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Wang K, Kim N, Bagherian M, Li K, Chou E, Colacino JA, Dolinoy DC, Sartor MA. Gene Target Prediction of Environmental Chemicals Using Coupled Matrix-Matrix Completion. Environ Sci Technol 2024; 58:5889-5898. [PMID: 38501580 DOI: 10.1021/acs.est.4c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Human exposure to toxic chemicals presents a huge health burden. Key to understanding chemical toxicity is knowledge of the molecular target(s) of the chemicals. Because a comprehensive safety assessment for all chemicals is infeasible due to limited resources, a robust computational method for discovering targets of environmental exposures is a promising direction for public health research. In this study, we implemented a novel matrix completion algorithm named coupled matrix-matrix completion (CMMC) for predicting direct and indirect exposome-target interactions, which exploits the vast amount of accumulated data regarding chemical exposures and their molecular targets. Our approach achieved an AUC of 0.89 on a benchmark data set generated using data from the Comparative Toxicogenomics Database. Our case studies with bisphenol A and its analogues, PFAS, dioxins, PCBs, and VOCs show that CMMC can be used to accurately predict molecular targets of novel chemicals without any prior bioactivity knowledge. Our results demonstrate the feasibility and promise of computationally predicting environmental chemical-target interactions to efficiently prioritize chemicals in hazard identification and risk assessment.
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Affiliation(s)
- Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicole Kim
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Maryam Bagherian
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kai Li
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Elysia Chou
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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Petroff RL, Dolinoy DC, Wang K, Montrose L, Padmanabhan V, Peterson KE, Ruden DM, Sartor MA, Svoboda LK, Téllez-Rojo MM, Goodrich JM. Translational toxicoepigenetic Meta-Analyses identify homologous gene DNA methylation reprogramming following developmental phthalate and lead exposure in mouse and human offspring. Environ Int 2024; 186:108575. [PMID: 38507935 DOI: 10.1016/j.envint.2024.108575] [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] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
Although toxicology uses animal models to represent real-world human health scenarios, a critical translational gap between laboratory-based studies and epidemiology remains. In this study, we aimed to understand the toxicoepigenetic effects on DNA methylation after developmental exposure to two common toxicants, the phthalate di(2-ethylhexyl) phthalate (DEHP) and the metal lead (Pb), using a translational paradigm that selected candidate genes from a mouse study and assessed them in four human birth cohorts. Data from mouse offspring developmentally exposed to DEHP, Pb, or control were used to identify genes with sex-specific sites with differential DNA methylation at postnatal day 21. Associations of human infant DNA methylation in homologous mouse genes with prenatal DEHP or Pb were examined with a meta-analysis. Differential methylation was observed on 6 cytosines (adjusted-p < 0.05) and 90 regions (adjusted-p < 0.001). This translational approach offers a unique method that can detect conserved epigenetic differences that are developmentally susceptible to environmental toxicants.
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Affiliation(s)
- Rebekah L Petroff
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Kai Wang
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Luke Montrose
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA; Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Karen E Peterson
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Douglas M Ruden
- Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Maureen A Sartor
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Laurie K Svoboda
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Martha M Téllez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Mexico
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA.
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Núñez FJ, Banerjee K, Mujeeb AA, Mauser A, Tronrud CE, Zhu Z, Taher A, Kadiyala P, Carney SV, Garcia-Fabiani MB, Comba A, Alghamri MS, McClellan BL, Faisal SM, Nwosu ZC, Hong HS, Qin T, Sartor MA, Ljungman M, Cheng SY, Appelman HD, Lowenstein PR, Lahann J, Lyssiotis CA, Castro MG. Epigenetic Reprogramming of Autophagy Drives Mutant IDH1 Glioma Progression and Response to Radiation. bioRxiv 2024:2024.03.08.584091. [PMID: 38559270 PMCID: PMC10979892 DOI: 10.1101/2024.03.08.584091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mutant isocitrate dehydrogenase 1 (mIDH1; IDH1 R132H ) exhibits a gain of function mutation enabling 2-hydroxyglutarate (2HG) production. 2HG inhibits DNA and histone demethylases, inducing epigenetic reprogramming and corresponding changes to the transcriptome. We previously demonstrated 2HG-mediated epigenetic reprogramming enhances DNA-damage response and confers radioresistance in mIDH1 gliomas harboring p53 and ATRX loss of function mutations. In this study, RNA-seq and ChIP-seq data revealed human and mouse mIDH1 glioma neurospheres have downregulated gene ontologies related to mitochondrial metabolism and upregulated autophagy. Further analysis revealed that the decreased mitochondrial metabolism was paralleled by a decrease in glycolysis, rendering autophagy as a source of energy in mIDH1 glioma cells. Analysis of autophagy pathways showed that mIDH1 glioma cells exhibited increased expression of pULK1-S555 and enhanced LC3 I/II conversion, indicating augmented autophagy activity. This dependence is reflected by increased sensitivity of mIDH1 glioma cells to autophagy inhibition. Blocking autophagy selectively impairs the growth of cultured mIDH1 glioma cells but not wild-type IDH1 (wtIDH1) glioma cells. Targeting autophagy by systemic administration of synthetic protein nanoparticles packaged with siRNA targeting Atg7 (SPNP-siRNA-Atg7) sensitized mIDH1 glioma cells to radiation-induced cell death, resulting in tumor regression, long-term survival, and immunological memory, when used in combination with IR. Our results indicate autophagy as a critical pathway for survival and maintenance of mIDH1 glioma cells, a strategy that has significant potential for future clinical translation. One Sentence Summary The inhibition of autophagy sensitizes mIDH1 glioma cells to radiation, thus creating a promising therapeutic strategy for mIDH1 glioma patients. Graphical abstract Our genetically engineered mIDH1 mouse glioma model harbors IDH1 R132H in the context of ATRX and TP53 knockdown. The production of 2-HG elicited an epigenetic reprogramming associated with a disruption in mitochondrial activity and an enhancement of autophagy in mIDH1 glioma cells. Autophagy is a mechanism involved in cell homeostasis related with cell survival under energetic stress and DNA damage protection. Autophagy has been associated with radio resistance. The inhibition of autophagy thus radio sensitizes mIDH1 glioma cells and enhances survival of mIDH1 glioma-bearing mice, representing a novel therapeutic target for this glioma subtype with potential applicability in combined clinical strategies.
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Wang K, Perera BPU, Morgan RK, Sala-Hamrick K, Geron V, Svoboda LK, Faulk C, Dolinoy DC, Sartor MA. piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation. Database (Oxford) 2024; 2024:baad096. [PMID: 38204359 PMCID: PMC10782149 DOI: 10.1093/database/baad096] [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: 08/14/2023] [Revised: 11/27/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly expressed and extensively studied from the germline. piRNAs associate with PIWI proteins to maintain DNA methylation for transposon silencing and transcriptional gene regulation for genomic stability. Mature germline piRNAs have distinct characteristics including a 24- to 32-nucleotide length and a 2'-O-methylation signature at the 3' end. Although recent studies have identified piRNAs in somatic tissues, they remain poorly characterized. For example, we recently demonstrated notable expression of piRNA in the murine soma, and while overall expression was lower than that of the germline, unique characteristics suggested tissue-specific functions of this class. While currently available databases commonly use length and association with PIWI proteins to identify piRNA, few have included a chemical oxidation method that detects piRNA based on its 3' modification. This method leads to reproducible and rigorous data processing when coupled with next-generation sequencing and bioinformatics analysis. Here, we introduce piOxi DB, a user-friendly web resource that provides a comprehensive analysis of piRNA, generated exclusively through sodium periodate treatment of small RNA. The current version of piOxi DB includes 435 749 germline and 9828 somatic piRNA sequences robustly identified from M. musculus, M. fascicularis and H. sapiens. The database provides species- and tissue-specific data that are further analyzed according to chromosome location and correspondence to gene and repetitive elements. piOxi DB is an informative tool to assist broad research applications in the fields of RNA biology, cancer biology, environmental toxicology and beyond. Database URL: https://pioxidb.dcmb.med.umich.edu/.
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Affiliation(s)
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Kimberley Sala-Hamrick
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Viviana Geron
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Department of Pharmacology, School of Medicine, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, 1988 Fitch Avenue, Saint Paul, MN 55108, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, 100 Washtenaw Ave, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, 100 Washtenaw Ave, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
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5
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Medeiros MCD, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY, D'Silva NJ. Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer. Microbiome 2023; 11:268. [PMID: 38037123 PMCID: PMC10687843 DOI: 10.1186/s40168-023-01677-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/26/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis. In this unique study, we compared pre- to post-treatment salivary microbiome in patients with SCC by 16S rRNA gene sequencing and examined how microbiome changes correlated with the expression of an anti-microbial protein. RESULTS Treatment of SCC was associated with a reduction in overall bacterial richness and diversity. There were significant changes in the microbial community structure, including a decrease in the abundance of Porphyromonaceae and Prevotellaceae and an increase in Lactobacillaceae. There were also significant changes in the microbial community structure before and after treatment with chemoradiotherapy, but not with surgery alone. In patients treated with chemoradiotherapy alone, several bacterial populations were differentially abundant between responders and non-responders before and after therapy. Microbiome changes were associated with a change in the expression of DMBT1, an anti-microbial protein in human saliva. Additionally, we found that salivary DMBT1, which increases after treatment, could serve as a post-treatment salivary biomarker that links to microbial changes. Specifically, post-treatment increases in human salivary DMBT1 correlated with increased abundance of Gemella spp., Pasteurellaceae spp., Lactobacillus spp., and Oribacterium spp. This is the first longitudinal study to investigate treatment-associated changes (chemoradiotherapy and surgery) in the oral microbiome in patients with SCC along with changes in expression of an anti-microbial protein in saliva. CONCLUSIONS The composition of the oral microbiota may predict treatment responses; salivary DMBT1 may have a role in modulating the oral microbiome in patients with SCC. After completion of treatment, 6 months after diagnosis, patients had a less diverse and less rich oral microbiome. Leptotrichia was a highly prevalent bacteria genus associated with disease. Expression of DMBT1 was higher after treatment and associated with microbiome changes, the most prominent genus being Gemella Video Abstract.
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Affiliation(s)
- Marcell Costa de Medeiros
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Stephanie The
- Cancer Data Science Shared Resource, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Emily Bellile
- Cancer Data Science Shared Resource, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Nickole Russo
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Ligia Schmitd
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Erika Danella
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Priyanka Singh
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Rajat Banerjee
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Christine Bassis
- Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 331248109, USA
| | - George R Murphy
- Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, 1011 N. University Ave, Ann Arbor, MI, USA
- Biointerfaces Institute, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Computational Medicine and Bioinformatics, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Isabelle Lombaert
- Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, 1011 N. University Ave, Ann Arbor, MI, USA
- Biointerfaces Institute, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- Microbiology and Immunology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Avi Eisbruch
- Radiation Oncology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Carol Anne Murdoch-Kinch
- Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, 1011 North Michigan St, Indianapolis, IN, USA
| | - Laura Rozek
- Environmental Health Sciences, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Gregory T Wolf
- Otolaryngology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Gen Li
- Biostatistics, University of Michigan School of Public Health, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Grace Y Chen
- Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 331248109, USA.
| | - Nisha J D'Silva
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA.
- Pathology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA.
- Rogel Cancer Center, Ann Arbor, MI, USA.
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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BP, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver Identifies Tissue- and Sex-Specific Changes with Implications for Genomic Imprinting. bioRxiv 2023:2023.09.29.560131. [PMID: 37873115 PMCID: PMC10592650 DOI: 10.1101/2023.09.29.560131] [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: 10/25/2023]
Abstract
Background Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. Objective We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. Methods Female mice were exposed to human relevant doses of either Pb (32ppm) via drinking water or DEHP (5 mg/kg-day) via chow for two weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and Chipenrich were used for genomic annotations and geneset enrichment tests of DMRs, respectively. Results The cortex contained the majority of DMRs associated with Pb (69%) and DEHP (58%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 17 and 14 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 79 and 47 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, with 15 and 17 ICR-located DMRs across cortex, blood, and liver in each gene, respectively. The ICRs were also the location of DMRs replicated across target and surrogate tissues, suggesting epigenetic changes these regions may be potentially viable biomarkers. Conclusions We observed Pb- and DEHP-specific DNAm changes in cortex, blood, and liver, and the greatest degree of overlap in DMR signatures was seen between exposures followed by sex and tissue type. DNAm at imprinted control regions was altered by both Pb and DEHP, highlighting the susceptibility of genomic imprinting to these exposures during the perinatal window of development.
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Affiliation(s)
- Rachel K. Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bambarendage P.U. Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Lim YX, Mierzwa ML, Sartor MA, D'Silva NJ. Clinical, morphologic and molecular heterogeneity of HPV-associated oropharyngeal cancer. Oncogene 2023; 42:2939-2955. [PMID: 37666939 PMCID: PMC10541327 DOI: 10.1038/s41388-023-02819-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023]
Abstract
The incidence of human papillomavirus-positive (HPV+) oropharyngeal squamous cell carcinoma (OPSCC) is rising rapidly and has exceeded cervical cancer to become the most common HPV-induced cancer in developed countries. Since patients with HPV + OPSCC respond very favorably to standard aggressive treatment, the emphasis has changed to reducing treatment intensity. However, recent multi-center clinical trials failed to show non-inferiority of de-escalation strategies on a population basis, highlighting the need to select low-risk patients likely to respond to de-intensified treatments. In contrast, there is a substantial proportion of patients who develop recurrent disease despite aggressive therapy. This supports that HPV + OPSCC is not a homogeneous disease, but comprises distinct subtypes with clinical and biological variations. The overall goal for this review is to identify biomarkers for HPV + OPSCC that may be relevant for patient stratification for personalized treatment. We discuss HPV + OPSCC as a heterogeneous disease from multifaceted perspectives including clinical behavior, tumor morphology, and molecular phenotype. Molecular profiling from bulk tumors as well as single-cell sequencing data are discussed as potential driving factors of heterogeneity between tumor subgroups. Finally, we evaluate key challenges that may impede in-depth investigations of HPV + OPSCC heterogeneity and outline potential future directions, including a section on racial and ethnic differences.
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Affiliation(s)
- Yvonne X Lim
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011N. University Ave, Ann Arbor, MI, USA
| | - Michelle L Mierzwa
- Rogel Cancer Center, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nisha J D'Silva
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011N. University Ave, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, USA.
- Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
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8
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Qin T, Li S, Henry LE, Chou E, Cavalcante RG, Garb BF, D'Silva NJ, Rozek LS, Sartor MA. Whole-genome CpG-resolution DNA Methylation Profiling of HNSCC Reveals Distinct Mechanisms of Carcinogenesis for Fine-scale HPV+ Cancer Subtypes. Cancer Res Commun 2023; 3:1701-1715. [PMID: 37654626 PMCID: PMC10467604 DOI: 10.1158/2767-9764.crc-23-0009] [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] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/24/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
DNA methylation is a vital early step in carcinogenesis. Most findings of aberrant DNA methylation in head and neck squamous cell carcinomas (HNSCC) are array based with limited coverage and resolution, and mainly explored by human papillomavirus (HPV) status, ignoring the high heterogeneity of this disease. In this study, we performed whole-genome bisulfite sequencing on a well-studied HNSCC cohort (n = 36) and investigated the methylation changes between fine-scaled HNSCC subtypes in relation to genomic instability, repetitive elements, gene expression, and key carcinogenic pathways. The previously observed hypermethylation phenotype in HPV-positive (HPV+) tumors compared with HPV-negative tumors was robustly present in the immune-strong (IMU) HPV+ subtype but absent in the highly keratinized (KRT) HPV+ subtype. Methylation levels of IMU tumors were significantly higher in repetitive elements, and methylation showed a significant correlation with genomic stability, consistent with the IMU subtype having more genomic stability and better prognosis. Expression quantitative trait methylation (cis-eQTM) analysis revealed extensive functionally-relevant differences, and differential methylation pathway analysis recapitulated gene expression pathway differences between subtypes. Consistent with their characteristics, KRT and HPV-negative tumors had high regulatory potential for multiple regulators of keratinocyte differentiation, which positively correlated with an expression-based keratinization score. Together, our findings revealed distinct mechanisms of carcinogenesis between subtypes in HPV+ HNSCC and uncovered previously ignored epigenomic differences and clinical implications, illustrating the importance of fine-scale subtype analysis in cancer. Significance This study revealed that the previously observed hypermethylation of HPV(+) HNSCC is due solely to the IMU subtype, illustrating the importance of fine-scale subtype analysis in such a heterogeneous disease. Particularly, IMU has significantly higher methylation of transposable elements, which can be tested as a prognosis biomarker in future translational studies.
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Affiliation(s)
- Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shiting Li
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Leanne E. Henry
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Elysia Chou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Raymond G. Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Bailey F. Garb
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Nisha J. D'Silva
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Laura S. Rozek
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
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9
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Petroff RL, Cavalcante RG, Colacino JA, Goodrich JM, Jones TR, Lalancette C, Morgan RK, Neier K, Perera BPU, Rygiel CA, Svoboda LK, Wang K, Sartor MA, Dolinoy DC. Developmental exposures to common environmental contaminants, DEHP and lead, alter adult brain and blood hydroxymethylation in mice. Front Cell Dev Biol 2023; 11:1198148. [PMID: 37384255 PMCID: PMC10294071 DOI: 10.3389/fcell.2023.1198148] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction: The developing epigenome changes rapidly, potentially making it more sensitive to toxicant exposures. DNA modifications, including methylation and hydroxymethylation, are important parts of the epigenome that may be affected by environmental exposures. However, most studies do not differentiate between these two DNA modifications, possibly masking significant effects. Methods: To investigate the relationship between DNA hydroxymethylation and developmental exposure to common contaminants, a collaborative, NIEHS-sponsored consortium, TaRGET II, initiated longitudinal mouse studies of developmental exposure to human-relevant levels of the phthalate plasticizer di(2-ethylhexyl) phthalate (DEHP), and the metal lead (Pb). Exposures to 25 mg DEHP/kg of food (approximately 5 mg DEHP/kg body weight) or 32 ppm Pb-acetate in drinking water were administered to nulliparous adult female mice. Exposure began 2 weeks before breeding and continued throughout pregnancy and lactation, until offspring were 21 days old. At 5 months, perinatally exposed offspring blood and cortex tissue were collected, for a total of 25 male mice and 17 female mice (n = 5-7 per tissue and exposure). DNA was extracted and hydroxymethylation was measured using hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq). Differential peak and pathway analysis was conducted comparing across exposure groups, tissue types, and animal sex, using an FDR cutoff of 0.15. Results: DEHP-exposed females had two genomic regions with lower hydroxymethylation in blood and no differences in cortex hydroxymethylation. For DEHP-exposed males, ten regions in blood (six higher and four lower) and 246 regions (242 higher and four lower) and four pathways in cortex were identified. Pb-exposed females had no statistically significant differences in blood or cortex hydroxymethylation compared to controls. Pb-exposed males, however, had 385 regions (all higher) and six pathways altered in cortex, but no differential hydroxymethylation was identified in blood. Discussion: Overall, perinatal exposure to human-relevant levels of two common toxicants showed differences in adult DNA hydroxymethylation that was specific to sex, exposure type, and tissue, but male cortex was most susceptible to hydroxymethylation differences by exposure. Future assessments should focus on understanding if these findings indicate potential biomarkers of exposure or are related to functional long-term health effects.
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Affiliation(s)
- Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Raymond G. Cavalcante
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Tamara R. Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Claudia Lalancette
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Rachel K. Morgan
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Kari Neier
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Bambarendage P. U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
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10
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Garcia-Fabiani MB, Haase S, Banerjee K, McClellan B, Zhu Z, Mujeeb A, Li Y, Yu J, Kadiyala P, Taher A, Núñez FJ, Alghamri MS, Comba A, Mendez FM, Nicola Candia AJ, Salazar B, Koschmann C, Nunez FM, Edwards M, Qin T, Sartor MA, Lowenstein PR, Castro MG. H3.3-G34R Mutation-Mediated Epigenetic Reprogramming Leads to Enhanced Efficacy of Immune Stimulatory Gene Therapy in Pediatric High-Grade Gliomas. bioRxiv 2023:2023.06.13.544658. [PMID: 37398299 PMCID: PMC10312611 DOI: 10.1101/2023.06.13.544658] [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: 07/04/2023]
Abstract
Pediatric high-grade gliomas (pHGGs) are diffuse and highly aggressive CNS tumors which remain incurable, with a 5-year overall survival of less than 20%. Within glioma, mutations in the genes encoding the histones H3.1 and H3.3 have been discovered to be age-restricted and specific of pHGGs. This work focuses on the study of pHGGs harboring the H3.3-G34R mutation. H3.3-G34R tumors represent the 9-15% of pHGGs, are restricted to the cerebral hemispheres, and are found predominantly in the adolescent population (median 15.0 years). We have utilized a genetically engineered immunocompetent mouse model for this subtype of pHGG generated via the Sleeping Beauty-transposon system. The analysis of H3.3-G34R genetically engineered brain tumors by RNA-Sequencing and ChIP-Sequencing revealed alterations in the molecular landscape associated to H3.3-G34R expression. In particular, the expression of H3.3-G34R modifies the histone marks deposited at the regulatory elements of genes belonging to the JAK/STAT pathway, leading to an increased activation of this pathway. This histone G34R-mediated epigenetic modifications lead to changes in the tumor immune microenvironment of these tumors, towards an immune-permissive phenotype, making these gliomas susceptible to TK/Flt3L immune-stimulatory gene therapy. The application of this therapeutic approach increased median survival of H3.3-G34R tumor bearing animals, while stimulating the development of anti-tumor immune response and immunological memory. Our data suggests that the proposed immune-mediated gene therapy has potential for clinical translation for the treatment of patients harboring H3.3-G34R high grade gliomas.
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Affiliation(s)
- Maria B. Garcia-Fabiani
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Current address: Leloir Institute Foundation, Buenos Aires, Argentina
| | - Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kaushik Banerjee
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brandon McClellan
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ziwen Zhu
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anzar Mujeeb
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yingxiang Li
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jin Yu
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Current address: Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Padma Kadiyala
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ayman Taher
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felipe J. Núñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mahmoud S. Alghamri
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Andrea Comba
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Flor M. Mendez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alejandro J. Nicola Candia
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brittany Salazar
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Cancer Biology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Carl Koschmann
- Department of Pediatrics, Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, MI 48109, USA
| | - Fernando M. Nunez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marta Edwards
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pedro R. Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Bioengineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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11
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Lee S, Deng L, Wang Y, Wang K, Sartor MA, Wang XS. IndepthPathway: an integrated tool for in-depth pathway enrichment analysis based on single-cell sequencing data. Bioinformatics 2023; 39:btad325. [PMID: 37243667 PMCID: PMC10275909 DOI: 10.1093/bioinformatics/btad325] [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: 07/30/2022] [Revised: 04/29/2023] [Accepted: 05/26/2023] [Indexed: 05/29/2023] Open
Abstract
MOTIVATION Single-cell sequencing enables exploring the pathways and processes of cells, and cell populations. However, there is a paucity of pathway enrichment methods designed to tolerate the high noise and low gene coverage of this technology. When gene expression data are noisy and signals are sparse, testing pathway enrichment based on the genes expression may not yield statistically significant results, which is particularly problematic when detecting the pathways enriched in less abundant cells that are vulnerable to disturbances. RESULTS In this project, we developed a Weighted Concept Signature Enrichment Analysis specialized for pathway enrichment analysis from single-cell transcriptomics (scRNA-seq). Weighted Concept Signature Enrichment Analysis took a broader approach for assessing the functional relations of pathway gene sets to differentially expressed genes, and leverage the cumulative signature of molecular concepts characteristic of the highly differentially expressed genes, which we termed as the universal concept signature, to tolerate the high noise and low coverage of this technology. We then incorporated Weighted Concept Signature Enrichment Analysis into an R package called "IndepthPathway" for biologists to broadly leverage this method for pathway analysis based on bulk and single-cell sequencing data. Through simulating technical variability and dropouts in gene expression characteristic of scRNA-seq as well as benchmarking on a real dataset of matched single-cell and bulk RNAseq data, we demonstrate that IndepthPathway presents outstanding stability and depth in pathway enrichment results under stochasticity of the data, thus will substantially improve the scientific rigor of the pathway analysis for single-cell sequencing data. AVAILABILITY AND IMPLEMENTATION The IndepthPathway R package is available through: https://github.com/wangxlab/IndepthPathway.
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Affiliation(s)
- Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, United States
| | - Letian Deng
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, United States
| | - Yue Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, United States
| | - Kai Wang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Maureen A Sartor
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, United States
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12
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Carney SV, Banerjee K, Mujeeb A, Zhu B, Haase S, Varela ML, Kadiyala P, Tronrud CE, Zhu Z, Mukherji D, Gorla P, Sun Y, Tagett R, Núñez FJ, Luo M, Luo W, Ljungman M, Liu Y, Xia Z, Schwendeman A, Qin T, Sartor MA, Costello JF, Cahill DP, Lowenstein PR, Castro MG. Zinc Finger MYND-Type Containing 8 (ZMYND8) Is Epigenetically Regulated in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma to Promote Radioresistance. Clin Cancer Res 2023; 29:1763-1782. [PMID: 36692427 PMCID: PMC10159884 DOI: 10.1158/1078-0432.ccr-22-1896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/27/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1 to confer therapeutic resistance to ionizing radiation (IR). EXPERIMENTAL DESIGN We evaluated changes in the transcriptome and epigenome in a radioresistant mIDH1 patient-derived glioma cell culture (GCC) following treatment with an mIDH1-specific inhibitor, AGI-5198. We identified Zinc Finger MYND-Type Containing 8 (ZMYND8) as a potential target of mIDH1 reprogramming. We suppressed ZMYND8 expression by shRNA knockdown and genetic knockout (KO) in mIDH1 glioma cells and then assessed cellular viability to IR. We assessed the sensitivity of mIDH1 GCCS to pharmacologic inhibition of ZMYND8-interacting partners: HDAC, BRD4, and PARP. RESULTS Inhibition of mIDH1 leads to an upregulation of gene networks involved in replication stress. We found that the expression of ZMYND8, a regulator of DNA damage response, was decreased in three patient-derived mIDH1 GCCs after treatment with AGI-5198. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 KO exhibit significant phosphorylation of ATM and sustained γH2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells. CONCLUSIONS These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma. See related commentary by Sachdev et al., p. 1648.
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Affiliation(s)
- Stephen V. Carney
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kaushik Banerjee
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anzar Mujeeb
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brandon Zhu
- Graduate Program in Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria L. Varela
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Padma Kadiyala
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Claire E. Tronrud
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ziwen Zhu
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Devarshi Mukherji
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Preethi Gorla
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Yilun Sun
- Department of Radiation Oncology, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Rebecca Tagett
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe J. Núñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maowu Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Environmental Health Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yayuan Liu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziyun Xia
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna Schwendeman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, California, 94143 USA
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston Massachusetts, 02114, USA
| | - Pedro R. Lowenstein
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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13
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Benjamin WJ, Wang K, Zarins K, Bellile E, Blostein F, Argirion I, Taylor JMG, D’Silva NJ, Chinn SB, Rifkin S, Sartor MA, Rozek LS. Oral Microbiome Community Composition in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:2549. [PMID: 37174014 PMCID: PMC10177240 DOI: 10.3390/cancers15092549] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 02/10/2023] [Revised: 03/13/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
The impact of the oral microbiome on head and neck cancer pathogenesis and outcomes requires further study. 16s rRNA was isolated and amplified from pre-treatment oral wash samples for 52 cases and 102 controls. The sequences were binned into operational taxonomic units (OTUs) at the genus level. Diversity metrics and significant associations between OTUs and case status were assessed. The samples were binned into community types using Dirichlet multinomial models, and survival outcomes were assessed by community type. Twelve OTUs from the phyla Firmicutes, Proteobacteria, and Acinetobacter were found to differ significantly between the cases and the controls. Beta-diversity was significantly higher between the cases than between the controls (p < 0.01). Two community types were identified based on the predominant sets of OTUs within our study population. The community type with a higher abundance of periodontitis-associated bacteria was more likely to be present in the cases (p < 0.01), in older patients (p < 0.01), and in smokers (p < 0.01). Significant differences between the cases and the controls in community type, beta-diversity, and OTUs indicate that the oral microbiome may play a role in HNSCC.
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Affiliation(s)
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine Zarins
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily Bellile
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Freida Blostein
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ilona Argirion
- Division of Cancer Epidemiology and Genomics, National Cancer Institute, Bethesda, MA 20814, USA
| | - Jeremy M. G. Taylor
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nisha J. D’Silva
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Steven B. Chinn
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samara Rifkin
- Department of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura S. Rozek
- Medical Center Department of Oncology, Georgetown University, Washington, DC 20007, USA
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14
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Svoboda LK, Wang K, Goodrich JM, Jones TR, Colacino JA, Peterson KE, Tellez-Rojo MM, Sartor MA, Dolinoy DC. Perinatal Lead Exposure Promotes Sex-Specific Epigenetic Programming of Disease-Relevant Pathways in Mouse Heart. Toxics 2023; 11:85. [PMID: 36668811 PMCID: PMC9860846 DOI: 10.3390/toxics11010085] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Environmental contaminants such as the metal lead (Pb) are associated with cardiovascular disease, but the underlying molecular mechanisms are poorly understood. In particular, little is known about how exposure to Pb during early development impacts the cardiac epigenome at any point across the life course and potential differences between sexes. In a mouse model of human-relevant perinatal exposures, we utilized RNA-seq and Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) to investigate the effects of Pb exposure during gestation and lactation on gene expression and DNA methylation, respectively, in the hearts of male and female mice at weaning. For ERRBS, we identified differentially methylated CpGs (DMCs) or differentially methylated 1000 bp regions (DMRs) based on a minimum absolute change in methylation of 10% and an FDR < 0.05. For gene expression data, an FDR < 0.05 was considered significant. No individual genes met the FDR cutoff for gene expression; however, we found that Pb exposure leads to significant changes in the expression of gene pathways relevant to cardiovascular development and disease. We further found that Pb promotes sex-specific changes in DNA methylation at hundreds of gene loci (280 DMCs and 99 DMRs in males, 189 DMCs and 121 DMRs in females), and pathway analysis revealed that these CpGs and regions collectively function in embryonic development. In males, differential methylation also occurred at genes related to immune function and metabolism. We then investigated whether genes exhibiting differential methylation at weaning were also differentially methylated in hearts from a cohort of Pb-exposed mice at adulthood. We found that a single gene, Galnt2, showed differential methylation in both sexes and time points. In a human cohort investigating the influence of prenatal Pb exposure on the epigenome, we also observed an inverse association between first trimester Pb concentrations and adolescent blood leukocyte DNA methylation at a locus in GALNT2, suggesting that this gene may represent a biomarker of Pb exposure across species. Together, these data, across two time points in mice and in a human birth cohort study, collectively demonstrate that Pb exposure promotes sex-specific programming of the cardiac epigenome, and provide potential mechanistic insight into how Pb causes cardiovascular disease.
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Affiliation(s)
- Laurie K. Svoboda
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jaclyn M. Goodrich
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Tamara R. Jones
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Karen E. Peterson
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Martha M. Tellez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca 62100, Mexico
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
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15
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Park BJ, Mattox AK, Clayburgh D, Patel M, Bell RB, Yueh B, Leidner R, Xiao H, Couey M, Li S, Qin T, Sartor MA, Cairns B, MacDonough T, Halliwill K, Deschler D, Lin DT, Faquin WC, Sadow PM, Pai SI. Chemoradiation therapy alters the PD-L1 score in locoregional recurrent squamous cell carcinomas of the head and neck. Oral Oncol 2022; 135:106183. [PMID: 36215771 PMCID: PMC10283355 DOI: 10.1016/j.oraloncology.2022.106183] [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: 07/12/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/07/2022]
Abstract
PD-L1 testing guides therapeutic decision-making for head and neck squamous cell carcinoma (HNSCC). We sought to understand whether chemoradiation therapy (CRT) influences the PD-L1 combined positive score (CPS) and other biomarkers of response to immunotherapy. PD-L1 expression was assessed using immunohistochemistry, and bulk RNA sequencing was performed on 146 HNSCC patients (65 primary sites, 50 paired local recurrences, and 31 paired regional recurrences). PD-L1 was scored using the CPS of ≥1, ≥20, and ≥50. Overall, 98 %, 54 %, and 17 % of HNSCCs had a CPS ≥1, ≥20, and ≥50, respectively. When using a cut-off of ≥1, CRT did not significantly change CPS at the locoregional recurrent site. However, there were significant changes when using CPS ≥20 or ≥50. The CPS changed for 32 % of patients when using a CPS ≥20 (p < 0.001). When using a CPS ≥50, there was a 20-23 % (p = 0.0058-0.00067) discordance rate at the site of locoregional recurrence. Oral cavity cancers had a significantly higher discordant rate than other primary sites for CPS ≥50, 44 % (8/18, p = 0.0058) and 58 % (7/12, p = 0.00067) discordance at the site of local and regional recurrence, respectively. When evaluating the 18 gene IFN-ɣ signature predictive of response to anti-PD-1 blockade, there was a statistically significant increase in the IFN-ɣ signature in recurrent larynx cancer (p = 0.02). Our study demonstrates that when using a higher cut-off of CPS ≥20 and ≥50, a repeat biopsy may be warranted after CRT for local and regional recurrent HNSCCs.
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Affiliation(s)
- Brian J Park
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Austin K Mattox
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Daniel Clayburgh
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health & Science University, Portland, OR, United States
| | - Mihir Patel
- Department of Otolaryngology-Head and Neck Surgery, Emory University, Atlanta, Georgia
| | - R Bryan Bell
- Earle A. Chiles Research Institute in the Robert W. Franz Cancer Center, Providence Cancer Institute, Portland, OR, United States
| | - Bevan Yueh
- Department of Otolaryngology, University of Minnesota, Minneapolis, MN, United States
| | - Rom Leidner
- Earle A. Chiles Research Institute in the Robert W. Franz Cancer Center, Providence Cancer Institute, Portland, OR, United States
| | - Hong Xiao
- Department of Pathology, Providence Health and Services-Oregon, Portland, OR, United States
| | - Marcus Couey
- Department of Pathology, Providence Health and Services-Oregon, Portland, OR, United States
| | - Shiting Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | | | | | | | - Daniel Deschler
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Derrick T Lin
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Sara I Pai
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States; Center for Systems Biology, Massachusetts General Hospital, Boston, MA, United States.
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16
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Qin T, Lee C, Li S, Cavalcante RG, Orchard P, Yao H, Zhang H, Wang S, Patil S, Boyle AP, Sartor MA. Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data. Genome Biol 2022; 23:105. [PMID: 35473573 PMCID: PMC9044877 DOI: 10.1186/s13059-022-02668-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 10/09/2020] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cell types, while the accuracy of genome-wide approaches remains elusive due to the lack of a systematic evaluation. We combined multiple spatial and in silico approaches for defining enhancer locations and linking them to their target genes aggregated across >500 cell types, generating 1860 human genome-wide distal enhancer-to-target gene definitions (EnTDefs). To evaluate performance, we used gene set enrichment (GSE) testing on 87 independent ENCODE ChIP-seq datasets of 34 transcription factors (TFs) and assessed concordance of results with known TF Gene Ontology annotations, and other benchmarks. RESULTS The top ranked 741 (40%) EnTDefs significantly outperform the common, naïve approach of linking distal regions to the nearest genes, and the top 10 EnTDefs perform well when applied to ChIP-seq data of other cell types. The GSE-based ranking of EnTDefs is highly concordant with ranking based on overlap with curated benchmarks of enhancer-gene interactions. Both our top general EnTDef and cell-type-specific EnTDefs significantly outperform seven independent computational and experiment-based enhancer-gene pair datasets. We show that using our top EnTDefs for GSE with either genome-wide DNA methylation or ATAC-seq data is able to better recapitulate the biological processes changed in gene expression data performed in parallel for the same experiment than our lower-ranked EnTDefs. CONCLUSIONS Our findings illustrate the power of our approach to provide genome-wide interpretation regardless of cell type.
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Affiliation(s)
- Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Christopher Lee
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shiting Li
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Raymond G Cavalcante
- Biomedical Research Core Facilities, Epigenomics Core, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Heming Yao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hanrui Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shuze Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Snehal Patil
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Biostatistics, School of Public Health, University of Michigan Medical School, Ann Arbor, MI, USA.
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17
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Qin T, Mullan B, Ravindran R, Messinger D, Siada R, Cummings JR, Harris M, Muruganand A, Pyaram K, Miklja Z, Reiber M, Garcia T, Tran D, Danussi C, Brosnan-Cashman J, Pratt D, Zhao X, Rehemtulla A, Sartor MA, Venneti S, Meeker AK, Huse JT, Morgan MA, Lowenstein PR, Castro MG, Yadav VN, Koschmann C. ATRX loss in glioma results in dysregulation of cell-cycle phase transition and ATM inhibitor radio-sensitization. Cell Rep 2022; 38:110216. [PMID: 35021084 DOI: 10.1016/j.celrep.2021.110216] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 06/11/2021] [Revised: 10/15/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
ATRX, a chromatin remodeler protein, is recurrently mutated in H3F3A-mutant pediatric glioblastoma (GBM) and isocitrate dehydrogenase (IDH)-mutant grade 2/3 adult glioma. Previous work has shown that ATRX-deficient GBM cells show enhanced sensitivity to irradiation, but the etiology remains unclear. We find that ATRX binds the regulatory elements of cell-cycle phase transition genes in GBM cells, and there is a marked reduction in Checkpoint Kinase 1 (CHEK1) expression with ATRX loss, leading to the early release of G2/M entry after irradiation. ATRX-deficient cells exhibit enhanced activation of master cell-cycle regulator ATM with irradiation. Addition of the ATM inhibitor AZD0156 doubles median survival in mice intracranially implanted with ATRX-deficient GBM cells, which is not seen in ATRX-wild-type controls. This study demonstrates that ATRX-deficient high-grade gliomas (HGGs) display Chk1-mediated dysregulation of cell-cycle phase transitions, which opens a window for therapies targeting this phenotype.
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Affiliation(s)
- Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Rogel Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brendan Mullan
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ramya Ravindran
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Dana Messinger
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ruby Siada
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jessica R Cummings
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Micah Harris
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ashwath Muruganand
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Kalyani Pyaram
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Zachary Miklja
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Mary Reiber
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Taylor Garcia
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Dustin Tran
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Carla Danussi
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Drew Pratt
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Xinyi Zhao
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alnawaz Rehemtulla
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sriram Venneti
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jason T Huse
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pedro R Lowenstein
- Departments of Neurosurgery and Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G Castro
- Departments of Neurosurgery and Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Viveka Nand Yadav
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Carl Koschmann
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of Michigan Medical School, 3520D MSRB 1, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA.
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18
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Chi X, Sartor MA, Lee S, Anurag M, Patil S, Hall P, Wexler M, Wang XS. Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways. Brief Bioinform 2021; 21:1717-1732. [PMID: 31631213 DOI: 10.1093/bib/bbz093] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/11/2019] [Revised: 05/23/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
Identifying new gene functions and pathways underlying diseases and biological processes are major challenges in genomics research. Particularly, most methods for interpreting the pathways characteristic of an experimental gene list defined by genomic data are limited by their dependence on assessing the overlapping genes or their interactome topology, which cannot account for the variety of functional relations. This is particularly problematic for pathway discovery from single-cell genomics with low gene coverage or interpreting complex pathway changes such as during change of cell states. Here, we exploited the comprehensive sets of molecular concepts that combine ontologies, pathways, interactions and domains to help inform the functional relations. We first developed a universal concept signature (uniConSig) analysis for genome-wide quantification of new gene functions underlying biological or pathological processes based on the signature molecular concepts computed from known functional gene lists. We then further developed a novel concept signature enrichment analysis (CSEA) for deep functional assessment of the pathways enriched in an experimental gene list. This method is grounded on the framework of shared concept signatures between gene sets at multiple functional levels, thus overcoming the limitations of the current methods. Through meta-analysis of transcriptomic data sets of cancer cell line models and single hematopoietic stem cells, we demonstrate the broad applications of CSEA on pathway discovery from gene expression and single-cell transcriptomic data sets for genetic perturbations and change of cell states, which complements the current modalities. The R modules for uniConSig analysis and CSEA are available through https://github.com/wangxlab/uniConSig.
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Affiliation(s)
- Xu Chi
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, U.S.A.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15232, U.S.A.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206, U.S.A.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Maureen A Sartor
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, U.S.A
| | - Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, U.S.A.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206, U.S.A
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, U.S.A
| | - Snehal Patil
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, U.S.A
| | - Pelle Hall
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, U.S.A
| | - Matthew Wexler
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, U.S.A.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15232, U.S.A.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206, U.S.A
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, U.S.A.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15232, U.S.A.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206, U.S.A.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, U.S.A
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19
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Liu S, Wang K, Svoboda LK, Rygiel CA, Neier K, Jones TR, Cavalcante RG, Colacino JA, Dolinoy DC, Sartor MA. Perinatal DEHP exposure induces sex- and tissue-specific DNA methylation changes in both juvenile and adult mice. Environ Epigenet 2021; 7:dvab004. [PMID: 33986952 PMCID: PMC8107644 DOI: 10.1093/eep/dvab004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/12/2021] [Accepted: 03/17/2021] [Indexed: 05/04/2023]
Abstract
Di(2-ethylhexyl) phthalate (DEHP) is a type of phthalate plasticizer found in a variety of consumer products and poses a public health concern due to its metabolic and endocrine disruption activities. Dysregulation of epigenetic modifications, including DNA methylation, has been shown to be an important mechanism for the pathogenic effects of prenatal exposures, including phthalates. In this study, we used an established mouse model to study the effect of perinatal DEHP exposure on the DNA methylation profile in liver (a primary target tissue of DEHP) and blood (a common surrogate tissue) of both juvenile and adult mice. Despite exposure ceasing at 3 weeks of age (PND21), we identified thousands of sex-specific differential DNA methylation events in 5-month old mice, more than identified at PND21, both in blood and liver. Only a small number of these differentially methylated cytosines (DMCs) overlapped between the time points, or between tissues (i.e. liver and blood), indicating blood may not be an appropriate surrogate tissue to estimate the effects of DEHP exposure on liver DNA methylation. We detected sex-specific DMCs common between 3-week and 5-month samples, pointing to specific DNA methylation alterations that are consistent between weanling and adult mice. In summary, this is the first study to assess the genome-wide DNA methylation profiles in liver and blood at two different aged cohorts in response to perinatal DEHP exposure. Our findings cast light on the implications of using surrogate tissue instead of target tissue in human population-based studies and identify epigenetic biomarkers for DEHP exposure.
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Affiliation(s)
- Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Laurie K Svoboda
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Christine A Rygiel
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Kari Neier
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Tamara R Jones
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Raymond G Cavalcante
- Epigenomics Core, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Justin A Colacino
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Dana C Dolinoy
- Correspondence address. Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, USA. Tel: +734-647-3155; Fax: +734-936-7283; E-mail: (D.C.D.); Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI 48109-2218, USA . Tel: +734-763-8013; Fax: +734-615-6553; E-mail: (M.A.S.)
| | - Maureen A Sartor
- Correspondence address. Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, USA. Tel: +734-647-3155; Fax: +734-936-7283; E-mail: (D.C.D.); Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI 48109-2218, USA . Tel: +734-763-8013; Fax: +734-615-6553; E-mail: (M.A.S.)
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20
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Huang SK, Tripathi P, Koneva LA, Cavalcante RG, Craig N, Scruggs AM, Sartor MA, Deng F, Chen Y. Effect of concentration and duration of particulate matter exposure on the transcriptome and DNA methylome of bronchial epithelial cells. Environ Epigenet 2021; 7:dvaa022. [PMID: 33692908 PMCID: PMC7928203 DOI: 10.1093/eep/dvaa022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/18/2020] [Accepted: 12/08/2020] [Indexed: 05/04/2023]
Abstract
Exposure to particulate matter (PM) from ambient air pollution is a well-known risk factor for many lung diseases, but the mechanism(s) for this is not completely understood. Bronchial epithelial cells, which line the airway of the respiratory tract, undergo genome-wide level changes in gene expression and DNA methylation particularly when exposed to fine (<2.5 µm) PM (PM2.5). Although some of these changes have been reported in other studies, a comparison of how different concentrations and duration of exposure affect both the gene transcriptome and DNA methylome has not been done. Here, we exposed BEAS-2B, a bronchial epithelial cell line, to different concentrations of PM2.5, and compared how single or repeated doses of PM2.5 affect both the transcriptome and methylome of cells. Widespread changes in gene expression occurred after cells were exposed to a single treatment of high-concentration (30 µg/cm2) PM2.5 for 24 h. These genes were enriched in pathways regulating cytokine-cytokine interactions, Mitogen-Activated Protein Kinase (MAPK) signaling, PI3K-Akt signaling, IL6, and P53. DNA methylomic analysis showed that nearly half of the differentially expressed genes were found to also have DNA methylation changes, with just a slightly greater trend toward overall hypomethylation across the genome. Cells exposed to a lower concentration (1 µg/cm2) of PM2.5 demonstrated a comparable, but more attenuated change in gene expression compared to cells exposed to higher concentrations. There were also many genes affected by lower concentrations of PM2.5, but not higher concentrations. Additionally, repeated exposure to PM2.5 (1 µg/cm2) for seven days resulted in transcriptomic and DNA methylomic changes that were distinct from cells treated with PM2.5 for only one day. Compared to single exposure, repeated exposure to PM2.5 caused a more notable degree of hypomethylation across the genome, though certain genes and regions demonstrated increased DNA methylation. The overall increase in hypomethylation, especially with repeated exposure to PM2.5, was associated with an increase in expression of ten-eleven translocation enzymes. These data demonstrate how variations in concentration and duration of PM2.5 exposure induce distinct differences in the transcriptomic and DNA methylomic profile of bronchial epithelial cells, which may have important implications in the development of both acute and chronic lung disease.
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Affiliation(s)
- Steven K Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, 6301 MSRB III, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
- Correspondence address: Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, 6301 MSRB III, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA. Tel: +1-734-647-6477; Fax: +1-734-764-4556; E-mail:
| | - Priya Tripathi
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, 6301 MSRB III, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Lada A Koneva
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Room 2017, Palmer Commons 100 Washtenaw Avenue Ann Arbor, MI 48109-2218, USA
| | - Raymond G Cavalcante
- Epigenomics Core, University of Michigan, Ann Arbor, Medical Science Research Building II Rm C568 1150 W. Medical Center Dr Ann Arbor, MI 48109, USA
| | - Nathan Craig
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, 6301 MSRB III, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Anne M Scruggs
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, 6301 MSRB III, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Room 2017, Palmer Commons 100 Washtenaw Avenue Ann Arbor, MI 48109-2218, USA
| | - Furong Deng
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Xueyuan Road 38, Haidian District, Beijing, China
| | - Yahong Chen
- Department of Respiratory Medicine, Peking University Third Hospital, No. 49, Huayuan North Road, Haidian District, Beijing, China
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21
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Neier K, Montrose L, Chen K, Malloy MA, Jones TR, Svoboda LK, Harris C, Song PXK, Pennathur S, Sartor MA, Dolinoy DC. Short- and long-term effects of perinatal phthalate exposures on metabolic pathways in the mouse liver. Environ Epigenet 2020; 6:dvaa017. [PMID: 33391822 PMCID: PMC7757125 DOI: 10.1093/eep/dvaa017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 07/19/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 06/12/2023]
Abstract
Phthalates have been demonstrated to interfere with metabolism, presumably by interacting with peroxisome proliferator-activated receptors (PPARs). However, mechanisms linking developmental phthalate exposures to long-term metabolic effects have not yet been elucidated. We investigated the hypothesis that developmental phthalate exposure has long-lasting impacts on PPAR target gene expression and DNA methylation to influence hepatic metabolic profiles across the life course. We utilized an established longitudinal mouse model of perinatal exposures to diethylhexyl phthalate and diisononyl phthalate, and a mixture of diethylhexyl phthalate+diisononyl phthalate. Exposure was through the diet and spanned from 2 weeks before mating until weaning at postnatal day 21 (PND21). Liver tissue was analyzed from the offspring of exposed and control mice at PND21 and in another cohort of exposed and control mice at 10 months of age. RNA-seq and pathway enrichment analyses indicated that acetyl-CoA metabolic processes were altered in diisononyl phthalate-exposed female livers at both PND21 and 10 months (FDR = 0.0018). Within the pathway, all 13 significant genes were potential PPAR target genes. Promoter DNA methylation was altered at three candidate genes, but persistent effects were only observed for Fasn. Targeted metabolomics indicated that phthalate-exposed females had decreased acetyl-CoA at PND21 and increased acetyl-CoA and acylcarnitines at 10 months. Together, our data suggested that perinatal phthalate exposures were associated with short- and long-term activation of PPAR target genes, which manifested as increased fatty acid production in early postnatal life and increased fatty acid oxidation in adulthood. This presents a novel molecular pathway linking developmental phthalate exposures and metabolic health outcomes.
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Affiliation(s)
- Kari Neier
- Environmental Health Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
| | - Luke Montrose
- Environmental Health Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
| | - Kathleen Chen
- Environmental Health Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
| | - Maureen A Malloy
- Environmental Health Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
| | - Tamara R Jones
- Environmental Health Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
| | - Laurie K Svoboda
- Environmental Health Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
| | - Craig Harris
- Environmental Health Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
| | - Peter X K Song
- Biostatistics, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, 1500 East Medical Center Drive 48109 MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, 1137 E. Catherine St. 48109 MI, USA
| | - Maureen A Sartor
- Biostatistics, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 100 Washtenaw Avenue 48109 MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
- Nutritional Sciences, University of Michigan, Ann Arbor, 1415 Washington Heights 48109 MI, USA
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22
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Liu S, de Medeiros MC, Fernandez EM, Zarins KR, Cavalcante RG, Qin T, Wolf GT, Figueroa ME, D'Silva NJ, Rozek LS, Sartor MA. 5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers. Clin Epigenetics 2020; 12:175. [PMID: 33203436 PMCID: PMC7672859 DOI: 10.1186/s13148-020-00965-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.
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Affiliation(s)
- Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | | | - Evan M Fernandez
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | - Gregory T Wolf
- Department of Otolaryngology-Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Maria E Figueroa
- Department of Human Genetics and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Nisha J D'Silva
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA. .,Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
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23
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Svoboda LK, Neier K, Wang K, Cavalcante RG, Rygiel CA, Tsai Z, Jones TR, Liu S, Goodrich JM, Lalancette C, Colacino JA, Sartor MA, Dolinoy DC. Tissue and sex-specific programming of DNA methylation by perinatal lead exposure: implications for environmental epigenetics studies. Epigenetics 2020; 16:1102-1122. [PMID: 33164632 DOI: 10.1080/15592294.2020.1841872] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 02/07/2023] Open
Abstract
Early developmental environment can influence long-term health through reprogramming of the epigenome. Human environmental epigenetics studies rely on surrogate tissues, such as blood, to assess the effects of environment on disease-relevant but inaccessible target tissues. However, the extent to which environment-induced epigenetic changes are conserved between these tissues is unclear. A better understanding of this conservation is imperative for effective design and interpretation of human environmental epigenetics studies. The Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET II) consortium was established by the National Institute of Environmental Health Sciences to address the utility of surrogate tissues as proxies for toxicant-induced epigenetic changes in target tissues. We and others have recently reported that perinatal exposure to lead (Pb) is associated with adverse metabolic outcomes. Here, we investigated the sex-specific effects of perinatal exposure to a human environmentally relevant level of Pb on DNA methylation in paired liver and blood samples from adult mice using enhanced reduced-representation bisulphite sequencing. Although Pb exposure ceased at 3 weeks of age, we observed thousands of sex-specific differentially methylated cytosines in the blood and liver of Pb-exposed animals at 5 months of age, including 44 genomically imprinted loci. We observed significant tissue overlap in the genes mapping to differentially methylated cytosines. A small but significant subset of Pb-altered genes exhibit basal sex differences in gene expression in the mouse liver. Collectively, these data identify potential molecular targets for Pb-induced metabolic diseases, and inform the design of more robust human environmental epigenomics studies.
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Affiliation(s)
- Laurie K Svoboda
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kari Neier
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | | | - Christine A Rygiel
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Zing Tsai
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | - Tamara R Jones
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Claudia Lalancette
- Epigenomics Core, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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24
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Wang K, Liu S, Svoboda LK, Rygiel CA, Neier K, Jones TR, Colacino JA, Dolinoy DC, Sartor MA. Tissue- and Sex-Specific DNA Methylation Changes in Mice Perinatally Exposed to Lead (Pb). Front Genet 2020; 11:840. [PMID: 32973866 PMCID: PMC7472839 DOI: 10.3389/fgene.2020.00840] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 04/15/2020] [Accepted: 07/10/2020] [Indexed: 12/22/2022] Open
Abstract
Lead (Pb) is a well-known toxicant that interferes with the development of a child’s nervous and metabolic systems and increases the risk of developing diseases later in life. Although studies have investigated epigenetic effects associated with Pb exposure, knowledge of genome-wide changes with in vivo low dose perinatal Pb exposure in multiple tissues is limited. Within the Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET II) consortium, we utilized a mouse model to investigate tissue- and sex-specific DNA methylation. Dams were assigned to control or Pb-acetate water, respectively. Exposures started 2 weeks prior to mating and continued until weaning at post-natal day 21 (PND21). Liver and blood were collected from PND21 mice, and the DNA methylome was assessed using enhanced reduced representation bisulfite sequencing (ERRBS). We identified ∼1000 perinatal Pb exposure related differentially methylated cytosines (DMCs) for each tissue- and sex-specific comparison, and hundreds of tissue- and sex-specific differentially methylated regions (DMRs). Several mouse imprinted genes were differentially methylated across both tissues in males and females. Overall, our findings demonstrate that perinatal Pb exposure can induce tissue- and sex-specific DNA methylation changes and provide information for future Pb studies in humans.
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Affiliation(s)
- Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Siyu Liu
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Christine A Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
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25
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Svoboda LK, Wang K, Cavalcante RG, Neier K, Colacino JA, Sartor MA, Dolinoy DC. Sex-Specific Programming of Cardiac DNA Methylation by Developmental Phthalate Exposure. Epigenet Insights 2020; 13:2516865720939971. [PMID: 32864567 PMCID: PMC7430087 DOI: 10.1177/2516865720939971] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 04/05/2020] [Accepted: 06/15/2020] [Indexed: 01/05/2023] Open
Abstract
Phthalate plasticizers are ubiquitous chemicals linked to several cardiovascular diseases in animal models and humans. Despite this, the mechanisms by which phthalate exposures cause adverse cardiac health outcomes are unclear. In particular, whether phthalate exposures during pregnancy interfere with normal developmental programming of the cardiovascular system, and the resulting implications this may have for long-term disease risk, are unknown. Recent studies suggest that the effects of phthalates on metabolic and neurobehavioral outcomes are sex-specific. However, the influence of sex on cardiac susceptibility to phthalate exposures has not been investigated. One mechanism by which developmental exposures may influence long-term health is through altered programming of DNA methylation. In this work, we utilized an established mouse model of human-relevant perinatal exposure and enhanced reduced representation bisulfite sequencing to investigate the long-term effects of diethylhexyl phthalate (DEHP) exposure on DNA methylation in the hearts of adult male and female offspring at 5 months of age (n = 5-7 mice per sex and exposure). Perinatal DEHP exposure led to hundreds of sex-specific, differentially methylated cytosines (DMCs) and differentially methylated regions (DMRs) in the heart. Pathway analysis of DMCs revealed enrichment for several pathways in females, including insulin signaling, regulation of histone methylation, and tyrosine phosphatase activity. In males, DMCs were enriched for glucose transport, energy generation, and developmental programs. Notably, many sex-specific genes differentially methylated with DEHP exposure in our mouse model were also differentially methylated in published data of heart tissues collected from human heart failure patients. Together, these data highlight the potential role for DNA methylation in DEHP-induced cardiac effects and emphasize the importance of sex as a biological variable in environmental health studies.
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Affiliation(s)
- Laurie K Svoboda
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Kari Neier
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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26
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Bakulski KM, Dou JF, Thompson RC, Lee C, Middleton LY, Perera BPU, Ferris SP, Jones TR, Neier K, Zhou X, Sartor MA, Hammoud SS, Dolinoy DC, Colacino JA. Single-Cell Analysis of the Gene Expression Effects of Developmental Lead (Pb) Exposure on the Mouse Hippocampus. Toxicol Sci 2020; 176:396-409. [PMID: 32458983 PMCID: PMC7416319 DOI: 10.1093/toxsci/kfaa069] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Lead (Pb) exposure is ubiquitous with permanent neurodevelopmental effects. The hippocampus brain region is involved in learning and memory with heterogeneous cellular composition. The hippocampus cell type-specific responses to Pb are unknown. The objective of this study is to examine perinatal Pb treatment effects on adult hippocampus gene expression, at the level of individual cells. In mice perinatally exposed to control water or a human physiologically relevant level (32 ppm in maternal drinking water) of Pb, 2 weeks prior to mating through weaning, we tested for hippocampus gene expression and cellular differences at 5 months of age. We sequenced RNA from 5258 hippocampal cells to (1) test for treatment gene expression differences averaged across all cells, (2) compare cell cluster composition by treatment, and (3) test for treatment gene expression and pathway differences within cell clusters. Gene expression patterns revealed 12 hippocampus cell clusters, mapping to major expected cell types (eg, microglia, astrocytes, neurons, and oligodendrocytes). Perinatal Pb treatment was associated with 12.4% more oligodendrocytes (p = 4.4 × 10-21) in adult mice. Across all cells, Pb treatment was associated with expression of cell cluster marker genes. Within cell clusters, Pb treatment (q < 0.05) caused differential gene expression in endothelial, microglial, pericyte, and astrocyte cells. Pb treatment upregulated protein folding pathways in microglia (p = 3.4 × 10-9) and stress response in oligodendrocytes (p = 3.2 × 10-5). Bulk tissue analysis may be influenced by changes in cell type composition, obscuring effects within vulnerable cell types. This study serves as a biological reference for future single-cell toxicant studies, to ultimately characterize molecular effects on cognition and behavior.
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Affiliation(s)
| | | | | | | | | | | | - Sean P Ferris
- Medical School, University of Michigan, Ann Arbor, Michigan 48109
| | | | | | | | - Maureen A Sartor
- School of Public Health
- Medical School, University of Michigan, Ann Arbor, Michigan 48109
| | - Saher S Hammoud
- Medical School, University of Michigan, Ann Arbor, Michigan 48109
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27
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Qin T, Koneva LA, Liu Y, Zhang Y, Arthur AE, Zarins KR, Carey TE, Chepeha D, Wolf GT, Rozek LS, Sartor MA. Significant association between host transcriptome-derived HPV oncogene E6* influence score and carcinogenic pathways, tumor size, and survival in head and neck cancer. Head Neck 2020; 42:2375-2389. [PMID: 32406560 DOI: 10.1002/hed.26244] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human papillomavirus (HPV) oncogenes E6, E7, and shorter isoforms of E6 (E6*) are known carcinogenic factors in head and neck squamous cell carcinoma (HNSCC). Little is known regarding E6* functions. METHODS We analyzed RNA-seq data from 68 HNSCC HPV type 16-positive tumors to determine host genes and pathways associated with E6+E7 expression (E6E7) or the percent of full-length E6 (E6%FL). Influence scores of E6E7 and E6%FL were used to test for associations with clinical variables. RESULTS For E6E7, we recapitulated all major known affected pathways and revealed additional pathways. E6%FL was found to affect mitochondrial processes, and E6%FL influence score was significantly associated with overall survival and tumor size. CONCLUSIONS HPV E6E7 and E6* result in extensive, dose-dependent compensatory effects and dysregulation of key cancer pathways. The switch from E6 to E6* promotes oxidative phosphorylation, larger tumor size, and worse prognosis, potentially serving as a prognostic factor for HPV-positive HNSCC.
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Affiliation(s)
- Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lada A Koneva
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Kennedy Institute of Rheumatology, University of Oxford, United Kingdom
| | - Yidan Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yanxiao Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Anna E Arthur
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA.,Department of Food Science and Human Nutrition, University of Illinois, Urbana-Champaign, IL, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas E Carey
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Douglas Chepeha
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA.,Department of Otolaryngology/Head & Neck Surgery, University of Toronto, Toronto, ON, Canada
| | - Gregory T Wolf
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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28
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Xu B, Qin T, Yu J, Giordano TJ, Sartor MA, Koenig RJ. Novel role of ASH1L histone methyltransferase in anaplastic thyroid carcinoma. J Biol Chem 2020; 295:8834-8845. [PMID: 32398261 DOI: 10.1074/jbc.ra120.013530] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Anaplastic thyroid cancer (ATC) is one of the most aggressive human malignancies, with an average life expectancy of ∼6 months from the time of diagnosis. The genetic and epigenetic changes that underlie this malignancy are incompletely understood. We found that ASH1-like histone lysine methyltransferase (ASH1L) is overexpressed in ATC relative to the much less aggressive and more common differentiated thyroid cancer. This increased expression was due at least in part to reduced levels of microRNA-200b-3p (miR-200b-3p), which represses ASH1L expression, in ATC. Genetic knockout of ASH1L protein expression in ATC cell lines decreased cell growth both in culture and in mouse xenografts. RNA-Seq analysis of ASH1L knockout versus WT ATC cell lines revealed that ASH1L is involved in the regulation of numerous cancer-related genes and gene sets. The pro-oncogenic long noncoding RNA colon cancer-associated transcript 1 (CCAT1) was one of the most highly (approximately 68-fold) down-regulated transcripts in ASH1L knockout cells. Therefore, we investigated CCAT1 as a potential mediator of the growth-inducing activity of ASH1L. Supporting this hypothesis, CCAT1 knockdown in ATC cells decreased their growth rate, and ChIP-Seq data indicated that CCAT1 is likely a direct target of ASH1L's histone methyltransferase activity. These results indicate that ASH1L contributes to the aggressiveness of ATC and suggest that ASH1L, along with its upstream regulator miR-200b-3p and its downstream mediator CCAT1, represents a potential therapeutic target in ATC.
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Affiliation(s)
- Bin Xu
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jingcheng Yu
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Thomas J Giordano
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ronald J Koenig
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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29
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Saha AK, Contreras-Galindo R, Niknafs YS, Iyer M, Qin T, Padmanabhan K, Siddiqui J, Palande M, Wang C, Qian B, Ward E, Tang T, Tomlins SA, Gitlin SD, Sartor MA, Omenn GS, Chinnaiyan AM, Markovitz DM. The role of the histone H3 variant CENPA in prostate cancer. J Biol Chem 2020; 295:8537-8549. [PMID: 32371391 PMCID: PMC7307189 DOI: 10.1074/jbc.ra119.010080] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 07/05/2019] [Revised: 04/14/2020] [Indexed: 01/26/2023] Open
Abstract
Overexpression of centromeric proteins has been identified in a number of human malignancies, but the functional and mechanistic contributions of these proteins to disease progression have not been characterized. The centromeric histone H3 variant centromere protein A (CENPA) is an epigenetic mark that determines centromere identity. Here, using an array of approaches, including RNA-sequencing and ChIP-sequencing analyses, immunohistochemistry-based tissue microarrays, and various cell biology assays, we demonstrate that CENPA is highly overexpressed in prostate cancer in both tissue and cell lines and that the level of CENPA expression correlates with the disease stage in a large cohort of patients. Gain-of-function and loss-of-function experiments confirmed that CENPA promotes prostate cancer cell line growth. The results from the integrated sequencing experiments suggested a previously unidentified function of CENPA as a transcriptional regulator that modulates expression of critical proliferation, cell-cycle, and centromere/kinetochore genes. Taken together, our findings show that CENPA overexpression is crucial to prostate cancer growth.
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Affiliation(s)
- Anjan K Saha
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Yashar S Niknafs
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Iyer
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Karthik Padmanabhan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Monica Palande
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Claire Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Brian Qian
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth Ward
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Tara Tang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott D Gitlin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Gilbert S Omenn
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Arul M Chinnaiyan
- Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - David M Markovitz
- Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA .,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA
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30
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Bagherian M, Kim RB, Jiang C, Sartor MA, Derksen H, Najarian K. Coupled matrix-matrix and coupled tensor-matrix completion methods for predicting drug-target interactions. Brief Bioinform 2020; 22:2161-2171. [PMID: 32186716 PMCID: PMC7986629 DOI: 10.1093/bib/bbaa025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/27/2020] [Accepted: 02/17/2020] [Indexed: 12/20/2022] Open
Abstract
Predicting the interactions between drugs and targets plays an important role in the process of new drug discovery, drug repurposing (also known as drug repositioning). There is a need to develop novel and efficient prediction approaches in order to avoid the costly and laborious process of determining drug–target interactions (DTIs) based on experiments alone. These computational prediction approaches should be capable of identifying the potential DTIs in a timely manner. Matrix factorization methods have been proven to be the most reliable group of methods. Here, we first propose a matrix factorization-based method termed ‘Coupled Matrix–Matrix Completion’ (CMMC). Next, in order to utilize more comprehensive information provided in different databases and incorporate multiple types of scores for drug–drug similarities and target–target relationship, we then extend CMMC to ‘Coupled Tensor–Matrix Completion’ (CTMC) by considering drug–drug and target–target similarity/interaction tensors. Results: Evaluation on two benchmark datasets, DrugBank and TTD, shows that CTMC outperforms the matrix-factorization-based methods: GRMF, \documentclass[12pt]{minimal}
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}{}$L_{2,1}$\end{document}-GRMF, NRLMF and NRLMF\documentclass[12pt]{minimal}
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}{}$\beta $\end{document}. Based on the evaluation, CMMC and CTMC outperform the above three methods in term of area under the curve, F1 score, sensitivity and specificity in a considerably shorter run time.
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Affiliation(s)
- Maryam Bagherian
- Corresponding author: Maryam Bagherian, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, USA.
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31
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Lee C, Wang K, Qin T, Sartor MA. Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing. Front Genet 2020; 11:199. [PMID: 32211031 PMCID: PMC7069355 DOI: 10.3389/fgene.2020.00199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Abstract
Large sets of genomic regions are generated by the initial analysis of various genome-wide sequencing data, such as ChIP-seq and ATAC-seq experiments. Gene set enrichment (GSE) methods are commonly employed to determine the pathways associated with them. Given the pathways and other gene sets (e.g., GO terms) of significance, it is of great interest to know the extent to which each is driven by binding near transcription start sites (TSS) or near enhancers. Currently, no tool performs such an analysis. Here, we present a method that addresses this question to complement GSE methods for genomic regions. Specifically, the new method tests whether the genomic regions in a gene set are significantly closer to a TSS (or to an enhancer) than expected by chance given the total list of genomic regions, using a non-parametric test. Combining the results from a GSE test with our novel method provides additional information regarding the mode of regulation of each pathway, and additional evidence that the pathway is truly enriched. We illustrate our new method with a large set of ENCODE ChIP-seq data, using the chipenrich Bioconductor package. The results show that our method is a powerful complementary approach to help researchers interpret large sets of genomic regions.
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Affiliation(s)
- Christopher Lee
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
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32
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Lee CT, Cavalcante RG, Lee C, Qin T, Patil S, Wang S, Tsai Z, Boyle AP, Sartor MA. Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. NAR Genom Bioinform 2020; 2:lqaa006. [PMID: 32051932 PMCID: PMC7003681 DOI: 10.1093/nargab/lqaa006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/12/2019] [Accepted: 01/30/2020] [Indexed: 12/13/2022] Open
Abstract
Gene set enrichment (GSE) testing enhances the biological interpretation of ChIP-seq data and other large sets of genomic regions. Our group has previously introduced two GSE methods for genomic regions: ChIP-Enrich for narrow regions and Broad-Enrich for broad regions. Here, we introduce Poly-Enrich, which has wider applicability, additional capabilities and models the number of peaks assigned to a gene using a generalized additive model with a negative binomial family to determine gene set enrichment, while adjusting for gene locus length. As opposed to ChIP-Enrich, Poly-Enrich works well even when nearly all genes have a peak, illustrated by using Poly-Enrich to characterize pathways and types of genic regions enriched with different families of repetitive elements. By comparing Poly-Enrich and ChIP-Enrich results with ENCODE ChIP-seq data, we found that the optimal test depends more on the pathway being regulated than on properties of the transcription factors. Using known transcription factor functions, we discovered clusters of related biological processes consistently better modeled with Poly-Enrich. This suggests that the regulation of certain processes may be modified by multiple binding events, better modeled by a count-based method. Our new hybrid method automatically uses the optimal method for each gene set, with correct FDR-adjustment.
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Affiliation(s)
- Christopher T Lee
- Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chee Lee
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Snehal Patil
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shuze Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zing T Y Tsai
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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33
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Núñez FJ, Mendez FM, Kadiyala P, Alghamri MS, Savelieff MG, Garcia-Fabiani MB, Haase S, Koschmann C, Calinescu AA, Kamran N, Saxena M, Patel R, Carney S, Guo MZ, Edwards M, Ljungman M, Qin T, Sartor MA, Tagett R, Venneti S, Brosnan-Cashman J, Meeker A, Gorbunova V, Zhao L, Kremer DM, Zhang L, Lyssiotis CA, Jones L, Herting CJ, Ross JL, Hambardzumyan D, Hervey-Jumper S, Figueroa ME, Lowenstein PR, Castro MG. IDH1-R132H acts as a tumor suppressor in glioma via epigenetic up-regulation of the DNA damage response. Sci Transl Med 2020; 11:11/479/eaaq1427. [PMID: 30760578 DOI: 10.1126/scitranslmed.aaq1427] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 08/08/2018] [Accepted: 12/28/2018] [Indexed: 01/01/2023]
Abstract
Patients with glioma whose tumors carry a mutation in isocitrate dehydrogenase 1 (IDH1R132H) are younger at diagnosis and live longer. IDH1 mutations co-occur with other molecular lesions, such as 1p/19q codeletion, inactivating mutations in the tumor suppressor protein 53 (TP53) gene, and loss-of-function mutations in alpha thalassemia/mental retardation syndrome X-linked gene (ATRX). All adult low-grade gliomas (LGGs) harboring ATRX loss also express the IDH1R132H mutation. The current molecular classification of LGGs is based, partly, on the distribution of these mutations. We developed a genetically engineered mouse model harboring IDH1R132H, TP53 and ATRX inactivating mutations, and activated NRAS G12V. Previously, we established that ATRX deficiency, in the context of wild-type IDH1, induces genomic instability, impairs nonhomologous end-joining DNA repair, and increases sensitivity to DNA-damaging therapies. In this study, using our mouse model and primary patient-derived glioma cultures with IDH1 mutations, we investigated the function of IDH1R132H in the context of TP53 and ATRX loss. We discovered that IDH1R132H expression in the genetic context of ATRX and TP53 gene inactivation (i) increases median survival in the absence of treatment, (ii) enhances DNA damage response (DDR) via epigenetic up-regulation of the ataxia-telangiectasia-mutated (ATM) signaling pathway, and (iii) elicits tumor radioresistance. Accordingly, pharmacological inhibition of ATM or checkpoint kinases 1 and 2, essential kinases in the DDR, restored the tumors' radiosensitivity. Translation of these findings to patients with IDH1132H glioma harboring TP53 and ATRX loss could improve the therapeutic efficacy of radiotherapy and, consequently, patient survival.
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Affiliation(s)
- Felipe J Núñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Flor M Mendez
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Padma Kadiyala
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mahmoud S Alghamri
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Masha G Savelieff
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria B Garcia-Fabiani
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Carl Koschmann
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Neha Kamran
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Meghna Saxena
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rohin Patel
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Stephen Carney
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marissa Z Guo
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marta Edwards
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Environmental Health Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rebecca Tagett
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sriram Venneti
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Alan Meeker
- Departments of Pathology, Oncology and Urology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lili Zhao
- Department of Biostatistics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Daniel M Kremer
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.,Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Costas A Lyssiotis
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lindsey Jones
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cameron J Herting
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Division of Molecular and Systems Pharmacology, Emory University, Atlanta, GA 30322, USA
| | - James L Ross
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Division of Cancer Biology, Emory University, Atlanta, GA 30322, USA
| | - Dolores Hambardzumyan
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shawn Hervey-Jumper
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria E Figueroa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136-1000, USA
| | - Pedro R Lowenstein
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA. .,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA. .,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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34
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Bagherian M, Sabeti E, Wang K, Sartor MA, Nikolovska-Coleska Z, Najarian K. Erratum to: Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. Brief Bioinform 2020; 22:606. [PMID: 32047893 PMCID: PMC7820856 DOI: 10.1093/bib/bbaa020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Bagherian M, Sabeti E, Wang K, Sartor MA, Nikolovska-Coleska Z, Najarian K. Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. Brief Bioinform 2020; 22:247-269. [PMID: 31950972 PMCID: PMC7820849 DOI: 10.1093/bib/bbz157] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 12/12/2022] Open
Abstract
The task of predicting the interactions between drugs and targets plays a key role in the process of drug discovery. There is a need to develop novel and efficient prediction approaches in order to avoid costly and laborious yet not-always-deterministic experiments to determine drug–target interactions (DTIs) by experiments alone. These approaches should be capable of identifying the potential DTIs in a timely manner. In this article, we describe the data required for the task of DTI prediction followed by a comprehensive catalog consisting of machine learning methods and databases, which have been proposed and utilized to predict DTIs. The advantages and disadvantages of each set of methods are also briefly discussed. Lastly, the challenges one may face in prediction of DTI using machine learning approaches are highlighted and we conclude by shedding some lights on important future research directions.
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Affiliation(s)
- Maryam Bagherian
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Elyas Sabeti
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kai Wang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maureen A Sartor
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Kayvan Najarian
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
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36
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Rocco SA, Koneva L, Middleton LYM, Thong T, Solanki S, Karram S, Nambunmee K, Harris C, Rozek LS, Sartor MA, Shah YM, Colacino JA. Cadmium Exposure Inhibits Branching Morphogenesis and Causes Alterations Consistent With HIF-1α Inhibition in Human Primary Breast Organoids. Toxicol Sci 2019; 164:592-602. [PMID: 29741670 DOI: 10.1093/toxsci/kfy112] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Developmental cadmium exposure in vivo disrupts mammary gland differentiation, while exposure of breast cell lines to cadmium causes invasion consistent with the epithelial-mesenchymal transition (EMT). The effects of cadmium on normal human breast stem cells have not been measured. Here, we quantified the effects of cadmium exposure on reduction mammoplasty patient-derived breast stem cell proliferation and differentiation. Using the mammosphere assay and organoid formation in 3D hydrogels, we tested 2 physiologically relevant doses of cadmium, 0.25 and 2.5 µM, and tested for molecular alterations using RNA-seq. We functionally validated our RNA-seq findings with a hypoxia-inducible factor (HIF)-1α activity reporter line and pharmaceutical inhibition of HIF-1α in organoid formation assays. 2.5 µM cadmium reduced primary mammosphere formation and branching structure organoid formation rates by 33% and 87%, respectively. Despite no changes in mammosphere formation, 0.25 µM cadmium inhibited branching organoid formation in hydrogels by 73%. RNA-seq revealed cadmium downregulated genes associated with extracellular matrix formation and EMT, while upregulating genes associated with metal response including metallothioneins and zinc transporters. In the RNA-seq data, cadmium downregulated HIF-1α target genes including LOXL2, ZEB1, and VIM. Cadmium significantly inhibited HIF-1α activity in a luciferase assay, and the HIF-1α inhibitor acriflavine ablated mammosphere and organoid formation. These findings show that cadmium, at doses relevant to human exposure, inhibited human mammary stem cell proliferation and differentiation, potentially through disruption of HIF-1α activity.
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Affiliation(s)
- Sabrina A Rocco
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Lada Koneva
- Department of Computational Medicine and Bioinformatics
| | - Lauren Y M Middleton
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Tasha Thong
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Sumeet Solanki
- Molecular and Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Sarah Karram
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Kowit Nambunmee
- Department of Occupational Health and Safety, Mae Fah Luong University, Chiang Rai, Thailand, 57100
| | - Craig Harris
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | | | - Yatrik M Shah
- Molecular and Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029.,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, 48109
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Capitano ML, Mor-Vaknin N, Saha AK, Cooper S, Legendre M, Guo H, Contreras-Galindo R, Kappes F, Sartor MA, Lee CT, Huang X, Markovitz DM, Broxmeyer HE. Secreted nuclear protein DEK regulates hematopoiesis through CXCR2 signaling. J Clin Invest 2019; 129:2555-2570. [PMID: 31107242 PMCID: PMC6546479 DOI: 10.1172/jci127460] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 01/15/2019] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Abstract
The nuclear protein DEK is an endogenous DNA-binding chromatin factor regulating hematopoiesis. DEK is one of only 2 known secreted nuclear chromatin factors, but whether and how extracellular DEK regulates hematopoiesis is not known. We demonstrated that extracellular DEK greatly enhanced ex vivo expansion of cytokine-stimulated human and mouse hematopoietic stem cells (HSCs) and regulated HSC and hematopoietic progenitor cell (HPC) numbers in vivo and in vitro as determined both phenotypically (by flow cytometry) and functionally (through transplantation and colony formation assays). Recombinant DEK increased long-term HSC numbers and decreased HPC numbers through a mechanism mediated by the CXC chemokine receptor CXCR2 and heparan sulfate proteoglycans (HSPGs) (as determined utilizing Cxcr2-/- mice, blocking CXCR2 antibodies, and 3 different HSPG inhibitors) that was associated with enhanced phosphorylation of ERK1/2, AKT, and p38 MAPK. To determine whether extracellular DEK required nuclear function to regulate hematopoiesis, we utilized 2 mutant forms of DEK: one that lacked its nuclear translocation signal and one that lacked DNA-binding ability. Both altered HSC and HPC numbers in vivo or in vitro, suggesting the nuclear function of DEK is not required. Thus, DEK acts as a hematopoietic cytokine, with the potential for clinical applicability.
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Affiliation(s)
- Maegan L. Capitano
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nirit Mor-Vaknin
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA
| | - Anjan K. Saha
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott Cooper
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Maureen Legendre
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA
| | - Haihong Guo
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Rafael Contreras-Galindo
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA
| | - Ferdinand Kappes
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, China
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher T. Lee
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Xinxin Huang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - David M. Markovitz
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA
| | - Hal E. Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Perera BPU, Tsai ZTY, Colwell ML, Jones TR, Goodrich JM, Wang K, Sartor MA, Faulk C, Dolinoy DC. Somatic expression of piRNA and associated machinery in the mouse identifies short, tissue-specific piRNA. Epigenetics 2019; 14:504-521. [PMID: 30955436 DOI: 10.1080/15592294.2019.1600389] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are small non-coding RNAs that associate with PIWI proteins for transposon silencing via DNA methylation and are highly expressed and extensively studied in the germline. Mature germline piRNAs typically consist of 24-32 nucleotides, with a strong preference for a 5' uridine signature, an adenosine signature at position 10, and a 2'-O-methylation signature at the 3' end. piRNA presence in somatic tissues, however, is not well characterized and requires further systematic evaluation. In the current study, we identified piRNAs and associated machinery from mouse somatic tissues representing the three germ layers. piRNA specificity was improved by combining small RNA size selection, sodium periodate treatment enrichment for piRNA over other small RNA, and small RNA next-generation sequencing. We identify PIWIL1, PIWIL2, and PIWIL4 expression in brain, liver, kidney, and heart. Of note, somatic piRNAs are shorter in length and tissue-specific, with increased occurrence of unique piRNAs in hippocampus and liver, compared to the germline. Hippocampus contains 5,494 piRNA-like peaks, the highest expression among all tested somatic tissues, followed by cortex (1,963), kidney (580), and liver (406). The study identifies 26 piRNA sequence species and 40 piRNA locations exclusive to all examined somatic tissues. Although piRNA expression has long been considered exclusive to the germline, our results support that piRNAs are expressed in several somatic tissues that may influence piRNA functions in the soma. Once confirmed, the PIWI/piRNA system may serve as a potential tool for future research in epigenome editing to improve human health by manipulating DNA methylation.
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Affiliation(s)
- Bambarendage P U Perera
- a Department of Environmental Health Sciences, School of Public Health , University of Michigan , Ann Arbor , MI , USA
| | - Zing Tsung-Yeh Tsai
- b Department of Computational Medicine and Bioinformatics , University of Michigan Medical School , Ann Arbor , MI , USA
| | - Mathia L Colwell
- c Department of Animal Science , University of Minnesota , St. Paul , MN , USA
| | - Tamara R Jones
- a Department of Environmental Health Sciences, School of Public Health , University of Michigan , Ann Arbor , MI , USA
| | - Jaclyn M Goodrich
- a Department of Environmental Health Sciences, School of Public Health , University of Michigan , Ann Arbor , MI , USA
| | - Kai Wang
- b Department of Computational Medicine and Bioinformatics , University of Michigan Medical School , Ann Arbor , MI , USA
| | - Maureen A Sartor
- b Department of Computational Medicine and Bioinformatics , University of Michigan Medical School , Ann Arbor , MI , USA.,d Department of Biostatistics, School of Public Health , University of Michigan , Ann Arbor , MI , USA
| | - Christopher Faulk
- c Department of Animal Science , University of Minnesota , St. Paul , MN , USA
| | - Dana C Dolinoy
- a Department of Environmental Health Sciences, School of Public Health , University of Michigan , Ann Arbor , MI , USA.,e Department of Nutritional Sciences, School of Public Health , University of Michigan , Ann Arbor , MI , USA
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39
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Rozek LS, Virani S, Bellile EL, Taylor JMG, Sartor MA, Zarins KR, Virani A, Cote C, Worden FP, Mark MEP, McLean SA, Duffy SA, Yoo GH, Saba NF, Shin DM, Kucuk O, Wolf GT. Soy Isoflavone Supplementation Increases Long Interspersed Nucleotide Element-1 (LINE-1) Methylation in Head and Neck Squamous Cell Carcinoma. Nutr Cancer 2019; 71:772-780. [PMID: 30862188 PMCID: PMC6513708 DOI: 10.1080/01635581.2019.1577981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 08/08/2018] [Revised: 11/13/2018] [Accepted: 12/26/2018] [Indexed: 12/20/2022]
Abstract
AIM Soy isoflavones have been suggested as epigenetic modulating agents with effects that could be important in carcinogenesis. Hypomethylation of LINE-1 has been associated with head and neck squamous cell carcinoma (HNSCC) development from oral premalignant lesions and with poor prognosis. To determine if neoadjuvant soy isoflavone supplementation could modulate LINE-1 methylation in HNSCC, we undertook a clinical trial. METHODS Thirty-nine patients received 2-3 weeks of soy isoflavone supplements (300 mg/day) orally prior to surgery. Methylation of LINE-1, and 6 other genes was measured by pyrosequencing in biopsy, resection, and whole blood (WB) specimens. Changes in methylation were tested using paired t tests and ANOVA. Median follow up was 45 months. RESULTS LINE-1 methylation increased significantly after soy isoflavone (P < 0.005). Amount of change correlated positively with days of isoflavone taken (P = 0.04). Similar changes were not seen in corresponding WB samples. No significant changes in tumor or blood methylation levels were seen in the other candidate genes. CONCLUSION This is the first demonstration of in vivo increases in tissue-specific global methylation associated with soy isoflavone intake in patients with HNSCC. Prior associations of LINE-1 hypomethylation with genetic instability, carcinogenesis, and prognosis suggest that soy isoflavones maybe potential chemopreventive agents in HNSCC.
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Affiliation(s)
- Laura S Rozek
- a University of Michigan , Ann Arbor , Michigan, USA
| | - Shama Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - A Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | - C Cote
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - George H Yoo
- c Karmanos Cancer Institute , Wayne State University , Detroit , Michigan 48201, USA
| | - Nabil F Saba
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Dong M Shin
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Omer Kucuk
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
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40
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Wang T, Pehrsson EC, Purushotham D, Li D, Zhuo X, Zhang B, Lawson HA, Province MA, Krapp C, Lan Y, Coarfa C, Katz TA, Tang WY, Wang Z, Biswal S, Rajagopalan S, Colacino JA, Tsai ZTY, Sartor MA, Neier K, Dolinoy DC, Pinto J, Hamanaka RB, Mutlu GM, Patisaul HB, Aylor DL, Crawford GE, Wiltshire T, Chadwick LH, Duncan CG, Garton AE, McAllister KA, Bartolomei MS, Walker CL, Tyson FL. The NIEHS TaRGET II Consortium and environmental epigenomics. Nat Biotechnol 2018; 36:225-227. [PMID: 29509741 DOI: 10.1038/nbt.4099] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Deepak Purushotham
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xiaoyu Zhuo
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bo Zhang
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael A Province
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher Krapp
- Epigenetics Institute, Center for Excellence in Environmental Toxicology, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yemin Lan
- Epigenetics Institute, Center for Excellence in Environmental Toxicology, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Tiffany A Katz
- Center for Precision Environmental Health, Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Wan Yee Tang
- Department of Environmental Health Sciences, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Zhibin Wang
- Department of Environmental Health Sciences, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Shyam Biswal
- Department of Environmental Health Sciences, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Sanjay Rajagopalan
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Zing Tsung-Yeh Tsai
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Kari Neier
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jayant Pinto
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Robert B Hamanaka
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Gokhan M Mutlu
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Heather B Patisaul
- Department of Biological Sciences, Center for Human Health and the Environment, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - David L Aylor
- Department of Biological Sciences, Center for Human Health and the Environment, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Gregory E Crawford
- Center for Genomic & Computational Biology, Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Tim Wiltshire
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Lisa H Chadwick
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Christopher G Duncan
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Amanda E Garton
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Kimberly A McAllister
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | | | - Marisa S Bartolomei
- Epigenetics Institute, Center for Excellence in Environmental Toxicology, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cheryl L Walker
- Center for Precision Environmental Health, Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Frederick L Tyson
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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41
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Kochmanski J, Marchlewicz EH, Cavalcante RG, Sartor MA, Dolinoy DC. Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood. Epigenetics 2018; 13:779-792. [PMID: 30079798 PMCID: PMC6224215 DOI: 10.1080/15592294.2018.1507198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 04/11/2018] [Revised: 07/13/2018] [Accepted: 07/25/2018] [Indexed: 01/10/2023] Open
Abstract
DNA methylation at cytosine-phosphate-guanine (CpG) dinucleotides changes as a function of age in humans and animal models, a process that may contribute to chronic disease development. Recent studies have investigated the role of an oxidized form of DNA methylation - 5-hydroxymethylcytosine (5hmC) - in the epigenome, but its contribution to age-related DNA methylation remains unclear. We tested the hypothesis that 5hmC changes with age, but in a direction opposite to 5-methylcytosine (5mC), potentially playing a distinct role in aging. To characterize epigenetic aging, genome-wide 5mC and 5hmC were measured in longitudinal blood samples (2, 4, and 10 months of age) from isogenic mice using two sequencing methods - enhanced reduced representation bisulfite sequencing and hydroxymethylated DNA immunoprecipitation sequencing. Examining the epigenome by age, we identified 28,196 unique differentially methylated CpGs (DMCs) and 8,613 differentially hydroxymethylated regions (DHMRs). Mouse blood showed a general pattern of epigenome-wide hypermethylation and hypo-hydroxymethylation with age. Comparing age-related DMCs and DHMRs, 1,854 annotated genes showed both differential 5mC and 5hmC, including one gene - Nfic - at five CpGs in the same 250 bp chromosomal region. At this region, 5mC and 5hmC levels both decreased with age. Reflecting these age-related epigenetic changes, Nfic RNA expression in blood decreased with age, suggesting that age-related regulation of this gene may be driven by 5hmC, not canonical DNA methylation. Combined, our genome-wide results show age-related differential 5mC and 5hmC, as well as some evidence that changes in 5hmC may drive age-related DNA methylation and gene expression.
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Affiliation(s)
- Joseph Kochmanski
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth H. Marchlewicz
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Raymond G. Cavalcante
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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42
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Qin T, Zhang Y, Zarins KR, Jones TR, Virani S, Peterson LA, McHugh JB, Chepeha D, Wolf GT, Rozek LS, Sartor MA. Expressed HNSCC variants by HPV-status in a well-characterized Michigan cohort. Sci Rep 2018; 8:11458. [PMID: 30061624 PMCID: PMC6065423 DOI: 10.1038/s41598-018-29599-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 03/12/2018] [Accepted: 07/12/2018] [Indexed: 12/16/2022] Open
Abstract
While whole-exome DNA sequencing is the most common technology to study genetic variants in tumors in known exonic regions, RNA-seq is cheaper, covers most of the same exonic regions, and is often more readily available. In this study, we show the utility of mRNA-seq-based variant analysis combined with targeted gene sequencing performed on both tumor and matched blood as an alternative when exome data is unavailable. We use the approach to study expressed variant profiles in the well-characterized University of Michigan (UM) head and neck squamous carcinoma (HNSCC) cohort (n = 36). We found that 441 out of 455 (~97%) identified cancer genes with an expressed variant in the UM cohort also harbor a somatic mutation in TCGA. Fourteen (39%) patients had a germline variant in a cancer-related Fanconi Anemia (FA) pathway gene. HPV-positive patients had more nonsynonymous, rare, and damaging (NRD) variants in those genes than HPV-negative patients. Moreover, the known mutational signatures for DNA mismatch repair and APOBEC activation were attributive to the UM expressed NRD variants, and the APOBEC signature contribution differed by HPV status. Our results provide additional support to certain TCGA findings and suggest an association of expressed variants in FA/DNA repair pathways with HPV-associated HNSCC tumorigenesis. These results will benefit future studies on this and other cohorts by providing the genetic variants of key cancer-related genes.
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Affiliation(s)
- Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Yanxiao Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Shama Virani
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Lisa A Peterson
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jonathan B McHugh
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Douglas Chepeha
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Otolaryngology, University of Toronto, Toronto, Ontario, Canada
| | - Gregory T Wolf
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA.
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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43
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Kochmanski JJ, Marchlewicz EH, Cavalcante RG, Perera BPU, Sartor MA, Dolinoy DC. Longitudinal Effects of Developmental Bisphenol A Exposure on Epigenome-Wide DNA Hydroxymethylation at Imprinted Loci in Mouse Blood. Environ Health Perspect 2018; 126:077006. [PMID: 30044229 PMCID: PMC6108846 DOI: 10.1289/ehp3441] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Epigenetic machinery plays an important role in genomic imprinting, a developmental process that establishes parent-of-origin-specific monoallelic gene expression. Although a number of studies have investigated the role of 5-methylcytosine in imprinting control, the contribution of 5-hydroxymethylcytosine (5-hmC) to this epigenetic phenomenon remains unclear. OBJECTIVES Using matched mouse blood samples (from mice at 2, 4, and 10 months of age), our objective was to examine the effects of perinatal bisphenol A (BPA) exposure (50 μg/kg diet) on longitudinal 5-hmC patterns at imprinted regions. We also aimed to test the hypothesis that 5-hmC would show defined patterns at imprinted genes that persist across the life course. METHODS Genome-wide 5-hmC levels were measured using hydroxymethylated DNA immunoprecipitation sequencing (HMeDIP-seq). Modeling of differential hydroxymethylation by BPA exposure was performed using a pipeline of bioinformatics tools, including the csaw R package. RESULTS Based on BPA exposure, we identified 5,950 differentially hydroxymethylated regions (DHMRs), including 12 DHMRs that were annotated to murine imprinted genes—Gnas, Grb10, Plagl1, Klf14, Pde10a, Snrpn, Airn, Cmah, Ppp1r9a, Kcnq1, Phactr2, and Pde4d. When visualized, these imprinted gene DHMRs showed clear, consistent patterns of differential 5-hmC by developmental BPA exposure that persisted throughout adulthood. CONCLUSIONS These data show long-term establishment of 5-hmC marks at imprinted loci during development. Further, the effect of perinatal BPA exposure on 5-hmC at specific imprinted loci indicates that developmental exposure to environmental toxicants may alter long-term imprinted gene regulation via an epigenetic mechanism. https://doi.org/10.1289/EHP3441.
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Affiliation(s)
- Joseph J Kochmanski
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Elizabeth H Marchlewicz
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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44
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Colacino JA, Azizi E, Brooks MD, Harouaka R, Fouladdel S, McDermott SP, Lee M, Hill D, Madden J, Boerner J, Cote ML, Sartor MA, Rozek LS, Wicha MS. Heterogeneity of Human Breast Stem and Progenitor Cells as Revealed by Transcriptional Profiling. Stem Cell Reports 2018; 10:1596-1609. [PMID: 29606612 PMCID: PMC5995162 DOI: 10.1016/j.stemcr.2018.03.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [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: 03/13/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 01/10/2023] Open
Abstract
During development, the mammary gland undergoes extensive remodeling driven by stem cells. Breast cancers are also hierarchically organized and driven by cancer stem cells characterized by CD44+CD24low/− or aldehyde dehydrogenase (ALDH) expression. These markers identify mesenchymal and epithelial populations both capable of tumor initiation. Less is known about these populations in non-cancerous mammary glands. From RNA sequencing, ALDH+ and ALDH−CD44+CD24− human mammary cells have epithelial-like and mesenchymal-like characteristics, respectively, with some co-expressing ALDH+ and CD44+CD24− by flow cytometry. At the single-cell level, these cells have the greatest mammosphere-forming capacity and express high levels of stemness and epithelial-to-mesenchymal transition-associated genes including ID1, SOX2, TWIST1, and ZEB2. We further identify single ALDH+ cells with a hybrid epithelial/mesenchymal phenotype that express genes associated with aggressive triple-negative breast cancers. These results highlight single-cell analyses to characterize tissue heterogeneity, even in marker-enriched populations, and identify genes and pathways that define this heterogeneity. Isolation and RNA-seq of ALDH+ and CD44+CD24− breast cells Unlike in cancer, there is substantial overlap in ALDH+ and CD44+CD24− populations Single-cell analysis of ALDH+ cells identifies unexpected subpopulation structure Hybrid epithelial/mesenchymal ALDH+ cells have a cancer-like expression signature
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Affiliation(s)
- Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA.
| | - Ebrahim Azizi
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael D Brooks
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ramdane Harouaka
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shamileh Fouladdel
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sean P McDermott
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Lee
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Julie Madden
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Julie Boerner
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Michele L Cote
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Population Sciences and Health Disparities Program, Karmanos Cancer Institute, Detroit, MI, USA
| | - Maureen A Sartor
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Max S Wicha
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
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45
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Abstract
Motivation Analysis of next-generation sequencing data often results in a list of genomic regions. These may include differentially methylated CpGs/regions, transcription factor binding sites, interacting chromatin regions, or GWAS-associated SNPs, among others. A common analysis step is to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.). Existing tools are limited by a lack of annotation sources and flexible options, the time it takes to annotate regions, an artificial one-to-one region-to-annotation mapping, a lack of visualization options to easily summarize data, or some combination thereof. Results We developed the annotatr Bioconductor package to flexibly and quickly summarize and plot annotations of genomic regions. The annotatr package reports all intersections of regions and annotations, giving a better understanding of the genomic context of the regions. A variety of graphics functions are implemented to easily plot numerical or categorical data associated with the regions across the annotations, and across annotation intersections, providing insight into how characteristics of the regions differ across the annotations. We demonstrate that annotatr is up to 27× faster than comparable R packages. Overall, annotatr enables a richer biological interpretation of experiments. Availability and Implementation http://bioconductor.org/packages/annotatr/ and https://github.com/rcavalcante/annotatr. Contact rcavalca@umich.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics.,Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
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46
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Cavalcante RG, Patil S, Park Y, Rozek LS, Sartor MA. Integrating DNA Methylation and Hydroxymethylation Data with the Mint Pipeline. Cancer Res 2017; 77:e27-e30. [PMID: 29092933 DOI: 10.1158/0008-5472.can-17-0330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/06/2017] [Accepted: 07/12/2017] [Indexed: 11/16/2022]
Abstract
DNA methylation (5mC) plays important roles in mammalian development, oncogenesis, treatment response, and responses to the environment. DNA hydroxymethylation (5hmC) is also an informative epigenetic mark with distinct roles in regulation and cancer. Gold-standard, widely used technologies (bisulfite conversion, followed by deep sequencing) cannot distinguish between 5mC and 5hmC. Therefore, additional experiments are required to differentiate the two marks, and in silico methods are needed to analyze, integrate, and interpret these data. We developed the Methylation INTegration (mint) pipeline to support the comprehensive analysis of bisulfite conversion and immunoprecipitation-based methylation and hydroxymethylation assays, with additional steps toward integration, visualization, and interpretation. The pipeline is available as both a command line and a Galaxy graphical user interface tool. Both implementations require minimal configuration while remaining flexible to experiment specific needs. Cancer Res; 77(21); e27-30. ©2017 AACR.
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Affiliation(s)
- Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Snehal Patil
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Yongseok Park
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.
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47
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Koneva LA, Zhang Y, Virani S, Hall PB, McHugh JB, Chepeha DB, Wolf GT, Carey TE, Rozek LS, Sartor MA. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res 2017; 16:90-102. [PMID: 28928286 DOI: 10.1158/1541-7786.mcr-17-0153] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/12/2017] [Accepted: 09/15/2017] [Indexed: 12/12/2022]
Abstract
The incidence of human papillomavirus (HPV)-related oropharynx cancer has steadily increased over the past two decades and now represents a majority of oropharyngeal cancer cases. Integration of the HPV genome into the host genome is a common event during carcinogenesis that has clinically relevant effects if the viral early genes are transcribed. Understanding the impact of HPV integration on clinical outcomes of head and neck squamous cell carcinoma (HNSCC) is critical for implementing deescalated treatment approaches for HPV+ HNSCC patients. RNA sequencing (RNA-seq) data from HNSCC tumors (n = 84) were used to identify and characterize expressed integration events, which were overrepresented near known head and neck, lung, and urogenital cancer genes. Five genes were recurrent, including CD274 (PD-L1) A significant number of genes detected to have integration events were found to interact with Tp63, ETS, and/or FOX1A. Patients with no detected integration had better survival than integration-positive and HPV- patients. Furthermore, integration-negative tumors were characterized by strongly heightened signatures for immune cells, including CD4+, CD3+, regulatory, CD8+ T cells, NK cells, and B cells, compared with integration-positive tumors. Finally, genes with elevated expression in integration-negative specimens were strongly enriched with immune-related gene ontology terms, while upregulated genes in integration-positive tumors were enriched for keratinization, RNA metabolism, and translation.Implications: These findings demonstrate the clinical relevancy of expressed HPV integration, which is characterized by a change in immune response and/or aberrant expression of the integration-harboring cancer-related genes, and suggest strong natural selection for tumor cells with expressed integration events in key carcinogenic genes. Mol Cancer Res; 16(1); 90-102. ©2017 AACR.
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Affiliation(s)
- Lada A Koneva
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Yanxiao Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Shama Virani
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan
| | - Pelle B Hall
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Jonathan B McHugh
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Douglas B Chepeha
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Gregory T Wolf
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Thomas E Carey
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan. .,Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.
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48
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Koneva LA, Vyas AK, McEachin RC, Puttabyatappa M, H-S W, Sartor MA, Padmanabhan V. Developmental programming: Interaction between prenatal BPA and postnatal overfeeding on cardiac tissue gene expression in female sheep. Environ Mol Mutagen 2017; 58:4-18. [PMID: 28079927 PMCID: PMC5730970 DOI: 10.1002/em.22071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 05/23/2023]
Abstract
Epidemiologic studies and studies in rodents point to potential risks from developmental exposure to BPA on cardiometabolic diseases. Furthermore, it is becoming increasingly evident that the manifestation and severity of adverse outcomes is the result of interaction between developmental insults and the prevailing environment. Consistent with this premise, recent studies in sheep found prenatal BPA treatment prevented the adverse effects of postnatal obesity in inducing hypertension. The gene networks underlying these complex interactions are not known. mRNA-seq of myocardium was performed on four groups of four female sheep to assess the effects of prenatal BPA exposure, postnatal overfeeding and their interaction on gene transcription, pathway perturbations and functional effects. The effects of prenatal exposure to BPA, postnatal overfeeding, and prenatal BPA with postnatal overfeeding all resulted in transcriptional changes (85-141 significant differentially expressed genes). Although the effects of prenatal BPA and postnatal overfeeding did not involve dysregulation of many of the same genes, they affected a remarkably similar set of biological pathways. Furthermore, an additive or synergistic effect was not found in the combined treatment group, but rather prenatal BPA treatment led to a partial reversal of the effects of overfeeding alone. Many genes previously known to be affected by BPA and involved in obesity, hypertension, or heart disease were altered following these treatments, and AP-1, EGR1, and EGFR were key hubs affected by BPA and/or overfeeding. Environ. Mol. Mutagen. 58:4-18, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- LA Koneva
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI
| | - AK Vyas
- Department of Pediatrics, Texas Tech Health Sciences Permian Basin, Odessa, TX
| | - RC McEachin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI
| | - M Puttabyatappa
- Department of Pediatrics, University of Michigan, Ann Arbor MI
| | - Wang H-S
- Department of Environmental Health, University of Cincinnati, Cincinnati OH
- Department of Pharmacology and Cell Biophysics, University of Cincinnati, Cincinnati OH
| | - MA Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI
| | - V Padmanabhan
- Department of Pediatrics, University of Michigan, Ann Arbor MI
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49
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Anderson OS, Kim JH, Peterson KE, Sanchez BN, Sant KE, Sartor MA, Weinhouse C, Dolinoy DC. Novel Epigenetic Biomarkers Mediating Bisphenol A Exposure and Metabolic Phenotypes in Female Mice. Endocrinology 2017; 158:31-40. [PMID: 27824486 PMCID: PMC5412976 DOI: 10.1210/en.2016-1441] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/03/2016] [Indexed: 12/29/2022]
Abstract
There is compelling evidence that epigenetic modifications link developmental environmental insults to adult disease susceptibility. Animal studies have associated perinatal bisphenol A (BPA) exposure to altered DNA methylation, but these studies are often limited to candidate gene and global non-loci-specific approaches. By using an epigenome-wide discovery platform, we elucidated epigenetic alterations in liver tissue from adult mice offspring (10 months) following perinatal BPA exposure at human physiologically relevant doses (50-ng, 50-μg, and 50-mg BPA/kg diet). Biological pathway analysis identified an enrichment of significant differentially methylated regions in metabolic pathways among females. Furthermore, through the use of top enriched biological pathways, 4 candidate genes were chosen to assess DNA methylation as a mediating factor linking the association of perinatal BPA exposure to metabolic phenotypes previously observed in female offspring. DNA methylation status at Janus kinase-2 (Jak-2), retinoid X receptor (Rxr), regulatory factor x-associated protein (Rfxap), and transmembrane protein 238 (Tmem238) was used within a mediational regression analysis. DNA methylation in all four of the candidate genes was identified as a mediator in the mechanistic pathway of developmental BPA exposure and female-specific energy expenditure, body weight, and body fat phenotypes. Data generated from this study are crucial for deciphering the mechanistic role of epigenetics in the pathogenesis of chronic disease and the development of epigenetic-based prevention and therapeutic strategies for complex human disease.
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Affiliation(s)
- Olivia S. Anderson
- Department of Environmental Health Sciences,
- Department of Nutritional Sciences,
| | - Jung H. Kim
- Department of Environmental Health Sciences,
| | | | | | | | - Maureen A. Sartor
- Department of Biostatistics, and
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, Michigan 48109
| | | | - Dana C. Dolinoy
- Department of Environmental Health Sciences,
- Department of Nutritional Sciences,
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50
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Koneva LA, Vyas AK, McEachin RC, Puttabyatappa M, Wang HS, Sartor MA, Padmanabhan V. Developmental programming: Interaction between prenatal BPA and postnatal overfeeding on cardiac tissue gene expression in female sheep. Environ Mol Mutagen 2017; 58:4-18. [PMID: 28079927 DOI: 10.1002/em] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 05/23/2023]
Abstract
Epidemiologic studies and studies in rodents point to potential risks from developmental exposure to BPA on cardiometabolic diseases. Furthermore, it is becoming increasingly evident that the manifestation and severity of adverse outcomes is the result of interaction between developmental insults and the prevailing environment. Consistent with this premise, recent studies in sheep found prenatal BPA treatment prevented the adverse effects of postnatal obesity in inducing hypertension. The gene networks underlying these complex interactions are not known. mRNA-seq of myocardium was performed on four groups of four female sheep to assess the effects of prenatal BPA exposure, postnatal overfeeding and their interaction on gene transcription, pathway perturbations and functional effects. The effects of prenatal exposure to BPA, postnatal overfeeding, and prenatal BPA with postnatal overfeeding all resulted in transcriptional changes (85-141 significant differentially expressed genes). Although the effects of prenatal BPA and postnatal overfeeding did not involve dysregulation of many of the same genes, they affected a remarkably similar set of biological pathways. Furthermore, an additive or synergistic effect was not found in the combined treatment group, but rather prenatal BPA treatment led to a partial reversal of the effects of overfeeding alone. Many genes previously known to be affected by BPA and involved in obesity, hypertension, or heart disease were altered following these treatments, and AP-1, EGR1, and EGFR were key hubs affected by BPA and/or overfeeding. Environ. Mol. Mutagen. 58:4-18, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- L A Koneva
- Departments of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - A K Vyas
- Department of Pediatrics, Texas Tech Health Sciences Permian Basin, Odessa, Texas
| | - R C McEachin
- Departments of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - M Puttabyatappa
- Departments of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - H-S Wang
- Departments of Environmental Health, University of Cincinnati, Cincinnati, Ohio
- Departments of Pharmacology and Cell Biophysics, University of Cincinnati, Cincinnati, Ohio
| | - M A Sartor
- Departments of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - V Padmanabhan
- Departments of Pediatrics, University of Michigan, Ann Arbor, Michigan
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