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Virolainen SJ, Satish L, Biagini JM, Chaib H, Chang WC, Dexheimer PJ, Dixon MR, Dunn KA, Fletcher D, Forney C, Granitto M, Hestand MS, Hurd M, Kaufman K, Lawson LP, Martin LJ, Peña LD, Phelan KJ, Shook MS, Weirauch MT, Khurana Hershey GK, Kottyan LC. Filaggrin loss-of-function variants are associated with atopic dermatitis phenotypes in a diverse, early life prospective cohort. JCI Insight 2024:e178258. [PMID: 38564302 DOI: 10.1172/jci.insight.178258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Loss-of-Function (LoF) variants in the filaggrin (FLG) gene are the strongest known genetic risk factor for atopic dermatitis (AD), but the impact of these variants on AD outcomes is poorly understood. We comprehensively identified genetic variants through targeted region sequencing of FLG in children (n = 438) participating in the Mechanisms of Progression of Atopic Dermatitis to Asthma in Children (MPAACH) cohort. Twenty FLG LoF variants were identified, including one novel variant and nine variants not previously associated with AD. FLG LoF variants were found in 13.6% of the cohort. Among these children, the presence of one or more FLG LoF variants was associated with moderate/severe AD (odds ratio (OR) = 2.00 (95% CI, 1.23-3.68) compared to those with mild AD. Children with FLG LoF variants had a higher SCORAD (SCORing for Atopic Dermatitis (SCORAD); P = 0.012) and higher likelihood of food allergy within the first 2.5 years of life (OR = 2.81, 1.50-5.26). LoF variants were associated with higher transepidermal Water Loss (TEWL) in both lesional (P = 0.018) and non-lesional skin (P = 0.015). Collectively, our study identifies established and novel AD-associated FLG LoF variants and associates FLG LoF with higher TEWL in lesional and non-lesional skin.
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Affiliation(s)
- Samuel J Virolainen
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Latha Satish
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Jocelyn M Biagini
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Hassan Chaib
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Wan Chi Chang
- Division of Asthma Research, Cincinnati Children Hospital Medical Center, Cincinnati, United States of America
| | - Phillip J Dexheimer
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Michael R Dixon
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Katelyn A Dunn
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - David Fletcher
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Carmy Forney
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Marissa Granitto
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | | | - Makenna Hurd
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Kenneth Kaufman
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Lucinda P Lawson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Loren Dm Peña
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Kieran J Phelan
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Molly S Shook
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Matthew T Weirauch
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Gurjit K Khurana Hershey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Leah C Kottyan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
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Dexheimer PJ, Pujato M, Roskin KM, Weirauch MT. VExD: a curated resource for human gene expression alterations following viral infection. G3 (Bethesda) 2023; 13:jkad176. [PMID: 37531635 PMCID: PMC10542171 DOI: 10.1093/g3journal/jkad176] [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] [Received: 11/22/2022] [Revised: 11/22/2022] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
Much of the host antiviral response is mediated through changes to host gene expression levels. Likewise, viruses induce changes to host gene expression levels in order to promote the viral life cycle and evade the host immune system. However, there is no resource that specifically collects human gene expression levels pre- and post-virus infection. Further, public gene expression repositories do not contain enough specialized metadata to easily find relevant experiments. Here, we present the Virus Expression Database (VExD), a freely available website and database, that collects human gene expression datasets in response to viral infection. VExD contains ∼8,000 uniformly processed samples obtained from 289 studies examining 51 distinct human viruses. We show that the VExD processing pipeline captures known antiviral responses in the form of interferon-stimulated genes. We further show that the datasets collected in VExD can be used to quickly identify supporting data for experiments performed in human cells or model organisms. VExD is freely available at https://vexd.cchmc.org/.
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Affiliation(s)
- Phillip J Dexheimer
- Division of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH 45221, USA
| | - Mario Pujato
- Division of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Krishna M Roskin
- Division of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Division of Immunobiology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45221, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45221, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Divisions of Human Genetics, Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
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Bedard MC, Chihanga T, Carlile A, Jackson R, Brusadelli MG, Lee D, VonHandorf A, Rochman M, Dexheimer PJ, Chalmers J, Nuovo G, Lehn M, Williams DEJ, Kulkarni A, Carey M, Jackson A, Billingsley C, Tang A, Zender C, Patil Y, Wise-Draper TM, Herzog TJ, Ferris RL, Kendler A, Aronow BJ, Kofron M, Rothenberg ME, Weirauch MT, Van Doorslaer K, Wikenheiser-Brokamp KA, Lambert PF, Adam M, Steven Potter S, Wells SI. Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer. Nat Commun 2023; 14:1975. [PMID: 37031202 PMCID: PMC10082832 DOI: 10.1038/s41467-023-37377-0] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 03/15/2023] [Indexed: 04/10/2023] Open
Abstract
Persistent HPV16 infection is a major cause of the global cancer burden. The viral life cycle is dependent on the differentiation program of stratified squamous epithelium, but the landscape of keratinocyte subpopulations which support distinct phases of the viral life cycle has yet to be elucidated. Here, single cell RNA sequencing of HPV16 infected compared to uninfected organoids identifies twelve distinct keratinocyte populations, with a subset mapped to reconstruct their respective 3D geography in stratified squamous epithelium. Instead of conventional terminally differentiated cells, an HPV-reprogrammed keratinocyte subpopulation (HIDDEN cells) forms the surface compartment and requires overexpression of the ELF3/ESE-1 transcription factor. HIDDEN cells are detected throughout stages of human carcinogenesis including primary human cervical intraepithelial neoplasias and HPV positive head and neck cancers, and a possible role in promoting viral carcinogenesis is supported by TCGA analyses. Single cell transcriptome information on HPV-infected versus uninfected epithelium will enable broader studies of the role of individual keratinocyte subpopulations in tumor virus infection and cancer evolution.
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Affiliation(s)
- Mary C Bedard
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Tafadzwa Chihanga
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Adrean Carlile
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Robert Jackson
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Denis Lee
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Andrew VonHandorf
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mark Rochman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Phillip J Dexheimer
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jeffrey Chalmers
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, 151 W. Woodruff Ave, Columbus, OH, 43210, USA
| | - Gerard Nuovo
- Department of Pathology, Ohio State University Medical Center, Columbus, OH, 43210, USA
| | - Maria Lehn
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - David E J Williams
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721, USA
- Medical Scientist Training M.D.-Ph.D. Program (MSTP), College of Medicine-Tucson, University of Arizona, Tucson, AZ, USA
| | - Aditi Kulkarni
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Molly Carey
- Department of Obstetrics and Gynecology, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA
| | - Amanda Jackson
- Department of Obstetrics and Gynecology, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA
| | - Caroline Billingsley
- Department of Obstetrics and Gynecology, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA
| | - Alice Tang
- Department of Otolaryngology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Chad Zender
- Department of Otolaryngology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Yash Patil
- Department of Otolaryngology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Trisha M Wise-Draper
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Thomas J Herzog
- Department of Obstetrics and Gynecology, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA
| | - Robert L Ferris
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Ady Kendler
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Matthew Kofron
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Divisions of Human Genetics, Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721, USA
- The BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
- Department of Immunobiology, University of Arizona, Tucson, AZ, 85721, USA
- UA Cancer Center, University of Arizona, Tucson, AZ, 85721, USA
| | - Kathryn A Wikenheiser-Brokamp
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Division of Pathology & Laboratory Medicine and The Perinatal Institute Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| | - Susanne I Wells
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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Rochman M, Wen T, Kotliar M, Dexheimer PJ, Ben-Baruch Morgenstern N, Caldwell JM, Lim HW, Rothenberg ME. Single-cell RNA sequencing of human esophageal epithelium in homeostasis and allergic inflammation. JCI Insight 2022; 7:159093. [PMID: 35472002 PMCID: PMC9208762 DOI: 10.1172/jci.insight.159093] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 02/03/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022] Open
Abstract
Inflammation of the esophageal epithelium is a hallmark of eosinophilic esophagitis (EoE), an emerging chronic allergic disease. Herein, we probed human esophageal epithelial cells at single-cell resolution during homeostasis and EoE. During allergic inflammation, the epithelial differentiation program was blocked, leading to loss of KRT6high differentiated populations and expansion of TOP2high proliferating and DSPhigh, SERPINB3high transitioning populations; however, there was stability of the stem cell-enriched PDPNhigh basal epithelial compartment. This differentiation program blockade was associated with dysregulation of transcription factors, including nuclear receptor signalers, in the most differentiated epithelial cells and altered NOTCH-related cell-to-cell communication. Each epithelial population expressed genes with allergic disease risk variants, supporting their functional interplay. The esophageal epithelium differed notably between EoE in histologic remission and controls, indicating that remission is a transitory state poised to relapse. Collectively, our data uncover the dynamic nature of the inflamed human esophageal epithelium and provide a framework to better understand esophageal health and disease.
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Affiliation(s)
- Mark Rochman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Ting Wen
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Phillip J Dexheimer
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Netali Ben-Baruch Morgenstern
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Julie M Caldwell
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
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5
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Ware SM, Bhatnagar S, Dexheimer PJ, Wilkinson JD, Sridhar A, Fan X, Shen Y, Tariq M, Schubert JA, Colan SD, Shi L, Canter CE, Hsu DT, Bansal N, Webber SA, Everitt MD, Kantor PF, Rossano JW, Pahl E, Rusconi P, Lee TM, Towbin JA, Lal AK, Chung WK, Miller EM, Aronow B, Martin LJ, Lipshultz SE. The genetic architecture of pediatric cardiomyopathy. Am J Hum Genet 2022; 109:282-298. [PMID: 35026164 DOI: 10.1016/j.ajhg.2021.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/10/2021] [Indexed: 01/27/2023] Open
Abstract
To understand the genetic contribution to primary pediatric cardiomyopathy, we performed exome sequencing in a large cohort of 528 children with cardiomyopathy. Using clinical interpretation guidelines and targeting genes implicated in cardiomyopathy, we identified a genetic cause in 32% of affected individuals. Cardiomyopathy sub-phenotypes differed by ancestry, age at diagnosis, and family history. Infants < 1 year were less likely to have a molecular diagnosis (p < 0.001). Using a discovery set of 1,703 candidate genes and informatic tools, we identified rare and damaging variants in 56% of affected individuals. We see an excess burden of damaging variants in affected individuals as compared to two independent control sets, 1000 Genomes Project (p < 0.001) and SPARK parental controls (p < 1 × 10-16). Cardiomyopathy variant burden remained enriched when stratified by ancestry, variant type, and sub-phenotype, emphasizing the importance of understanding the contribution of these factors to genetic architecture. Enrichment in this discovery candidate gene set suggests multigenic mechanisms underlie sub-phenotype-specific causes and presentations of cardiomyopathy. These results identify important information about the genetic architecture of pediatric cardiomyopathy and support recommendations for clinical genetic testing in children while illustrating differences in genetic architecture by age, ancestry, and sub-phenotype and providing rationale for larger studies to investigate multigenic contributions.
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Haberman Y, Iqbal NT, Ghandikota S, Mallawaarachchi I, Tzipi Braun, Dexheimer PJ, Rahman N, Hadar R, Sadiq K, Ahmad Z, Idress R, Iqbal J, Ahmed S, Hotwani A, Umrani F, Ehsan L, Medlock G, Syed S, Moskaluk C, Ma JZ, Jegga AG, Moore SR, Ali SA, Denson LA. Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction. Gastroenterology 2021; 160:2055-2071.e0. [PMID: 33524399 PMCID: PMC8113748 DOI: 10.1053/j.gastro.2021.01.221] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Environmental enteric dysfunction (EED) limits the Sustainable Development Goals of improved childhood growth and survival. We applied mucosal genomics to advance our understanding of EED. METHODS The Study of Environmental Enteropathy and Malnutrition (SEEM) followed 416 children from birth to 24 months in a rural district in Pakistan. Biomarkers were measured at 9 months and tested for association with growth at 24 months. The duodenal methylome and transcriptome were determined in 52 undernourished SEEM participants and 42 North American controls and patients with celiac disease. RESULTS After accounting for growth at study entry, circulating insulin-like growth factor-1 (IGF-1) and ferritin predicted linear growth, whereas leptin correlated with future weight gain. The EED transcriptome exhibited suppression of antioxidant, detoxification, and lipid metabolism genes, and induction of anti-microbial response, interferon, and lymphocyte activation genes. Relative to celiac disease, suppression of antioxidant and detoxification genes and induction of antimicrobial response genes were EED-specific. At the epigenetic level, EED showed hyper-methylation of epithelial metabolism and barrier function genes, and hypo-methylation of immune response and cell proliferation genes. Duodenal coexpression modules showed association between lymphocyte proliferation and epithelial metabolic genes and histologic severity, fecal energy loss, and wasting (weight-for-length/height Z < -2.0). Leptin was associated with expression of epithelial carbohydrate metabolism and stem cell renewal genes. Immune response genes were attenuated by giardia colonization. CONCLUSIONS Children with reduced circulating IGF-1 are more likely to experience stunting. Leptin and a gene signature for lymphocyte activation and dysregulated lipid metabolism are implicated in wasting, suggesting new approaches for EED refractory to nutritional intervention. ClinicalTrials.gov, Number: NCT03588013. (https://clinicaltrials.gov/ct2/show/NCT03588013).
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Affiliation(s)
- Yael Haberman
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio,Department of Pediatrics, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Israel
| | - Najeeha T. Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Sudhir Ghandikota
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center Cincinnati, Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, Ohio
| | | | - Tzipi Braun
- Department of Pediatrics, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Israel
| | - Phillip J. Dexheimer
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Najeeb Rahman
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Rotem Hadar
- Department of Pediatrics, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Israel
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Zubair Ahmad
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Romana Idress
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fayyaz Umrani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Lubaina Ehsan
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Greg Medlock
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Sana Syed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan,Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Chris Moskaluk
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Anil G. Jegga
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center Cincinnati, Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, Ohio
| | - Sean R. Moore
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia,Sean R. Moore, MD, MS, Division of Pediatric Gastroenterology, Hepatology, & Nutrition, University of Virginia, 409 Lane Rd., Charlottesville, VA 22908.
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan.
| | - Lee A. Denson
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio,Correspondence Address correspondence to: Lee A Denson, MD, Division of Pediatric Gastroenterology, Hepatology, & Nutrition, Cincinnati Children’s Hospital Medical Center, MLC 2010, 3333 Burnet Avenue, Cincinnati, Ohio 45229. fax: (513) 636-558.
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7
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Ware SM, Wilkinson JD, Tariq M, Schubert JA, Sridhar A, Colan SD, Shi L, Canter CE, Hsu DT, Webber SA, Dodd DA, Everitt MD, Kantor PF, Addonizio LJ, Jefferies JL, Rossano JW, Pahl E, Rusconi P, Chung WK, Lee T, Towbin JA, Lal AK, Bhatnagar S, Aronow B, Dexheimer PJ, Martin LJ, Miller EM, Sleeper LA, Razoky H, Czachor J, Lipshultz SE. Genetic Causes of Cardiomyopathy in Children: First Results From the Pediatric Cardiomyopathy Genes Study. J Am Heart Assoc 2021; 10:e017731. [PMID: 33906374 PMCID: PMC8200745 DOI: 10.1161/jaha.120.017731] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Pediatric cardiomyopathy is a genetically heterogeneous disease with substantial morbidity and mortality. Current guidelines recommend genetic testing in children with hypertrophic, dilated, or restrictive cardiomyopathy, but practice variations exist. Robust data on clinical testing practices and diagnostic yield in children are lacking. This study aimed to identify the genetic causes of cardiomyopathy in children and to investigate clinical genetic testing practices. Methods and Results Children with familial or idiopathic cardiomyopathy were enrolled from 14 institutions in North America. Probands underwent exome sequencing. Rare sequence variants in 37 known cardiomyopathy genes were assessed for pathogenicity using consensus clinical interpretation guidelines. Of the 152 enrolled probands, 41% had a family history of cardiomyopathy. Of 81 (53%) who had undergone clinical genetic testing for cardiomyopathy before enrollment, 39 (48%) had a positive result. Genetic testing rates varied from 0% to 97% between sites. A positive family history and hypertrophic cardiomyopathy subtype were associated with increased likelihood of genetic testing (P=0.005 and P=0.03, respectively). A molecular cause was identified in an additional 21% of the 63 children who did not undergo clinical testing, with positive results identified in both familial and idiopathic cases and across all phenotypic subtypes. Conclusions A definitive molecular genetic diagnosis can be made in a substantial proportion of children for whom the cause and heritable nature of their cardiomyopathy was previously unknown. Practice variations in genetic testing are great and should be reduced. Improvements can be made in comprehensive cardiac screening and predictive genetic testing in first‐degree relatives. Overall, our results support use of routine genetic testing in cases of both familial and idiopathic cardiomyopathy. Registration URL: https://www.clinicaltrials.gov; Unique identifier: NCT01873963.
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Affiliation(s)
- Stephanie M Ware
- Departments of Pediatrics and Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | | | - Muhammad Tariq
- Faculty of Applied Medical Sciences University of Tabuk Kingdom of Saudi Arabia
| | - Jeffrey A Schubert
- Departments of Pediatrics and Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | - Arthi Sridhar
- Departments of Pediatrics and Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | - Steven D Colan
- Department of Cardiology and Harvard Medical School Boston Children's Hospital Boston MA
| | - Ling Shi
- New England Research Institutes Watertown MA
| | | | - Daphne T Hsu
- Albert Einstein College of Medicine and Children's Hospital at Montefiore Bronx NY
| | - Steven A Webber
- Monroe Carell Jr. Children's Hospital at Vanderbilt Nashville TN
| | - Debra A Dodd
- Monroe Carell Jr. Children's Hospital at Vanderbilt Nashville TN
| | | | - Paul F Kantor
- Keck School of Medicine and Children's Hospital Los Angeles University of Southern California Los Angeles CA
| | | | | | | | - Elfriede Pahl
- Ann and Robert H. Lurie Children's Hospital Chicago IL
| | - Paolo Rusconi
- University of Miami Miller School of Medicine Miami FL
| | | | - Teresa Lee
- Columbia University Medical Center New York NY
| | | | | | - Surbhi Bhatnagar
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Bruce Aronow
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Phillip J Dexheimer
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Lisa J Martin
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Erin M Miller
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Lynn A Sleeper
- Department of Cardiology and Harvard Medical School Boston Children's Hospital Boston MA
| | - Hiedy Razoky
- Wayne State University School of Medicine Detroit MI
| | - Jason Czachor
- Wayne State University School of Medicine Detroit MI
| | - Steven E Lipshultz
- Jacobs School of Medicine and Biomedical Sciences at University at Buffalo NY.,John R. Oishei Children's Hospital Buffalo NY
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8
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Lazow MA, Johnson SL, Johnson ND, Breneman JC, Dexheimer PJ, Szabo S, Pressey JG. Genome-Driven Therapy for Chemotherapy-Resistant Metastatic CDK6-Amplified Osteosarcoma. JCO Precis Oncol 2020; 4:498-504. [PMID: 35050742 DOI: 10.1200/po.20.00032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Margot A Lazow
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sheryl L Johnson
- Division of Pathology and Laboratory Medicine, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pathology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Neil D Johnson
- Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - John C Breneman
- Department of Radiation Oncology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Phillip J Dexheimer
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sara Szabo
- Division of Pathology and Laboratory Medicine, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pathology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Joseph G Pressey
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
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9
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Haberman Y, Minar P, Karns R, Dexheimer PJ, Ghandikota S, Tegge S, Shapiro D, Shuler B, Venkateswaran S, Braun T, Ta A, Walters TD, Baldassano RN, Noe JD, Rosh J, Markowitz J, Dotson JL, Mack DR, Kellermayer R, Griffiths AM, Heyman MB, Baker SS, Moulton D, Patel AS, Gulati AS, Steiner SJ, LeLeiko N, Otley A, Oliva-Hemker M, Ziring D, Gokhale R, Kim S, Guthery SL, Cohen SA, Snapper S, Aronow BJ, Stephens M, Gibson G, Dillman JR, Dubinsky M, Hyams JS, Kugathasan S, Jegga AG, Denson LA. Mucosal Inflammatory and Wound Healing Gene Programs Reveal Targets for Stricturing Behavior in Pediatric Crohn's Disease. J Crohns Colitis 2020; 15:jjaa166. [PMID: 32770196 PMCID: PMC7904088 DOI: 10.1093/ecco-jcc/jjaa166] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND AND AIMS Ileal strictures are the major indication for resective surgery in Crohn's disease (CD). We aimed to define ileal gene programs present at diagnosis linked with future stricturing behavior during five year follow-up, and to identify potential small molecules to reverse these gene signatures. METHODS Antimicrobial serologies and pre-treatment ileal gene expression were assessed in a representative subset of 249 CD patients within the RISK multicenter pediatric CD inception cohort study, including 113 that are unique to this report. These data were used to define genes associated with stricturing behavior and for model testing to predict stricturing behavior. A bioinformatics approach to define small molecules which may reverse the stricturing gene signature was applied. RESULTS 19 of the 249 patients developed isolated B2 stricturing behavior during follow-up, while 218 remained B1 inflammatory. Using deeper RNA sequencing than in our prior report, we have now defined an inflammatory gene signature including an oncostatin M co-expression signature, tightly associated with extra-cellular matrix (ECM) gene expression in those who developed stricturing complications. We further computationally prioritize small molecules targeting macrophage and fibroblast activation and angiogenesis which may reverse the stricturing gene signature. A model containing ASCA and CBir1 serologies and a refined eight ECM gene set was significantly associated with stricturing development by year five after diagnosis (AUC (95th CI) = 0.82 (0.7-0.94)). CONCLUSION An ileal gene program for macrophage and fibroblast activation is linked to stricturing complications in treatment naïve pediatric CD, and may inform novel small molecule therapeutic approaches.
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Affiliation(s)
- Yael Haberman
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Phillip Minar
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Rebekah Karns
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Phillip J Dexheimer
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sudhir Ghandikota
- Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, OH, USA
| | - Samuel Tegge
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Daniel Shapiro
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Brianne Shuler
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Tzipi Braun
- Department of Pediatrics, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Allison Ta
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Thomas D Walters
- Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Robert N Baldassano
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua D Noe
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Joel Rosh
- Department of Pediatrics, Goryeb Children’s Hospital/Atlantic Health, Morristown, NJ, USA
| | - James Markowitz
- Department of Pediatrics, Cohen Children’s Medical Center of New York, New Hyde Park, NY, USA
| | - Jennifer L Dotson
- Department of Pediatrics, Nationwide Children’s Hospital, Columbus, OH, USA
| | - David R Mack
- Department of Pediatrics, Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Richard Kellermayer
- Department of Pediatrics, Texas Children’s Hospital, Baylor College School of Medicine, Houston, TX, USA
| | - Anne M Griffiths
- Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Melvin B Heyman
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Susan S Baker
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Dedrick Moulton
- Department of Pediatrics, Monroe Carell Jr Children’s Hospital, Nashville, TN, USA
| | - Ashish S Patel
- Department of Pediatrics, UT Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Ajay S Gulati
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC, USA
| | - Steven J Steiner
- Department of Pediatrics, Riley Children’s Hospital, Indianapolis, IN, USA
| | - Neal LeLeiko
- Department of Pediatrics, Hasbro Children’s Hospital, Providence, RI, USA
| | - Anthony Otley
- Department of Pediatrics, IWK Health Centre, Halifax, NS, Canada
| | | | - David Ziring
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ranjana Gokhale
- Department of Pediatrics, University of Chicago Comer Children’s Hospital, Chicago, IL, USA
| | - Sandra Kim
- Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah and Intermountain Primary Children’s Hospital, Salt Lake City, UT, USA
| | - Stanley A Cohen
- Department of Pediatrics, Children’s Center for Digestive Health Medicine, Atlanta, GA, USA
| | - Scott Snapper
- Department of Pediatrics, Children’s Hospital ‐ Boston, Boston, MA, USA
| | - Bruce J Aronow
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Greg Gibson
- Center for for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jonathan R Dillman
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Marla Dubinsky
- Department of Pediatrics, Mount Sinai Hospital New York, NY, USA
| | - Jeffrey S Hyams
- Department of Pediatrics, Connecticut Children’s Medical Center, Hartford, CT, USA
| | | | - Anil G Jegga
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
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10
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Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, Nistel M, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, Leleiko NS, Heyman MB, Grifiths AM, Patel AS, Noe JD, Aronow BJ, Kugathasan S, Walters TD, Gibson G, Thomas SD, Mollen K, Shen-Orr S, Huttenhower C, Xavier RJ, Hyams JS, Denson LA. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nat Commun 2019; 10:38. [PMID: 30604764 PMCID: PMC6318335 DOI: 10.1038/s41467-018-07841-3] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 02/07/2023] Open
Abstract
Molecular mechanisms driving disease course and response to therapy in ulcerative colitis (UC) are not well understood. Here, we use RNAseq to define pre-treatment rectal gene expression, and fecal microbiota profiles, in 206 pediatric UC patients receiving standardised therapy. We validate our key findings in adult and paediatric UC cohorts of 408 participants. We observe a marked suppression of mitochondrial genes and function across cohorts in active UC, and that increasing disease severity is notable for enrichment of adenoma/adenocarcinoma and innate immune genes. A subset of severity genes improves prediction of corticosteroid-induced remission in the discovery cohort; this gene signature is also associated with response to anti-TNFα and anti-α4β7 integrin in adults. The severity and therapeutic response gene signatures were in turn associated with shifts in microbes previously implicated in mucosal homeostasis. Our data provide insights into UC pathogenesis, and may prioritise future therapies for nonresponders to current approaches.
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Affiliation(s)
- Yael Haberman
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
- Sheba Medical Center, Tel Hashomer, affiliated with the Tel Aviv University, Tel Aviv, 5265601, Israel
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Phillip J Dexheimer
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Melanie Schirmer
- Broad Institute of MIT and Harvard University, Cambridge, 02142, MA, USA
| | - Judith Somekh
- Faculty of Medicine, Technion, Haifa, 3109601, Israel
- Department of Information Systems, University of Haifa, Haifa, 3498838, Israel
| | - Ingrid Jurickova
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Tzipi Braun
- Sheba Medical Center, Tel Hashomer, affiliated with the Tel Aviv University, Tel Aviv, 5265601, Israel
| | - Elizabeth Novak
- Children's Hospital of Pittsburgh, Pittsburgh, 15224, PA, USA
| | - Laura Bauman
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, 92162, CA, USA
| | - Margaret H Collins
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Angela Mo
- Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Michael J Rosen
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Erin Bonkowski
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Nathan Gotman
- Collaborative Studies Coordinating Center, University of North Carolina, Chapel Hill, 27516, NC, USA
| | - Alison Marquis
- Collaborative Studies Coordinating Center, University of North Carolina, Chapel Hill, 27516, NC, USA
| | - Mason Nistel
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | - Paul A Rufo
- Harvard-Children's Hospital Boston, Boston, 02115, MA, USA
| | - Susan S Baker
- Women & Children's Hospital of Buffalo WCHOB, Buffalo, 14222, NY, USA
| | | | - James Markowitz
- Cohen Children's Medical Center of New York, 11040, New Hyde Park, NY, USA
| | | | - Joel R Rosh
- Goryeb Children's Hospital-Atlantic Health, Morristown, 07960, NJ, USA
| | | | - David R Mack
- Children's Hospital of East Ontario, Ottawa, Ontario, K1P 1J1, Canada
| | | | - Sapana Shah
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, 15224, PA, USA
| | | | - Melvin B Heyman
- University of California at San Francisco, San Francisco, 94143, CA, USA
| | | | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, 53226, WI, USA
| | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
| | | | | | - Greg Gibson
- Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Sonia Davis Thomas
- Collaborative Studies Coordinating Center, University of North Carolina, Chapel Hill, 27516, NC, USA
- RTI International, Research Triangle Park, 27709, NC, USA
| | - Kevin Mollen
- Children's Hospital of Pittsburgh, Pittsburgh, 15224, PA, USA
| | - Shai Shen-Orr
- Faculty of Medicine, Technion, Haifa, 3109601, Israel
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard University, Cambridge, 02142, MA, USA
- Harvard School of Public Health, Boston, 02115, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard University, Cambridge, 02142, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, 02114, MA, USA
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, 06106, CT, USA
| | - Lee A Denson
- Cincinnati Children's Hospital Medical Center, and the University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA.
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11
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Sherrill JD, Kc K, Wang X, Wen T, Chamberlin A, Stucke EM, Collins MH, Abonia JP, Peng Y, Wu Q, Putnam PE, Dexheimer PJ, Aronow BJ, Kottyan LC, Kaufman KM, Harley JB, Huang T, Rothenberg ME. Whole-exome sequencing uncovers oxidoreductases DHTKD1 and OGDHL as linkers between mitochondrial dysfunction and eosinophilic esophagitis. JCI Insight 2018; 3:99922. [PMID: 29669943 DOI: 10.1172/jci.insight.99922] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/14/2018] [Indexed: 12/20/2022] Open
Abstract
Eosinophilic esophagitis (EoE) is an allergic inflammatory esophageal disorder with a complex underlying genetic etiology often associated with other comorbidities. Using whole-exome sequencing (WES) of 63 patients with EoE and 60 unaffected family members and family-based trio analysis, we sought to uncover rare coding variants. WES analysis identified 5 rare, damaging variants in dehydrogenase E1 and transketolase domain-containing 1 (DHTKD1). Rare variant burden analysis revealed an overabundance of putative, potentially damaging DHTKD1 mutations in EoE (P = 0.01). Interestingly, we also identified 7 variants in the DHTKD1 homolog oxoglutarate dehydrogenase-like (OGDHL). Using shRNA-transduced esophageal epithelial cells and/or patient fibroblasts, we further showed that disruption of normal DHTKD1 or OGDHL expression blunts mitochondrial function. Finally, we demonstrated that the loss of DHTKD1 expression increased ROS production and induced the expression of viperin, a gene previously shown to be involved in production of Th2 cytokines in T cells. Viperin had increased expression in esophageal biopsies of EoE patients compared with control individuals and was upregulated by IL-13 in esophageal epithelial cells. These data identify a series of rare genetic variants implicating DHTKD1 and OGDHL in the genetic etiology of EoE and underscore a potential pathogenic role for mitochondrial dysfunction in EoE.
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Affiliation(s)
| | - Kiran Kc
- Division of Allergy and Immunology and
| | - Xinjian Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center (CCHMC), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Ting Wen
- Division of Allergy and Immunology and
| | - Adam Chamberlin
- Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | | | | | | | - Yanyan Peng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center (CCHMC), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Qiang Wu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center (CCHMC), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | | | | | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, CCHMC, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, CCHMC, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, CCHMC, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center (CCHMC), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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12
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Haberman Y, BenShoshan M, Di Segni A, Dexheimer PJ, Braun T, Weiss B, Walters TD, Baldassano RN, Noe JD, Markowitz J, Rosh J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Kellermayer R, Patel A, Otley A, Steiner SJ, Gulati AS, Guthery SL, LeLeiko N, Moulton D, Kirschner BS, Snapper S, Avivi C, Barshack I, Oliva-Hemker M, Cohen SA, Keljo DJ, Ziring D, Anikster Y, Aronow B, Hyams JS, Kugathasan S, Denson LA. Long ncRNA Landscape in the Ileum of Treatment-Naive Early-Onset Crohn Disease. Inflamm Bowel Dis 2018; 24:346-360. [PMID: 29361088 PMCID: PMC6231367 DOI: 10.1093/ibd/izx013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Long noncoding RNAs (lncRNA) are key regulators of gene transcription and many show tissue-specific expression. We previously defined a novel inflammatory and metabolic ileal gene signature in treatment-naive pediatric Crohn disease (CD). We now extend our analyses to include potential regulatory lncRNA. METHODS Using RNAseq, we systematically profiled lncRNAs and protein-coding gene expression in 177 ileal biopsies. Co-expression analysis was used to identify functions and tissue-specific expression. RNA in situ hybridization was used to validate expression. Real-time polymerase chain reaction was used to test lncRNA regulation by IL-1β in Caco-2 enterocytes. RESULTS We characterize widespread dysregulation of 459 lncRNAs in the ileum of CD patients. Using only the lncRNA in discovery and independent validation cohorts showed patient classification as accurate as the protein-coding genes, linking lncRNA to CD pathogenesis. Co-expression and functional annotation enrichment analyses across several tissues and cell types 1showed that the upregulated LINC01272 is associated with a myeloid pro-inflammatory signature, whereas the downregulated HNF4A-AS1 exhibits association with an epithelial metabolic signature. We confirmed tissue-specific expression in biopsies using in situ hybridization, and validated regulation of prioritized lncRNA upon IL-1β exposure in differentiated Caco-2 cells. Finally, we identified significant correlations between LINC01272 and HNF4A-AS1 expression and more severe mucosal injury. CONCLUSIONS We systematically define differentially expressed lncRNA in the ileum of newly diagnosed pediatric CD. We show lncRNA utility to correctly classify disease or healthy states and demonstrate their regulation in response to an inflammatory signal. These lncRNAs, after mechanistic exploration, may serve as potential new tissue-specific targets for RNA-based interventions.
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Affiliation(s)
- Yael Haberman
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Sheba Medical Center, Israel,Address correspondence to: Yael Haberman, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, MLC 2010, 3333 Burnet Avenue, Cincinnati, OH 45229 ()
| | | | | | | | | | - Batia Weiss
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | - Thomas D Walters
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Joel Rosh
- Goryeb Children’s Hospital/Atlantic Health, Morristown, New Jersey
| | - Melvin B Heyman
- University of California, San Francisco, San Francisco, California
| | - Anne M Griffiths
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | | | - David R Mack
- Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | | | - Ashish Patel
- UT Southwestern Medical Center at Dallas, Dallas, Texas
| | | | | | - Ajay S Gulati
- University of North Carolina, Chapel Hill, North Carolina
| | | | | | | | | | | | | | - Iris Barshack
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | | | - Stanley A Cohen
- Children’s Center for Digestive Healthcare, Atlanta, Georgia
| | - David J Keljo
- Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Yair Anikster
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | - Bruce Aronow
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Jeffrey S Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut
| | | | - Lee A Denson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
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13
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Salomonis N, Dexheimer PJ, Omberg L, Schroll R, Bush S, Huo J, Schriml L, Ho Sui S, Keddache M, Mayhew C, Shanmukhappa SK, Wells J, Daily K, Hubler S, Wang Y, Zambidis E, Margolin A, Hide W, Hatzopoulos AK, Malik P, Cancelas JA, Aronow BJ, Lutzko C. Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium. Stem Cell Reports 2016; 7:110-25. [PMID: 27293150 PMCID: PMC4944587 DOI: 10.1016/j.stemcr.2016.05.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 01/07/2023] Open
Abstract
The rigorous characterization of distinct induced pluripotent stem cells (iPSC) derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources of variability and downstream potential. To achieve this goal, the Progenitor Cell Biology Consortium performed comprehensive experimental and genomic analyses of 58 iPSC from ten laboratories generated using a variety of reprogramming genes, vectors, and cells. Associated global molecular characterization studies identified functionally informative correlations in gene expression, DNA methylation, and/or copy-number variation among key developmental and oncogenic regulators as a result of donor, sex, line stability, reprogramming technology, and cell of origin. Furthermore, X-chromosome inactivation in PSC produced highly correlated differences in teratoma-lineage staining and regulator expression upon differentiation. All experimental results, and raw, processed, and metadata from these analyses, including powerful tools, are interactively accessible from a new online portal at https://www.synapse.org to serve as a reusable resource for the stem cell community. Comprehensive portal for diverse iPSC, protocols, metadata, and genomic assays Recurrent CNV occur during reprogramming, impact oncogenes and tumor suppressors DNA methylation is influenced by cell of origin in iPSC PSC X-chromosome inactivation impacts lineage differentiation outcomes
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Affiliation(s)
- Nathan Salomonis
- Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Phillip J Dexheimer
- Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | | | - Robin Schroll
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Stacy Bush
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Jeffrey Huo
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Lynn Schriml
- Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shannan Ho Sui
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Mehdi Keddache
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Christopher Mayhew
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | | | - James Wells
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | | | | | - Yuliang Wang
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elias Zambidis
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Adam Margolin
- Sage Bionetworks, Seattle, WA 98109, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Winston Hide
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Antonis K Hatzopoulos
- Division of Cardiovascular Medicine, Departments of Medicine and Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Jose A Cancelas
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA; Hoxworth Blood Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Bruce J Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Carolyn Lutzko
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA; Hoxworth Blood Center, University of Cincinnati, Cincinnati, OH 45229, USA.
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Chen S, Brunskill EW, Potter SS, Dexheimer PJ, Salomonis N, Aronow BJ, Hong CI, Zhang T, Kopan R. Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan. Dev Cell 2016; 35:49-62. [PMID: 26460946 DOI: 10.1016/j.devcel.2015.09.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [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: 02/04/2015] [Revised: 07/22/2015] [Accepted: 09/14/2015] [Indexed: 01/24/2023]
Abstract
During fetal development, nephrons of the metanephric kidney form from a mesenchymal progenitor population that differentiates en masse before or shortly after birth. We explored intrinsic and extrinsic mechanisms controlling progenitor lifespan in a transplantation assay that allowed us to compare engraftment of old and young progenitors into the same young niche. The progenitors displayed an age-dependent decrease in proliferation and concomitant increase in niche exit rates. Single-cell transcriptome profiling revealed progressive age-dependent changes, with heterogeneity increasing in older populations. Age-dependent elevation in mTor and reduction in Fgf20 could contribute to increased exit rates. Importantly, 30% of old progenitors remained in the niche for up to 1 week post engraftment, a net gain of 50% to their lifespan, but only if surrounded by young neighbors. We provide evidence in support of a model in which intrinsic age-dependent changes affect inter-progenitor interactions that drive cessation of nephrogenesis.
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Affiliation(s)
- Shuang Chen
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45220, USA
| | - Eric W Brunskill
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45220, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45220, USA
| | - Phillip J Dexheimer
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45220, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45220, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45220, USA
| | - Christian I Hong
- Department of Molecular and Cellular Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Tongli Zhang
- Department of Molecular and Cellular Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Raphael Kopan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45220, USA.
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15
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Adams AK, Bolanos LC, Dexheimer PJ, Karns RA, Aronow BJ, Komurov K, Jegga AG, Casper KA, Patil YJ, Wilson KM, Starczynowski DT, Wells SI. IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival. Oncotarget 2015; 6:43395-407. [PMID: 26527316 PMCID: PMC4791239 DOI: 10.18632/oncotarget.6028] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/13/2015] [Indexed: 12/20/2022] Open
Abstract
The chromatin-binding DEK protein was recently reported to promote the growth of HPV+ and HPV- head and neck squamous cell carcinomas (HNSCCs). Relevant cellular and molecular mechanism(s) controlled by DEK in HNSCC remain poorly understood. While DEK is known to regulate specific transcriptional targets, global DEK-dependent gene networks in HNSCC are unknown. To identify DEK transcriptional signatures we performed RNA-Sequencing (RNA-Seq) in HNSCC cell lines that were either proficient or deficient for DEK. Bioinformatic analyses and subsequent validation revealed that IRAK1, a regulator of inflammatory signaling, and IRAK1-dependent regulatory networks were significantly repressed upon DEK knockdown in HNSCC. According to TCGA data, 14% of HNSCC specimens overexpressed IRAK1, thus supporting possible oncogenic functions. Furthermore, genetic or pharmacologic inhibition of IRAK1 in HNSCC cell lines was sufficient to attenuate downstream signaling such as ERK1/2 and to induce HNSCC cell death by apoptosis. Finally, targeting DEK and IRAK1 simultaneously enhanced cell death as compared to targeting either alone. Our findings reveal that IRAK1 promotes cell survival and is an attractive therapeutic target in HNSCC cells. Thus, we propose a model wherein IRAK1 stimulates tumor signaling and phenotypes both independently and in conjunction with DEK.
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Affiliation(s)
- Allie K. Adams
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lyndsey C. Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Phillip J. Dexheimer
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Rebekah A. Karns
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kakajan Komurov
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anil G. Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Keith A. Casper
- Department of Otolaryngology, Head and Neck Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Yash J. Patil
- Department of Otolaryngology, Head and Neck Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Keith M. Wilson
- Department of Otolaryngology, Head and Neck Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Daniel T. Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Susanne I. Wells
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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16
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Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA. Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest 2015; 125:1363. [PMID: 25729854 DOI: 10.1172/jci79657] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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17
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Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest 2014; 124:3617-33. [PMID: 25003194 DOI: 10.1172/jci75436] [Citation(s) in RCA: 357] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/29/2014] [Indexed: 12/13/2022] Open
Abstract
Interactions between the host and gut microbial community likely contribute to Crohn disease (CD) pathogenesis; however, direct evidence for these interactions at the onset of disease is lacking. Here, we characterized the global pattern of ileal gene expression and the ileal microbial community in 359 treatment-naive pediatric patients with CD, patients with ulcerative colitis (UC), and control individuals. We identified core gene expression profiles and microbial communities in the affected CD ilea that are preserved in the unaffected ilea of patients with colon-only CD but not present in those with UC or control individuals; therefore, this signature is specific to CD and independent of clinical inflammation. An abnormal increase of antimicrobial dual oxidase (DUOX2) expression was detected in association with an expansion of Proteobacteria in both UC and CD, while expression of lipoprotein APOA1 gene was downregulated and associated with CD-specific alterations in Firmicutes. The increased DUOX2 and decreased APOA1 gene expression signature favored oxidative stress and Th1 polarization and was maximally altered in patients with more severe mucosal injury. A regression model that included APOA1 gene expression and microbial abundance more accurately predicted month 6 steroid-free remission than a model using clinical factors alone. These CD-specific host and microbe profiles identify the ileum as the primary inductive site for all forms of CD and may direct prognostic and therapeutic approaches.
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18
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Myronovych A, Kirby M, Ryan KK, Zhang W, Jha P, Setchell KDR, Dexheimer PJ, Aronow B, Seeley RJ, Kohli R. Vertical sleeve gastrectomy reduces hepatic steatosis while increasing serum bile acids in a weight-loss-independent manner. Obesity (Silver Spring) 2014; 22:390-400. [PMID: 23804416 PMCID: PMC3836901 DOI: 10.1002/oby.20548] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/08/2013] [Accepted: 06/03/2013] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Our objective was to investigate the role of bile acids in hepatic steatosis reduction after vertical sleeve gastrectomy (VSG). DESIGN AND METHODS High fat diet (HFD)-induced obese C57Bl/6 mice were randomized to VSG, Sham operation (Sham), Sham operation with pair feeding to VSG (Sham-PF), or nonsurgical controls (Naïve). All mice were on HFD until sacrifice. Mice were observed postsurgery and data for body weight, body composition, metabolic parameters, serum bile acid level and composition were collected. Further hepatic gene expression by mRNA-seq and RT-PCR analysis was assessed. RESULTS VSG and Sham-PF mice lost equal weight postsurgery while VSG mice had the lowest hepatic triglyceride content at sacrifice. The VSG mice had elevated serum bile acid levels that positively correlated with maximal weight loss. Serum bile composition in the VSG group had increased cholic and tauroursodeoxycholic acid. These bile acid composition changes in VSG mice explained observed downregulation of hepatic lipogenic and bile acid synthetic genes. CONCLUSION VSG in obese mice results in greater hepatic steatosis reduction than seen with caloric restriction alone. VSG surgery increases serum bile acids that correlate with weight lost postsurgery and changes serum bile composition that could explain suppression of hepatic genes responsible for lipogenesis.
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Affiliation(s)
- Andriy Myronovych
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Michelle Kirby
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Karen K. Ryan
- Metabolic Diseases Institute, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Wujuan Zhang
- Department of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Pinky Jha
- Department of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kenneth DR Setchell
- Department of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Phillip J Dexheimer
- Department of Pediatrics, Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Bruce Aronow
- Department of Pediatrics, Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Randy J Seeley
- Metabolic Diseases Institute, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rohit Kohli
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
- Metabolic Diseases Institute, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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19
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Ding D, Scott NM, Thompson EE, Chaiworapongsa T, Torres R, Billstrand C, Murray K, Dexheimer PJ, Ismail M, Kay H, Levy S, Romero R, Lindheimer MD, Nicolae DL, Ober C. Increased protein-coding mutations in the mitochondrial genome of African American women with preeclampsia. Reprod Sci 2012; 19:1343-51. [PMID: 22902742 DOI: 10.1177/1933719112450337] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Preeclampsia occurs more frequently in women of African ancestry. The cause of this hypertensive complication is unclear, but placental oxidative stress may play a role. Because mitochondria are the major sites of oxidative phosphorylation, we hypothesized that placentas of preeclamptic pregnancies harbor mitochondrial DNA (mtDNA) mutations. Next-generation sequencing of placental mtDNA in African American preeclamptics (N = 30) and controls (N = 38) from Chicago revealed significant excesses in preeclamptics of nonsynonymous substitutions in protein-coding genes and mitochondrially encoded nicotinamide adenine dinucleotide dehydrogenase 5 gene and an increase in the substitution rate (P = .0001). Moreover, 88% of preeclamptics and 53% of controls carried at least one nonsynonymous substitution (P = .005; odds ratio [OR] = 6.36, 95% confidence interval [CI]: 1.5-39.1). These results were not replicated in a sample of African American preeclamptics (N = 162) and controls (N = 171) from Detroit. Differences in study design and heterogeneity may account for this lack of replication. Nonsynonymous substitutions in mtDNA may be risk factors for preeclampsia in some African American women, but additional studies are required to establish this relationship.
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Affiliation(s)
- David Ding
- Department of Obstetrics and Gynecology, The University of Chicago, Chicago, IL 60637, USA
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20
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Recchia FM, Xu L, Penn JS, Boone B, Dexheimer PJ. Identification of genes and pathways involved in retinal neovascularization by microarray analysis of two animal models of retinal angiogenesis. Invest Ophthalmol Vis Sci 2009; 51:1098-105. [PMID: 19834031 DOI: 10.1167/iovs.09-4006] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Comparative retinal gene expression analysis in two rodent models of oxygen-induced retinopathy (OIR) was performed to identify the genes and pathways involved in retinal neovascularization. METHODS Three independent experimental runs were conducted for each species, according to standard protocols for induction of OIR. Total retinal RNA was isolated at two time points, corresponding to the early response to relative hypoxia (P13 in mouse, P15 in rat) and to the later phase of maximum retinal neovascularization (P18 in mouse, P20 in rat) and was used to prepare labeled probes for hybridization. Gene expression was compared between normal and experimental conditions for each species at each time point. Probesets with a false-discovery rate of <or=0.05 were considered significantly different and were classified as cellular functions or biological pathways. Changes in expression of selected genes were confirmed by quantitative rtPCR. RESULTS At the early time point, there were changes in 43 genes in each species, with two in common. Increased expression of members of the VEGF and ephrin receptor signaling pathways were identified in both models. At the later time point, there were changes in 26 genes in the rat and in 1622 in the mouse, with 13 in common. Four pathways were identified in both models. CONCLUSIONS Genes and pathways known to be involved in angiogenesis, as well as other biologically plausible genes and pathways, were identified. This work serves as a comprehensive resource for the study of retinal neovascularization and identification of potential rational targets for antiangiogenic therapy.
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Affiliation(s)
- Franco M Recchia
- Retina Division, Vanderbilt Eye Institute, Nashville, Tennessee 37232, USA.
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21
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Watson JD, Wang S, Von Stetina SE, Spencer WC, Levy S, Dexheimer PJ, Kurn N, Heath JD, Miller DM. Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system. BMC Genomics 2008; 9:84. [PMID: 18284693 PMCID: PMC2263045 DOI: 10.1186/1471-2164-9-84] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2007] [Accepted: 02/19/2008] [Indexed: 11/14/2022] Open
Abstract
Background DNA microarrays provide a powerful method for global analysis of gene expression. The application of this technology to specific cell types and tissues, however, is typically limited by small amounts of available mRNA, thereby necessitating amplification. Here we compare microarray results obtained with two different methods of RNA amplification to profile gene expression in the C. elegans larval nervous system. Results We used the mRNA-tagging strategy to isolate transcripts specifically from C. elegans larval neurons. The WT-Ovation Pico System (WT-Pico) was used to amplify 2 ng of pan-neural RNA to produce labeled cDNA for microarray analysis. These WT-Pico-derived data were compared to microarray results obtained with a labeled aRNA target generated by two rounds of In Vitro Transcription (IVT) of 25 ng of pan-neural RNA. WT-Pico results in a higher fraction of present calls than IVT, a finding consistent with the proposal that DNA-DNA hybridization results in lower mismatch signals than the RNA-DNA heteroduplexes produced by IVT amplification. Microarray data sets from these samples were compared to a reference profile of all larval cells to identify transcripts with elevated expression in neurons. These results were validated by the high proportion of known neuron-expressed genes detected in these profiles and by promoter-GFP constructs for previously uncharacterized genes in these data sets. Together, the IVT and WT-Pico methods identified 2,173 unique neuron-enriched transcripts. Only about half of these transcripts (1,044), however, are detected as enriched by both IVT and WT-Pico amplification. Conclusion We show that two different methods of RNA amplification, IVT and WT-Pico, produce valid microarray profiles of gene expression in the C. elegans larval nervous system with a low rate of false positives. However, our results also show that each method of RNA amplification detects a unique subset of bona fide neural-enriched transcripts and thus a wider array of authentic neural genes are identified by the combination of these data sets than by the microarray profiles obtained with either method of RNA amplification alone. With its relative ease of implementation and greater sensitivity, WT-Pico is the preferred method of amplification for cases in which sample RNA is limiting.
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Affiliation(s)
- Joseph D Watson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232-8240, USA.
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