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Baker BH, Zhang S, Simon JM, McLarnan SM, Chung WK, Pearson BL. Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders. Front Neurosci 2023; 17:1106573. [PMID: 37599994 PMCID: PMC10435087 DOI: 10.3389/fnins.2023.1106573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction De novo mutations contribute to a large proportion of sporadic psychiatric and developmental disorders, yet the potential role of environmental carcinogens as drivers of causal de novo mutations in neurodevelopmental disorders is poorly studied. Methods To explore environmental mutation vulnerability of disease-associated gene sets, we analyzed publicly available whole genome sequencing datasets of mutations in human induced pluripotent stem cell clonal lines exposed to 12 classes of environmental carcinogens, and human lung cancers from individuals living in highly polluted regions. We compared observed rates of exposure-induced mutations in disease-related gene sets with the expected rates of mutations based on control genes randomly sampled from the genome using exact binomial tests. To explore the role of sequence characteristics in mutation vulnerability, we modeled the effects of sequence length, gene expression, and percent GC content on mutation rates of entire genes and gene coding sequences using multivariate Quasi-Poisson regressions. Results We demonstrate that several mutagens, including radiation and polycyclic aromatic hydrocarbons, disproportionately mutate genes related to neurodevelopmental disorders including autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder. Other disease genes including amyotrophic lateral sclerosis, Alzheimer's disease, congenital heart disease, orofacial clefts, and coronary artery disease were generally not mutated more than expected. Longer sequence length was more strongly associated with elevated mutations in entire genes compared with mutations in coding sequences. Increased expression was associated with decreased coding sequence mutation rate, but not with the mutability of entire genes. Increased GC content was associated with increased coding sequence mutation rates but decreased mutation rates in entire genes. Discussion Our findings support the possibility that neurodevelopmental disorder genetic etiology is partially driven by a contribution of environment-induced germ line and somatic mutations.
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Affiliation(s)
- Brennan H. Baker
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shaoyi Zhang
- Master of Public Health Program, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeremy M. Simon
- Department of Genetics and Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah M. McLarnan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Brandon L. Pearson
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
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Tang L, Li W, Xu H, Zheng X, Qiu S, He W, Wei Q, Ai J, Yang L, Liu J. Mutator-Derived lncRNA Landscape: A Novel Insight Into the Genomic Instability of Prostate Cancer. Front Oncol 2022; 12:876531. [PMID: 35860569 PMCID: PMC9291324 DOI: 10.3389/fonc.2022.876531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Increasing evidence has emerged to reveal the correlation between genomic instability and long non-coding RNAs (lncRNAs). The genomic instability-derived lncRNA landscape of prostate cancer (PCa) and its critical clinical implications remain to be understood. Methods Patients diagnosed with PCa were recruited from The Cancer Genome Atlas (TCGA) program. Genomic instability-associated lncRNAs were identified by a mutator hypothesis-originated calculative approach. A signature (GILncSig) was derived from genomic instability-associated lncRNAs to classify PCa patients into high-risk and low-risk groups. The biochemical recurrence (BCR) model of a genomic instability-derived lncRNA signature (GILncSig) was established by Cox regression and stratified analysis in the train set. Then its prognostic value and association with clinical features were verified by Kaplan–Meier (K-M) analysis and receiver operating characteristic (ROC) curve in the test set and the total patient set. The regulatory network of transcription factors (TFs) and lncRNAs was established to evaluate TF–lncRNA interactions. Results A total of 95 genomic instability-associated lncRNAs of PCa were identified. We constructed the GILncSig based on 10 lncRNAs with independent prognostic value. GILncSig separated patients into the high-risk (n = 121) group and the low-risk (n = 121) group in the train set. Patients with high GILncSig score suffered from more frequent BCR than those with low GILncSig score. The results were further validated in the test set, the whole TCGA cohort, and different subgroups stratified by age and Gleason score (GS). A high GILncSig risk score was significantly associated with a high mutation burden and a low critical gene expression (PTEN and CDK12) in PCa. The predictive performance of our BCR model based on GILncSig outperformed other existing BCR models of PCa based on lncRNAs. The GILncSig also showed a remarkable ability to predict BCR in the subgroup of patients with TP53 mutation or wild type. Transcription factors, such as FOXA1, JUND, and SRF, were found to participate in the regulation of lncRNAs with prognostic value. Conclusion In summary, we developed a prognostic signature of BCR based on genomic instability-associated lncRNAs for PCa, which may provide new insights into the epigenetic mechanism of BCR.
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Affiliation(s)
- Liansha Tang
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- West China Medical School of Sichuan University, Chengdu, China
| | - Wanjiang Li
- Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Hang Xu
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
- Institute of System Genetics, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaonan Zheng
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
- Institute of System Genetics, West China Hospital of Sichuan University, Chengdu, China
| | - Shi Qiu
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Wenbo He
- West China Medical School of Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Jianzhong Ai
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Lu Yang
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Lu Yang, ; Jiyan Liu,
| | - Jiyan Liu
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Lu Yang, ; Jiyan Liu,
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Gafurov A, Brejová B, Medvedev P. OUP accepted manuscript. Bioinformatics 2022; 38:i203-i211. [PMID: 35758770 PMCID: PMC9235476 DOI: 10.1093/bioinformatics/btac255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Motivation Genome annotations are a common way to represent genomic features such as genes, regulatory elements or epigenetic modifications. The amount of overlap between two annotations is often used to ascertain if there is an underlying biological connection between them. In order to distinguish between true biological association and overlap by pure chance, a robust measure of significance is required. One common way to do this is to determine if the number of intervals in the reference annotation that intersect the query annotation is statistically significant. However, currently employed statistical frameworks are often either inefficient or inaccurate when computing P-values on the scale of the whole human genome. Results We show that finding the P-values under the typically used ‘gold’ null hypothesis is NP-hard. This motivates us to reformulate the null hypothesis using Markov chains. To be able to measure the fidelity of our Markovian null hypothesis, we develop a fast direct sampling algorithm to estimate the P-value under the gold null hypothesis. We then present an open-source software tool MCDP that computes the P-values under the Markovian null hypothesis in O(m2+n) time and O(m) memory, where m and n are the numbers of intervals in the reference and query annotations, respectively. Notably, MCDP runtime and memory usage are independent from the genome length, allowing it to outperform previous approaches in runtime and memory usage by orders of magnitude on human genome annotations, while maintaining the same level of accuracy. Availability and implementation The software is available at https://github.com/fmfi-compbio/mc-overlaps. All data for reproducibility are available at https://github.com/fmfi-compbio/mc-overlaps-reproducibility. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Broňa Brejová
- Department of Computer Science, Comenius University, Bratislava 84248, Slovakia
| | - Paul Medvedev
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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4
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Devailly G, Joshi A. Comprehensive analysis of epigenetic signatures of human transcription control. Mol Omics 2021; 17:692-705. [PMID: 34291238 DOI: 10.1039/d0mo00130a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Advances in sequencing technologies have enabled exploration of epigenetic and transcriptional profiles at a genome-wide level. The epigenetic and transcriptional landscapes are now available in hundreds of mammalian cell and tissue contexts. Many studies have performed multi-omics analyses using these datasets to enhance our understanding of relationships between epigenetic modifications and transcription regulation. Nevertheless, most studies so far have focused on the promoters/enhancers and transcription start sites, and other features of transcription control including exons, introns and transcription termination remain underexplored. We investigated the interplay between epigenetic modifications and diverse transcription features using the data generated by the Roadmap Epigenomics project. A comprehensive analysis of histone modifications, DNA methylation, and RNA-seq data of thirty-three human cell lines and tissue types allowed us to confirm the generality of previously described relationships, as well as to generate new hypotheses about the interplay between epigenetic modifications and transcription features. Importantly, our analysis included previously under-explored features of transcription control, namely, transcription termination sites, exon-intron boundaries, and the exon inclusion ratio. We have made the analyses freely available to the scientific community at joshiapps.cbu.uib.no/perepigenomics_app/ for easy exploration, validation and hypothesis generation.
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Affiliation(s)
- Guillaume Devailly
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France.
| | - Anagha Joshi
- Computational Biology Unit, Department of Clinical Science, University of Bergen, 5021, Bergen, Norway.
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Mirhashemi ME, Shah RV, Kitchen RR, Rong J, Spahillari A, Pico AR, Vitseva O, Levy D, Demarco D, Shah S, Iafrati MD, Larson MG, Tanriverdi K, Freedman JE. The Dynamic Platelet Transcriptome in Obesity and Weight Loss. Arterioscler Thromb Vasc Biol 2021; 41:854-864. [PMID: 33297754 PMCID: PMC8105277 DOI: 10.1161/atvbaha.120.315186] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Adiposity is associated with oxidative stress, inflammation, and glucose intolerance. Previous data suggest that platelet gene expression is associated with key cardiometabolic phenotypes, including body mass index but stable in healthy individuals over time. However, modulation of gene expression in platelets in response to metabolic shifts (eg, weight reduction) is unknown and may be important to defining mechanism. Approach and Results: Platelet RNA sequencing and aggregation were performed from 21 individuals with massive weight loss (>45 kg) following bariatric surgery. Based on RNA sequencing data, we measured the expression of 67 genes from isolated platelet RNA using high-throughput quantitative reverse transcription quantitative PCR in 1864 FHS (Framingham Heart Study) participants. Many transcripts not previously studied in platelets were differentially expressed with bariatric surgical weight loss, appeared specific to platelets (eg, not differentially expressed in leukocytes), and were enriched for a nonalcoholic fatty liver disease pathway. Platelet aggregation studies did not detect alteration in platelet function after significant weight loss. Linear regression models demonstrated several platelet genes modestly associated with cross-sectional cardiometabolic phenotypes, including body mass index. There were no associations between studied transcripts and incident diabetes or cardiovascular end points. CONCLUSIONS In summary, while there is no change in platelet aggregation function after significant weight loss, the human platelet experiences a dramatic transcriptional shift that implicates pathways potentially relevant to improved cardiometabolic risk postweight loss (eg, nonalcoholic fatty liver disease). Further studies are needed to determine the mechanistic importance of these observations.
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Affiliation(s)
- Marzieh Ezzaty Mirhashemi
- Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Ravi V. Shah
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Robert R. Kitchen
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jian Rong
- Department of Biostatistics, Boston University, Boston, MA
| | - Aferdita Spahillari
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Alexander R. Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA
| | - Olga Vitseva
- Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Daniel Levy
- The Framingham Heart Study, Framingham, MA, USA; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | | | - Sajani Shah
- Department of Surgery, Tufts University, Boston, MA
| | | | | | - Kahraman Tanriverdi
- Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Jane E. Freedman
- Department of Medicine, Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA
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6
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Longitudinal saliva omics responses to immune perturbation: a case study. Sci Rep 2021; 11:710. [PMID: 33436912 PMCID: PMC7804305 DOI: 10.1038/s41598-020-80605-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/23/2020] [Indexed: 01/03/2023] Open
Abstract
Saliva omics has immense potential for non-invasive diagnostics, including monitoring very young or elderly populations, or individuals in remote locations. In this study, multiple saliva omics from an individual were monitored over three periods (100 timepoints) involving: (1) hourly sampling over 24 h without intervention, (2) hourly sampling over 24 h including immune system activation using the standard 23-valent pneumococcal polysaccharide vaccine, (3) daily sampling for 33 days profiling the post-vaccination response. At each timepoint total saliva transcriptome and proteome, and small RNA from salivary extracellular vesicles were profiled, including mRNA, miRNA, piRNA and bacterial RNA. The two 24-h periods were used in a paired analysis to remove daily variation and reveal vaccination responses. Over 18,000 omics longitudinal series had statistically significant temporal trends compared to a healthy baseline. Various immune response and regulation pathways were activated following vaccination, including interferon and cytokine signaling, and MHC antigen presentation. Immune response timeframes were concordant with innate and adaptive immunity development, and coincided with vaccination and reported fever. Overall, mRNA results appeared more specific and sensitive (timewise) to vaccination compared to other omics. The results suggest saliva omics can be consistently assessed for non-invasive personalized monitoring and immune response diagnostics.
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Srinivasan S, Treacy R, Herrero T, Olsen R, Leonardo TR, Zhang X, DeHoff P, To C, Poling LG, Fernando A, Leon-Garcia S, Knepper K, Tran V, Meads M, Tasarz J, Vuppala A, Park S, Laurent CD, Bui T, Cheah PS, Tabitha Overcash R, Ramos GA, Roeder H, Ghiran I, Parast M, Breakefield XO, Lueth AJ, Rust SR, Dufford MT, Fox AC, Hickok DE, Burchard J, Boniface JJ, Laurent LC. Discovery and Verification of Extracellular miRNA Biomarkers for Non-invasive Prediction of Pre-eclampsia in Asymptomatic Women. Cell Rep Med 2020; 1:100013. [PMID: 32864636 PMCID: PMC7455024 DOI: 10.1016/j.xcrm.2020.100013] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/01/2019] [Accepted: 04/21/2020] [Indexed: 12/16/2022]
Abstract
Development of effective prevention and treatment strategies for pre-eclampsia is limited by the lack of accurate methods for identification of at-risk pregnancies. We performed small RNA sequencing (RNA-seq) of maternal serum extracellular RNAs (exRNAs) to discover and verify microRNAs (miRNAs) differentially expressed in patients who later developed pre-eclampsia. Sera collected from 73 pre-eclampsia cases and 139 controls between 17 and 28 weeks gestational age (GA), divided into separate discovery and verification cohorts, are analyzed by small RNA-seq. Discovery and verification of univariate and bivariate miRNA biomarkers reveal that bivariate biomarkers verify at a markedly higher rate than univariate biomarkers. The majority of verified biomarkers contain miR-155-5p, which has been reported to mediate the pre-eclampsia-associated repression of endothelial nitric oxide synthase (eNOS) by tumor necrosis factor alpha (TNF-α). Deconvolution analysis reveals that several verified miRNA biomarkers come from the placenta and are likely carried by placenta-specific extracellular vesicles.
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Affiliation(s)
- Srimeenakshi Srinivasan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ryan Treacy
- Sera Prognostics, 2749 East Parleys Way, Salt Lake City, UT 84109, USA
| | - Tiffany Herrero
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
- Department of Obstetrics and Gynecology, Stanford University, Palo Alto, CA 94305, USA
| | - Richelle Olsen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
- Franciscan Maternal-Fetal Medicine Associates at St. Joseph, Tacoma, WA 98405, USA
| | - Trevor R. Leonardo
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xuan Zhang
- Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Cuong To
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lara G. Poling
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Aileen Fernando
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Sandra Leon-Garcia
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Katharine Knepper
- Department of Pathology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Vy Tran
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Morgan Meads
- Department of Pathology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jennifer Tasarz
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Aishwarya Vuppala
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Soojin Park
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Clara D. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Tony Bui
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Pike See Cheah
- Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02115, USA
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
| | - Rachael Tabitha Overcash
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Gladys A. Ramos
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hilary Roeder
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
- Kaiser Permanente San Diego, San Diego, CA 92120, USA
| | - Ionita Ghiran
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Mana Parast
- Department of Pathology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Xandra O. Breakefield
- Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Amir J. Lueth
- Sera Prognostics, 2749 East Parleys Way, Salt Lake City, UT 84109, USA
| | - Sharon R. Rust
- Sera Prognostics, 2749 East Parleys Way, Salt Lake City, UT 84109, USA
| | - Max T. Dufford
- Sera Prognostics, 2749 East Parleys Way, Salt Lake City, UT 84109, USA
| | - Angela C. Fox
- Sera Prognostics, 2749 East Parleys Way, Salt Lake City, UT 84109, USA
| | - Durlin E. Hickok
- Sera Prognostics, 2749 East Parleys Way, Salt Lake City, UT 84109, USA
| | - Julja Burchard
- Sera Prognostics, 2749 East Parleys Way, Salt Lake City, UT 84109, USA
| | - J. Jay Boniface
- Sera Prognostics, 2749 East Parleys Way, Salt Lake City, UT 84109, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92037, USA
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Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol 2019; 20:209. [PMID: 31610796 PMCID: PMC6792267 DOI: 10.1186/s13059-019-1818-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration. While recent studies have defined broad patterns of association involving gene transcription and nearby SSV breakpoints, global alterations in DNA methylation in the context of SSVs remain largely unexplored. Results By data integration of whole genome sequencing, RNA sequencing, and DNA methylation arrays from more than 1400 human cancers, we identify hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of a somatic structural variant (SSV) breakpoint is recurrently associated with altered expression or DNA methylation, respectively, independently of copy number alterations. CGIs with SSV-associated increased methylation are predominantly promoter-associated, while CGIs with SSV-associated decreased methylation are enriched for gene body CGIs. Rearrangement of genomic regions normally having higher or lower methylation is often involved in SSV-associated CGI methylation alterations. Across cancers, the overall structural variation burden is associated with a global decrease in methylation, increased expression in methyltransferase genes and DNA damage response genes, and decreased immune cell infiltration. Conclusion Genomic rearrangement appears to have a major role in shaping the cancer DNA methylome, to be considered alongside commonly accepted mechanisms including histone modifications and disruption of DNA methyltransferases.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lixing Yang
- Ben May Department for Cancer Research and Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Melanie Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angela Hadjipanayis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angeliki Pantazi
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Christopher A Bristow
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Harshad S Mahadeshwar
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jiabin Tang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sahil Seth
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Semin Lee
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaojia Ren
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xingzhi Song
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Huandong Sun
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jonathan Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lovelace J Luquette
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ruibin Xi
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lynda Chin
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Eli and Edythe L. Broad Institute of Massachusetts Institute Of Technology and Harvard University, Cambridge, MA, 02142, USA
| | | | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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Zanfardino M, Franzese M, Pane K, Cavaliere C, Monti S, Esposito G, Salvatore M, Aiello M. Bringing radiomics into a multi-omics framework for a comprehensive genotype-phenotype characterization of oncological diseases. J Transl Med 2019; 17:337. [PMID: 31590671 PMCID: PMC6778975 DOI: 10.1186/s12967-019-2073-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/18/2019] [Indexed: 02/07/2023] Open
Abstract
Genomic and radiomic data integration, namely radiogenomics, can provide meaningful knowledge in cancer diagnosis, prognosis and treatment. Despite several data structures based on multi-layer architecture proposed to combine multi-omic biological information, none of these has been designed and assessed to include radiomic data as well. To meet this need, we propose to use the MultiAssayExperiment (MAE), an R package that provides data structures and methods for manipulating and integrating multi-assay experiments, as a suitable tool to manage radiogenomic experiment data. To this aim, we first examine the role of radiogenomics in cancer phenotype definition, then the current state of radiogenomics data integration in public repository and, finally, challenges and limitations of including radiomics in MAE, designing an extended framework and showing its application on a case study from the TCGA-TCIA archives. Radiomic and genomic data from 91 patients have been successfully integrated in a single MAE object, demonstrating the suitability of the MAE data structure as container of radiogenomic data.
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10
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Waller R, Wyles M, Heath PR, Kazoka M, Wollff H, Shaw PJ, Kirby J. Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity. Front Neurosci 2018; 11:731. [PMID: 29375285 PMCID: PMC5767269 DOI: 10.3389/fnins.2017.00731] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a clinical subtype of motor neurone disease (MND), a fatal neurodegenerative disease involving the loss of both the upper and lower motor neurones from the motor cortex, brainstem, and spinal cord. Identifying specific disease biomarkers would help to not only improve diagnostic delay but also to classify disease subtypes, monitor response to therapeutic drugs and track disease progression. miRNAs are small non-coding RNA responsible for regulating gene expression and ultimately protein expression and have been used as biomarkers for many cancers and neurodegenerative disorders. Investigating the detection of miRNAs in cerebrospinal fluid (CSF), the fluid that bathes the central nervous system (CNS) is a prime target for identifying potential biomarkers for ALS. This is the first study to investigate the expression of miRNAs in the CSF of ALS patients using small RNA sequencing. We detected 11 differentially expressed miRNAs in the CSF of sporadic ALS (sALS) patients related to neural and glial activity. Additionally, miRNAs involved in glucose metabolism and the regulation of oxidative stress were also identified. Detecting the presence of potential CSF derived miRNA biomarkers in sALS could open up a whole new area of knowledge to help gain a better understanding of disease pathophysiology. Additionally, with further investigation, the tracking of CSF miRNA over the disease course could be used to follow the disease progression and monitor the effect of novel therapeutics that could be personalized to an individual disease phenotype.
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Affiliation(s)
- Rachel Waller
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Matthew Wyles
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Paul R Heath
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Mbombe Kazoka
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Helen Wollff
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Pamela J Shaw
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Janine Kirby
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, United Kingdom
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11
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Kozak RA, Majer A, Biondi MJ, Medina SJ, Goneau LW, Sajesh BV, Slota JA, Zubach V, Severini A, Safronetz D, Hiebert SL, Beniac DR, Booth TF, Booth SA, Kobinger GP. MicroRNA and mRNA Dysregulation in Astrocytes Infected with Zika Virus. Viruses 2017; 9:v9100297. [PMID: 29036922 PMCID: PMC5691648 DOI: 10.3390/v9100297] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 09/30/2017] [Accepted: 10/10/2017] [Indexed: 12/31/2022] Open
Abstract
The Zika virus (ZIKV) epidemic is an ongoing public health concern. ZIKV is a flavivirus reported to be associated with microcephaly, and recent work in animal models demonstrates the ability of the virus to cross the placenta and affect fetal brain development. Recent findings suggest that the virus preferentially infects neural stem cells and thereby deregulates gene expression, cell cycle progression, and increases cell death. However, neuronal stem cells are not the only brain cells that are susceptible to ZIKV and infection of other brain cells may contribute to disease progression. Herein, we characterized ZIKV replication in astrocytes, and profiled temporal changes in host microRNAs (miRNAs) and transcriptomes during infection. We observed the deregulation of numerous processes known to be involved in flavivirus infection, including genes involved in the unfolded protein response pathway. Moreover, a number of miRNAs were upregulated, including miR-30e-3p, miR-30e-5p, and, miR-17-5p, which have been associated with other flavivirus infections. This study highlights potential miRNAs that may be of importance in ZIKV pathogenesis.
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Affiliation(s)
- Robert A Kozak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Anna Majer
- Molecular Patho Biology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
- Viral Diseases Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Mia J Biondi
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada; Winnipeg, MB R3E 3R2, Canada, .
| | - Sarah J Medina
- Molecular Patho Biology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Lee W Goneau
- Medical Microbiology, Public Health Ontario Laboratory, Toronto, ON M5G 1M1, Canada.
| | - Babu V Sajesh
- Research Institute in Oncology and Hematology, Cancer Care Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Jessy A Slota
- Molecular Patho Biology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Vanessa Zubach
- Viral Exanthemata and STD, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Alberto Severini
- Viral Exanthemata and STD, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - David Safronetz
- Viral Zoonoses, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Shannon L Hiebert
- Viral Diseases Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Daniel R Beniac
- Viral Diseases Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Timothy F Booth
- Viral Diseases Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Stephanie A Booth
- Molecular Patho Biology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Gary P Kobinger
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
- Infectious Diseases Research Centre, Université Laval, Quebec, QC G1V 4G2, Canada.
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12
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Simon L, Chen E, Edelstein L, Kong X, Bhatlekar S, Rigoutsos I, Bray P, Shaw C. Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2. Am J Hum Genet 2016; 98:883-897. [PMID: 27132591 DOI: 10.1016/j.ajhg.2016.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/11/2016] [Indexed: 02/07/2023] Open
Abstract
Platelets play a central role in ischemic cardiovascular events. Cardiovascular disease (CVD) is a major cause of death worldwide. Numerous genome-wide association studies (GWASs) have identified loci associated with CVD risk. However, our understanding of how these variants contribute to disease is limited. Using data from the platelet RNA and expression 1 (PRAX1) study, we analyzed cis expression quantitative trait loci (eQTLs) in platelets from 154 normal human subjects. We confirmed these results in silico by performing allele-specific expression (ASE) analysis, which demonstrated that the allelic directionality of eQTLs and ASE patterns correlate significantly. Comparison of platelet eQTLs with data from the Genotype-Tissue Expression (GTEx) project revealed that a number of platelet eQTLs are platelet specific and that platelet eQTL peaks localize to the gene body at a higher rate than eQTLs from other tissues. Upon integration with data from previously published GWASs, we found that the trait-associated variant rs1474868 coincides with the eQTL peak for mitofusin 2 (MFN2). Additional experimental and computational analyses revealed that this eQTL is linked to an unannotated alternate MFN2 start site preferentially expressed in platelets. Integration of phenotype data from the PRAX1 study showed that MFN2 expression levels were significantly associated with platelet count. This study links the variant rs1474868 to a platelet-specific regulatory role for MFN2 and demonstrates the utility of integrating multi-omic data with eQTL analysis in disease-relevant tissues for interpreting GWAS results.
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13
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Reardon ES, Hong JA, Straughan DM, Azoury SC, Zhang M, Schrump DS. Pulmonary Metastases Exhibit Epigenetic Clonality: Implications for Precision Cancer Therapy. Ann Thorac Surg 2015; 100:1839-48; discussion 1848. [PMID: 26298164 DOI: 10.1016/j.athoracsur.2015.05.089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/12/2015] [Accepted: 05/15/2015] [Indexed: 12/29/2022]
Abstract
BACKGROUND Development of effective cancer therapies may be limited by intratumoral heterogeneity, which facilitates outgrowth and organ-specific dissemination of treatment resistant clones. At present, limited information is available regarding epigenetic landscapes of pulmonary metastases. This study was undertaken to characterize epigenetic signatures of pulmonary metastases and to identify potential therapeutic targets. METHODS RNA and DNA were extracted from 65 pulmonary metastases resected from 12 patients (5 with sarcoma, 7 with adrenocortical carcinoma). Quantitative reverse transcription polymerase chain reaction techniques were used to evaluate expression levels of cancer-testis (CT) genes (NY-ESO-1, MAGE-A3, MAGE-A9, MAGE-A12, GAGE1, CT-45, SSX-1, and SSX-2), tumor suppressor (TS) genes (p16 and RASSF1A), and genes encoding epigenetic modifiers (DNMT1, DNMT3A, DNMT3B, EZH2, EED, and SUZ12), aberrantly expressed in human malignant diseases. Pyrosequencing techniques were used to quantitate DNA methylation levels in LINE1, NBL2, and D4Z4 repetitive sequences and promoter methylation status of differentially regulated genes. Results of these analyses were compared with a standardized panel of normal lung tissues. RESULTS Pulmonary metastases exhibited histologically related and patient-specific global DNA demethylation. Significant interpatient heterogeneity of gene expression was observed even among patients with similar tumor histologic features. Epigenetic signatures appeared consistent among metastases from the same patient, irrespective of the time of resection (synchronous/metachronous) or the anatomic location. EZH2, EED, and SUZ12 (core components of Polycomb repressive complex-2 [PRC-2]) were upregulated in the majority of metastases. CONCLUSIONS Pulmonary metastases exhibit patient-specific epigenetic clonality, which may be exploited for precision therapies targeting aberrant CT or TS gene expression. PRC-2 may be a shared target for epigenetic therapy of pulmonary metastases.
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Affiliation(s)
- Emily S Reardon
- Thoracic Epigenetics Laboratory, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Julie A Hong
- Thoracic Epigenetics Laboratory, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - David M Straughan
- Thoracic Epigenetics Laboratory, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Saïd C Azoury
- Thoracic Epigenetics Laboratory, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Mary Zhang
- Thoracic Epigenetics Laboratory, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - David S Schrump
- Thoracic Epigenetics Laboratory, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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