.ajp.2015.15091171] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Increased risk of psychopathology is observed in children exposed to maternal prenatal distress, and elevated maternal cortisol and epigenetic regulation of placental glucocorticoid-pathway genes are potential mechanisms. The authors examined maternal distress and salivary cortisol in relation to fetal movement and heart rate ("coupling") and DNA methylation of three glucocorticoid pathway genes-HSD11B2, NR3C1, and FKBP5-in term placentas. METHOD Mood questionnaires and salivary cortisol were collected from 61 women between 24-27 gestational weeks, and fetal assessment was conducted at 34-37 weeks. Placental CpG methylation in the three genes was analyzed using 450K Beadchips and bisulfite sequencing; correlations between maternal and fetal variables and DNA methylation were tested; and maternal distress effects on fetal behavior via DNA methylation were investigated. RESULTS Perceived stress (Perceived Stress Scale), but not cortisol, was associated with altered CpG methylation in placentas. In the highest tertile of the Perceived Stress Scale, the Beadchip data revealed modestly elevated methylation of HSD11B2, associated with lower fetal coupling (β=-0.51), and modestly elevated methylation of FKBP5, also with lower fetal coupling (β=-0.47). These increases in methylation were validated by bisulfite sequencing, where they occurred in a minority of clones. CONCLUSIONS This is the first study to link the effects of pregnant women's distress on the fetus and epigenetic changes in placental genes. Since increased DNA methylation in HSD11B2 and FKBP5 are seen in a minority of bisulfite sequencing clones, these epigenetic changes, and functional consequences, may affect subpopulations of placental cells.
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38
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Mendioroz M, Do C, Jiang X, Liu C, Darbary HK, Lang CF, Lin J, Thomas A, Abu-Amero S, Stanier P, Temkin A, Yale A, Liu MM, Li Y, Salas M, Kerkel K, Capone G, Silverman W, Yu YE, Moore G, Wegiel J, Tycko B. Erratum to: Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. Genome Biol 2016; 17:123. [PMID: 27282916 PMCID: PMC4901436 DOI: 10.1186/s13059-016-0949-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/13/2016] [Indexed: 11/17/2022] Open
Affiliation(s)
- Maite Mendioroz
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Catherine Do
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Xiaoling Jiang
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | - Chunhong Liu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | - Huferesh K Darbary
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Charles F Lang
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - John Lin
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Anna Thomas
- Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Sayeda Abu-Amero
- Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Philip Stanier
- Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Alexis Temkin
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Alexander Yale
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Meng-Min Liu
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Yang Li
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Martha Salas
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - Kristi Kerkel
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA
| | - George Capone
- Department of Psychology, Kennedy Kreiger Institute, John Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wayne Silverman
- Department of Psychology, Kennedy Kreiger Institute, John Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program and Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | - Gudrun Moore
- Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Jerzy Wegiel
- Department of Developmental Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, 10314, USA
| | - Benjamin Tycko
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, 10032, USA. .,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
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Do C, Lang C, Lin J, Darbary H, Krupska I, Gaba A, Petukhova L, Vonsattel JP, Gallagher M, Goland R, Clynes R, Dwork A, Kral J, Monk C, Christiano A, Tycko B. Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation. Am J Hum Genet 2016; 98:934-955. [PMID: 27153397 DOI: 10.1016/j.ajhg.2016.03.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/25/2016] [Indexed: 10/21/2022] Open
Abstract
Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease susceptibility, but maps of this phenomenon using stringent criteria in disease-relevant tissues remain sparse. Here we apply array-based and Methyl-Seq approaches to multiple human tissues and cell types, including brain, purified neurons and glia, T lymphocytes, and placenta, and identify 795 hap-ASM differentially methylated regions (DMRs) and 3,082 strong methylation quantitative trait loci (mQTLs), most not previously reported. More than half of these DMRs have cell type-restricted ASM, and among them are 188 hap-ASM DMRs and 933 mQTLs located near GWAS signals for immune and neurological disorders. Targeted bis-seq confirmed hap-ASM in 12/13 loci tested, including CCDC155, CD69, FRMD1, IRF1, KBTBD11, and S100A(∗)-ILF2, associated with immune phenotypes, MYT1L, PTPRN2, CMTM8 and CELF2, associated with neurological disorders, NGFR and HLA-DRB6, associated with both immunological and brain disorders, and ZFP57, a trans-acting regulator of genomic imprinting. Polymorphic CTCF and transcription factor (TF) binding sites were over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to macaques, indicated that CTCF and TF binding likelihood predicts the strength and direction of the allelic methylation asymmetry. These results show that hap-ASM is highly tissue specific; an important trans-acting regulator of genomic imprinting is regulated by this phenomenon; and variation in CTCF and TF binding sites is an underlying mechanism, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supra- and sub-threshold GWAS peaks in immunological and neurological disorders.
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Wang E, Do C, Tycko B, Christiano A. 409 Epigenetic regulation of alopecia areata. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.02.443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Maldonado Gonzalez LF, VandenBussche C, Roden R, Wu T, Tycko B, Trimble CL. Abstract 1320: PD-L1: the hand brake of immune responses in cervical intraepithelial neoplasia and cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1320] [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: Prospective cohort studies have reported spontaneous regression rates of high-grade cervical intraepithelial Neoplasia (CIN2/3) close to 35%, over a period of 4-6 months. These regressions are presumably immunologically mediated. It is now well recognized that PD-L1 is an immune checkpoint used by neoplastic cells to evade the immune system, particularly T cells that are specific for tumor antigens. PD-L1 and several other immune checkpoints consist of inhibitory pathways that tightly regulate the immune system to control the duration and amplitude of immune responses in peripheral tissues in order to minimize collateral tissue damage.
Design: Immunohistochemistry with anti-TBX21 and anti-PD-L1 antibodies was performed in formalin-fixed paraffin-embedded tissue sections from a tissue microarray consisting of invasive cervical carcinomas (ICCs) (n = 22), CIN2/3 (n = 4) and benign cervical tissues (n = 4). Expression of TBX21 and PD-L1 was reviewed and scored by a trained pathologist blinded to the clinical outcome of each case. Statistical correlations between these markers’ score and available demographic and clinicopathologic data from each case were performed, as well as disease-free survival curves. Moreover, PD-L1 staining was performed in three patients with CIN2/3 that received peripheral (IM) therapeutic HPV vaccination. PD-L1 expression differences in pre and post-vaccination tissues were compared.
Results: Increased expression of TBX21+ T-cells and PD-L1 was observed from benign to CIN2/3 to ICCs. Association analysis (fisher exact test) showed a significant correlation between increased intraepithelial and stromal infiltration of TBX21+ T-cells (score 2,3) and higher PD-L1 membrane expression (p = 0.04 and p = 0.005, respectively). No significant associations were found between PD-L1 expression and demographic and clinicopathologic information, likely due to small number of samples. In our vaccine cohort, we observed a stronger membrane PD-L1 expression in the epithelium and stroma of the post-vaccination tissue compared to the pre-vaccination biopsy.
Conclusion: Increased membrane expression of PD-L1 is tightly correlated with an increased epithelial and stromal infiltration of TBX21+ T cells in CIN2/3 and ICCs. This correlation was also observed in our vaccination cohort when compared to our previous published findings of immune activation after HPV therapeutic vaccination. This association could represent an immune response control mechanism induced presumably by interferons released by TBX21+ T cells. We are currently evaluating the expression of PD-L1 and B7-H4, a recently discovered inhibitory ligand, in a larger cohort of benign, CIN2/3 and ICCs. Finally, we will further explore, quantitate and compare the expression changes of these immune checkpoints in the remaining CIN2/3 cases of our vaccination cohort (n = 12) in pre and post-vaccination tissues.
Citation Format: Leonel F. Maldonado Gonzalez, Christopher VandenBussche, Richard Roden, T.C. Wu, Benjamin Tycko, Cornelia L. Trimble. PD-L1: the hand brake of immune responses in cervical intraepithelial neoplasia and cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1320. doi:10.1158/1538-7445.AM2015-1320
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Affiliation(s)
| | | | - Richard Roden
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - T.C. Wu
- 1Johns Hopkins University School of Medicine, Baltimore, MD
| | - Benjamin Tycko
- 2Columbia University Institute for Cancer Genetics, New York, NY
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Schupf N, Dang LH, Lee A, Pang D, Zigman WB, Luchsinger JA, Krinsky-McHale S, Silverman W, Tycko B, Kisselev S, Clark L, Lee JH. P1‐268: Variants in candidate genes for Alzheimer's disease are associated with declining plasma abeta peptides in adults with down syndrome. Alzheimers Dement 2015. [DOI: 10.1016/j.jalz.2015.06.469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | - Lam-Ha Dang
- Columbia Univeristy Medical CenterNew YorkNYUSA
| | - Annie Lee
- Columbia University Medical CenterNew YorkNYUSA
| | - Deborah Pang
- NYS Institute for Basic ReseachStaten IslandNYUSA
| | | | | | | | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins UniversityBaltimoreMDUSA
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Schupf N, Lee A, Park N, Dang LH, Pang D, Yale A, Oh DKT, Krinsky-McHale SJ, Jenkins EC, Luchsinger JA, Zigman WB, Silverman W, Tycko B, Kisselev S, Clark L, Lee JH. Candidate genes for Alzheimer's disease are associated with individual differences in plasma levels of beta amyloid peptides in adults with Down syndrome. Neurobiol Aging 2015; 36:2907.e1-10. [PMID: 26166206 DOI: 10.1016/j.neurobiolaging.2015.06.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 10/01/2014] [Revised: 06/08/2015] [Accepted: 06/14/2015] [Indexed: 01/08/2023]
Abstract
We examined the contribution of candidates genes for Alzheimer's disease (AD) to individual differences in levels of beta amyloid peptides in adults with Down syndrom, a population at high risk for AD. Participants were 254 non-demented adults with Down syndrome, 30-78 years of age. Genomic deoxyribonucleic acid was genotyped using an Illumina GoldenGate custom array. We used linear regression to examine differences in levels of Aβ peptides associated with the number of risk alleles, adjusting for age, sex, level of intellectual disability, race and/or ethnicity, and the presence of the APOE ε4 allele. For Aβ42 levels, the strongest gene-wise association was found for a single nucleotide polymorphism (SNP) on CAHLM1; for Aβ40 levels, the strongest gene-wise associations were found for SNPs in IDE and SOD1, while the strongest gene-wise associations with levels of the Aβ42/Aβ40 ratio were found for SNPs in SORCS1. Broadly classified, variants in these genes may influence amyloid precursor protein processing (CALHM1, IDE), vesicular trafficking (SORCS1), and response to oxidative stress (SOD1).
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Affiliation(s)
- Nicole Schupf
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; G.H. Sergievsky Center, New York, NY, USA; Department of Epidemiology, Columbia University Medical Center, New York, NY, USA; Department of Psychiatry, Columbia University Medical Center, New York, NY, USA.
| | - Annie Lee
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Naeun Park
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Lam-Ha Dang
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Deborah Pang
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Alexander Yale
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - David Kyung-Taek Oh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Sharon J Krinsky-McHale
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Edmund C Jenkins
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - José A Luchsinger
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Warren B Zigman
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Tycko
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Sergey Kisselev
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Lorraine Clark
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Joseph H Lee
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; G.H. Sergievsky Center, New York, NY, USA; Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
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Shen J, LeFave C, Sirosh I, Siegel AB, Tycko B, Santella RM. Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas. BMC Med Genomics 2015; 8:28. [PMID: 26059414 PMCID: PMC4460673 DOI: 10.1186/s12920-015-0105-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 11/11/2014] [Accepted: 06/01/2015] [Indexed: 02/05/2023] Open
Abstract
Background Epigenome-wide studies in hepatocellular carcinoma (HCC) have identified numerous genes with aberrant DNA methylation. However, methods for triaging functional candidate genes as useful biomarkers for epidemiological study have not yet been developed. Methods We conducted targeted next-generation bisulfite sequencing (bis-seq) to investigate associations of DNA methylation and mRNA expression in HCC. Integrative analyses of epigenetic profiles with DNA copy number analysis were used to pinpoint functional genes regulated mainly by altered DNA methylation. Results Significant differences between HCC tumor and adjacent non-tumor tissue were observed for 28 bis-seq amplicons, with methylation differences varying from 12% to 43%. Available mRNA expression data in Oncomine were evaluated. Two candidate genes (GRASP and TSPYL5) were significantly under-expressed in HCC tumors in comparison with precursor and normal liver tissues. The expression levels in tumor tissues were, respectively, 1.828 and − 0.148, significantly lower than those in both precursor and normal liver tissue. Validations in an additional 42 paired tissues showed consistent under-expression in tumor tissue for GRASP (−7.49) and TSPYL5 (−9.71). A highly consistent DNA hypermethylation and mRNA repression pattern was obtained for both GRASP (69%) and TSPYL5 (73%), suggesting that their biological function is regulated by DNA methylation. Another two genes (RGS17 and NR2E1) at Chr6q showed significantly decreased DNA methylation in tumors with loss of DNA copy number compared to those without, suggesting alternative roles of DNA copy number losses and hypermethylation in the regulation of RGS17 and NR2E1. Conclusions These results suggest that integrative analyses of epigenomic and genomic data provide an efficient way to filter functional biomarkers for future epidemiological studies in human cancers. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0105-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Shen
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Clare LeFave
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Iryna Sirosh
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Abby B Siegel
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA. .,Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA.
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, 10032, USA.
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Hartley D, Blumenthal T, Carrillo M, DiPaolo G, Esralew L, Gardiner K, Granholm AC, Iqbal K, Krams M, Lemere C, Lott I, Mobley W, Ness S, Nixon R, Potter H, Reeves R, Sabbagh M, Silverman W, Tycko B, Whitten M, Wisniewski T. Down syndrome and Alzheimer's disease: Common pathways, common goals. Alzheimers Dement 2014; 11:700-9. [PMID: 25510383 DOI: 10.1016/j.jalz.2014.10.007] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [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: 03/09/2014] [Revised: 08/26/2014] [Accepted: 10/02/2014] [Indexed: 12/17/2022]
Abstract
In the United States, estimates indicate there are between 250,000 and 400,000 individuals with Down syndrome (DS), and nearly all will develop Alzheimer's disease (AD) pathology starting in their 30s. With the current lifespan being 55 to 60 years, approximately 70% will develop dementia, and if their life expectancy continues to increase, the number of individuals developing AD will concomitantly increase. Pathogenic and mechanistic links between DS and Alzheimer's prompted the Alzheimer's Association to partner with the Linda Crnic Institute for Down Syndrome and the Global Down Syndrome Foundation at a workshop of AD and DS experts to discuss similarities and differences, challenges, and future directions for this field. The workshop articulated a set of research priorities: (1) target identification and drug development, (2) clinical and pathological staging, (3) cognitive assessment and clinical trials, and (4) partnerships and collaborations with the ultimate goal to deliver effective disease-modifying treatments.
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Affiliation(s)
- Dean Hartley
- Medical and Scientific Relations, Alzheimer's Association, Chicago, IL, USA.
| | - Thomas Blumenthal
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Maria Carrillo
- Medical and Scientific Relations, Alzheimer's Association, Chicago, IL, USA
| | - Gilbert DiPaolo
- Department of Pathology and Cell Biology, Columbia University Medical Center and The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, New York, NY, USA
| | - Lucille Esralew
- Department of Behavioral Health, Trinitas Regional Medical Center, Elizabeth, NJ, USA
| | - Katheleen Gardiner
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, USA; Department of Pediatrics, University of Colorado, Denver, CO, USA
| | - Ann-Charlotte Granholm
- Department of Neuroscience and the Center on Aging, Medical University of South Carolina, Columbia, SC, USA
| | - Khalid Iqbal
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, New York, NY, USA
| | | | - Cynthia Lemere
- Department of Neurology and the Anne Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ira Lott
- Department of Pediatrics, University of California, Irvine, CA, USA
| | - William Mobley
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Seth Ness
- Janssen Research & Development, Raritan, NJ, USA
| | - Ralph Nixon
- Department of Psychiatry and Cell Biology, New York University, Langone Medical Center, New York, NY, USA
| | - Huntington Potter
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, USA; Department of Neurology, University of Colorado, Denver, CO, USA
| | - Roger Reeves
- Department of Physiology, McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marwan Sabbagh
- Banner Sun Health Research Institute, Banner Health, Sun City, AZ, USA
| | - Wayne Silverman
- Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Tycko
- Department of Pathology and Cell Biology, Columbia University Medical Center and The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, New York, NY, USA
| | | | - Thomas Wisniewski
- Department of Neurology, Pathology, and Psychiatry, New York University, Langone Medical Center, New York, NY, USA
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Maldonado L, Teague JE, Morrow MP, Jotova I, Wu TC, Wang C, Desmarais C, Boyer JD, Tycko B, Robins HS, Clark RA, Trimble CL. Intramuscular therapeutic vaccination targeting HPV16 induces T cell responses that localize in mucosal lesions. Sci Transl Med 2014; 6:221ra13. [PMID: 24477000 DOI: 10.1126/scitranslmed.3007323] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
About 25% of high-grade cervical intraepithelial neoplasias (CIN2/3) caused by human papillomavirus serotype 16 (HPV16) undergo complete spontaneous regression. However, to date, therapeutic vaccination strategies for HPV disease have yielded limited success when measured by their ability to induce robust peripheral blood T cell responses to vaccine antigen. We report marked immunologic changes in the target lesion microenvironment after intramuscular therapeutic vaccination targeting HPV16 E6/E7 antigens, in subjects with CIN2/3 who had modest detectable responses in circulating T lymphocytes. Histologic and molecular changes, including markedly (average threefold) increased intensity of CD8(+) T cell infiltrates in both the stromal and epithelial compartments, suggest an effector response to vaccination. Postvaccination cervical tissue immune infiltrates included organized tertiary lymphoid-like structures in the stroma subjacent to residual intraepithelial lesions and, unlike infiltrates in unvaccinated lesions, showed evidence of proliferation induced by recognition of cognate antigen. At a molecular level, these histologic changes in the stroma were characterized by increased expression of genes associated with immune activation (CXCR3) and effector function (Tbet and IFNβ), and were also associated with an immunologic signature in the overlying dysplastic epithelium. High-throughput T cell receptor sequencing of unmanipulated specimens identified clonal expansions in the tissue that were not readily detectable in peripheral blood. Together, these findings indicate that peripheral therapeutic vaccination to HPV antigens can induce a robust tissue-localized effector immune response, and that analyses of immune responses at sites of antigen are likely to be much more informative than analyses of cells that remain in the circulation.
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Affiliation(s)
- Leonel Maldonado
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Jessica E Teague
- Harvard Skin Disease Research Center and the Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Matthew P Morrow
- Inovio Pharmaceuticals Inc., 1787 Sentry Parkway West, Building 18, Suite 400, Blue Bell, PA 19422, USA
| | - Iveta Jotova
- Department of Pathology and Cell Biology and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10025, USA
| | - T C Wu
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Chenguang Wang
- Oncology Biostatistics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Cindy Desmarais
- Adaptive Biotechnologies, 1551 Eastlake Avenue, Seattle, WA 98102, USA
| | - Jean D Boyer
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin Tycko
- Department of Pathology and Cell Biology and Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10025, USA
| | - Harlan S Robins
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rachael A Clark
- Harvard Skin Disease Research Center and the Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Cornelia L Trimble
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
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Maldonado L, Diaz-Montes T, Sinno A, Tanner EJ, VandenBussche C, Roden R, Yotova I, Tycko B, Trimble CL. Abstract 3672: Role and presence of cancer associated fibroblasts and M2 macrophages in high grade cervical intraepithelial neoplasia and invasive cervical carcinomas. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3672] [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
The interactions between neoplastic cells and their tumor microenvironment (TME) have become increasingly evident. Cancer-associated fibroblasts (CAFs) and M2 macrophages (M2 Mθ) are important components of the TME that have been recognized to orchestrate tumor-promoting inflammation and thereby tumor growth and progression. Here, we aim to determine the presence and role of CAFs and M2 Mθ in high grade cervical intraepithelial neoplasia (CIN 2/3) and invasive cervical carcinomas (SCCx).
We optimized immunohistochemistry (IHC) markers for M2 Mθ (CD163, ARG1), CAFs (αSMA) and Th1 T cells (TBX21) in paraffin-embedded tissue sections from CIN2/3 (n=6) and SCCx cases (n=4). We found an increased infiltration of TBX21+ cells in the epithelium and stroma of CIN2/3 and SCCx cases compared to their normal adjacent stroma. This suggests that despite increased Th1 T cells, the progression from normal to CIN2/3 to SCCx might be facilitated by M2 Mθ and CAFs. Moreover, by performing double staining Immunofluorescence (IF) we found that M2 Mθ (CD163+) were the cells responsible for ARG1 production, an immunesuppressive mechanism utilized by these cells. We recently stained by IHC a cervical tissue microarray (TMA) of normal, CIN2/3 and SCCx cases (n=63) with CD163, αSMA and TBX21, and we are currently analyzing the correlation of these markers with clinicopathological data available for these cases (HPV status, tumor stage, therapy response, overall survival).
With the hypothesis in mind that CAFs induce the polarization of macrophages into a M2 Mθ phenotype, we isolated fibroblasts from normal (n=2), CIN2/3 (n=1) and SCCx (n=2) fresh tissue explants obtained from surgery. We performed Immunocytochemistry (ICC) with αSMA, and observed a progressive increase in αSMA+ fibroblasts from normal to CIN2/3 and from CIN2/3 to SCCx fibroblasts, suggesting that CAFs might play an important role in the transformation of normal cervix into CIN2/3 and SCCx. Furthermore, we are currently performing co-culture experiments with normal, CIN2/3 and SCCx isolated fibroblasts and peripheral blood monocytes obtained from healthy donors. We will perform triple staining IF with vimentin, αSMA and CD163 in the slides generated from the co-culture, to evaluate if monocytes acquired a M2 Mθ phenotype with the presence of any of these 3 subsets of fibroblasts. Moreover, we will perform a cytokine analysis in the supernatants of these co-cultures to evaluate for potential cytokines produced by CAFs, implicated in M2 Mθ polarization.
In this study we provide evidence regarding the role of CAFs in SCCx initiation and progression. Although the mechanisms that regulate fibroblast activation have not been elucidated, it is possible that CAFs might serve as novel therapeutic targets in cancer, either alone or in combination with existing anti-cancer therapies.
Citation Format: Leonel Maldonado, Teresa Diaz-Montes, Abdulrahman Sinno, Edward J. Tanner, Christopher VandenBussche, Richard Roden, Iveta Yotova, Benjamin Tycko, Cornelia L. Trimble. Role and presence of cancer associated fibroblasts and M2 macrophages in high grade cervical intraepithelial neoplasia and invasive cervical carcinomas. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3672. doi:10.1158/1538-7445.AM2014-3672
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Affiliation(s)
| | | | | | | | | | | | - Iveta Yotova
- 3Columbia University, Institute for Cancer Genetics, New York, NY
| | - Benjamin Tycko
- 3Columbia University, Institute for Cancer Genetics, New York, NY
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Hobbs CA, Chowdhury S, Cleves MA, Erickson S, MacLeod SL, Shaw GM, Shete S, Witte JS, Tycko B. Genetic epidemiology and nonsyndromic structural birth defects: from candidate genes to epigenetics. JAMA Pediatr 2014; 168:371-7. [PMID: 24515445 PMCID: PMC3981910 DOI: 10.1001/jamapediatrics.2013.4858] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Birth defects are a leading cause of infant morbidity and mortality worldwide. The vast majority of birth defects are nonsyndromic, and although their etiologies remain mostly unknown, evidence supports the hypothesis that they result from the complex interaction of genetic, epigenetic, environmental, and lifestyle factors. Since our last review published in 2002 describing the basic tools of genetic epidemiology used to study nonsyndromic structural birth defects, many new approaches have become available and have been used with varying success. Through rapid advances in genomic technologies, investigators are now able to investigate large portions of the genome at a fraction of previous costs. With next-generation sequencing, research has progressed from assessing a small percentage of single-nucleotide polymorphisms to assessing the entire human protein-coding repertoire (exome)-an approach that is starting to uncover rare but informative mutations associated with nonsyndromic birth defects. Herein, we report on the current state of the genetic epidemiology of birth defects and comment on future challenges and opportunities. We consider issues of study design, and we discuss common variant approaches, including candidate gene studies and genome-wide association studies. We also discuss the complexities embedded in exploring interactions between genes and the environment. We complete our review by describing new and promising next-generation sequencing technologies and examining how the study of epigenetic mechanisms could become the key to unraveling the complex etiologies of nonsyndromic structural birth defects.
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Affiliation(s)
- Charlotte A. Hobbs
- Department of Pediatrics, University of Arkansas for Medical Sciences, College of Medicine, Little Rock
| | - Shimul Chowdhury
- Department of Pediatrics, University of Arkansas for Medical Sciences, College of Medicine, Little Rock
| | - Mario A. Cleves
- Department of Pediatrics, University of Arkansas for Medical Sciences, College of Medicine, Little Rock
| | - Stephen Erickson
- Department of Pediatrics, University of Arkansas for Medical Sciences, College of Medicine, Little Rock
| | - Stewart L. MacLeod
- Department of Pediatrics, University of Arkansas for Medical Sciences, College of Medicine, Little Rock
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Sanjay Shete
- Department of Epidemiology, University of Texas M. D. Anderson Cancer Center, Houston
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - Benjamin Tycko
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University Medical Center, New York, New York
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Paroly SS, Wang F, Spraggon L, Merregaert J, Batourina E, Tycko B, Schmidt-Ott KM, Grimmond S, Little M, Mendelsohn C. Stromal protein Ecm1 regulates ureteric bud patterning and branching. PLoS One 2013; 8:e84155. [PMID: 24391906 PMCID: PMC3877229 DOI: 10.1371/journal.pone.0084155] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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: 08/30/2013] [Accepted: 11/12/2013] [Indexed: 01/28/2023] Open
Abstract
The interactions between the nephrogenic mesenchyme and the ureteric bud during kidney development are well documented. While recent studies have shed some light on the importance of the stroma during renal development, many of the signals generated in the stroma, the genetic pathways and interaction networks involving the stroma are yet to be identified. Our previous studies demonstrate that retinoids are crucial for branching of the ureteric bud and for patterning of the cortical stroma. In the present study we demonstrate that autocrine retinoic acid (RA) signaling in stromal cells is critical for their survival and patterning, and show that Extracellular matrix 1, Ecm1, a gene that in humans causes irritable bowel syndrome and lipoid proteinosis, is a novel RA-regulated target in the developing kidney, which is secreted from the cortical stromal cells surrounding the cap mesenchyme and ureteric bud. Our studies suggest that Ecm1 is required in the ureteric bud for regulating the distribution of Ret which is normally restricted to the tips, as inhibition of Ecm1 results in an expanded domain of Ret expression and reduced numbers of branches. We propose a model in which retinoid signaling in the stroma activates expression of Ecm1, which in turn down-regulates Ret expression in the ureteric bud cleft, where bifurcation normally occurs and normal branching progresses.
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Affiliation(s)
- Suneeta S. Paroly
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
- * E-mail:
| | - Fengwei Wang
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
| | - Lee Spraggon
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
| | - Joseph Merregaert
- Laboratory of Molecular Biotechnology, Department of Biochemistry, University of Antwerp, Wilrijk, Belgium
| | - Ekatherina Batourina
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
| | - Benjamin Tycko
- Institute for Cancer Genetics & Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York, United States of America
| | - Kai M. Schmidt-Ott
- Max-Delbrueck Center for Molecular Medicine Robert-Roessle-Str. Berlin, Germany
| | - Sean Grimmond
- Institute for Molecular Bioscience, The University of Queensland St Lucia QLD, Australia
| | - Melissa Little
- Institute for Molecular Bioscience, The University of Queensland St Lucia QLD, Australia
| | - Cathy Mendelsohn
- Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America
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Tycko B. Abstract ED02-02: Interaction between genetics, epigenetics, and environment in cancer prevention. Cancer Prev Res (Phila) 2013. [DOI: 10.1158/1940-6215.prev-13-ed02-02] [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 recent convergence of genomic and epigenomic findings has brought the study of DNA methylation to the forefront of cancer research. In this session I will review our knowledge to date and suggest future directions for translational research and clinical applications in two key areas – (i) dietary methyl donors and DNA methylation in cancer prevention, (ii) allele-specific DNA methylation mapping as a tool for improving the yield of true-positive signals from genome-wide association studies (GWAS) for cancer susceptibility. These topics will highlight the importance of cis- and trans-acting influences of the genetic background on epigenetic patterns and cancer susceptibility.
References:
1. Kerkel K, Spadola A, Yuan E, Kosek J, Jiang L, Hod E, Li K, Murty VV, Schupf N, Vilain E, Morris M, Haghighi F, Tycko B (2008) Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 40:904-908. PMID:18568024
2. Tycko B (2010). Allele-specific DNA methylation: beyond imprinting. Hum Mol Genet. 19:R210-220.
3. Gonda TA, Kim Y-I, Salas M, Gamble MV, Shibata W, Muthupalani S, Sohn K-J, Abram J, Fox JG, Wang TC, Tycko B (2012). Folic acid increases global DNA methylation and reduces inflammation to prevent Helicobacter-associated gastric cancer in mice. Gastroenterology. 142(4):824-833 PMID:22474448
4. Paliwal A, Temkin A, Kerkel K, Yale A, Yotova I , Drost N, Lax S, Nhan-Chang C-L, Powell C, Borczuk A, Aviv A, Wapner R, Chen X, Nagy P, Schork N, Do C, Torkamani A, Tycko B. (2013) Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation. PLoS Genet. 9(8):e1003622.
Citation Format: Benjamin Tycko. Interaction between genetics, epigenetics, and environment in cancer prevention. [abstract]. In: Proceedings of the Twelfth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2013 Oct 27-30; National Harbor, MD. Philadelphia (PA): AACR; Can Prev Res 2013;6(11 Suppl): Abstract nr ED02-02.
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