1
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Gaddis N, Fortriede J, Guo M, Bardes EE, Kouril M, Tabar S, Burns K, Ardini-Poleske ME, Loos S, Schnell D, Jin K, Iyer B, Du Y, Huo BX, Bhattacharjee A, Korte J, Munshi R, Smith V, Herbst A, Kitzmiller JA, Clair GC, Carson JP, Adkins J, Morrisey EE, Pryhuber GS, Misra R, Whitsett JA, Sun X, Heathorn T, Paten B, Prasath VBS, Xu Y, Tickle T, Aronow BJ, Salomonis N. LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. Am J Respir Cell Mol Biol 2024; 70:129-139. [PMID: 36413377 PMCID: PMC10848697 DOI: 10.1165/rcmb.2022-0165oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular imaging, and pathological datasets. To centralize and standardize information across broad lung research efforts, we expanded the LungMAP.net website into a new gateway portal. This portal connects a broad spectrum of research networks, bulk and single-cell multiomics data, and a diverse collection of image data that span mammalian lung development and disease. The data are standardized across species and technologies using harmonized data and metadata models that leverage recent advances, including those from the Human Cell Atlas, diverse ontologies, and the LungMAP CellCards initiative. To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, and mouse) to enable consistent queries across technologies, cohorts, age, disease, and drug treatment. These atlases are provided as independent and integrated queryable datasets, with an emphasis on dynamic visualization, figure generation, reanalysis, cell-type curation, and automated reference-based classification of user-provided single-cell genomics datasets (Azimuth). As this resource grows, we intend to increase the breadth of available interactive interfaces, supported data types, data portals and datasets from LungMAP, and external research efforts.
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Affiliation(s)
- Nathan Gaddis
- RTI International, Research Triangle Park, North Carolina
| | - Joshua Fortriede
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Minzhe Guo
- Division of Pulmonary Biology, The Perinatal Institute, and
| | - Eric E. Bardes
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Scott Tabar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kevin Burns
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | | | - Stephanie Loos
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Daniel Schnell
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Balaji Iyer
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
| | - Yina Du
- Division of Pulmonary Biology, The Perinatal Institute, and
| | - Bing-Xing Huo
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Anukana Bhattacharjee
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Jeff Korte
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ruchi Munshi
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Victoria Smith
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Andrew Herbst
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Geremy C. Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | - James P. Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas
| | - Joshua Adkins
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Edward E. Morrisey
- Department of Medicine and
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Ravi Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Jeffrey A. Whitsett
- Division of Pulmonary Biology, The Perinatal Institute, and
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Xin Sun
- Department of Pediatrics and
- Department of Biological Sciences, University of California, San Diego, San Diego, California; and
| | - Trevor Heathorn
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Yan Xu
- Division of Pulmonary Biology, The Perinatal Institute, and
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Tim Tickle
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
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2
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Jin K, Zhang Z, Zhang K, Viggiani F, Callahan C, Tang J, Aronow BJ, Shu J. Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings. bioRxiv 2023:2023.09.19.558548. [PMID: 37786667 PMCID: PMC10541596 DOI: 10.1101/2023.09.19.558548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Single-cell spatial transcriptomics such as in-situ hybridization or sequencing technologies can provide subcellular resolution that enables the identification of individual cell identities, locations, and a deep understanding of subcellular mechanisms. However, accurate segmentation and annotation that allows individual cell boundaries to be determined remains a major challenge that limits all the above and downstream insights. Current machine learning methods heavily rely on nuclei or cell body staining, resulting in the significant loss of both transcriptome depth and the limited ability to learn latent representations of spatial colocalization relationships. Here, we propose Bering, a graph deep learning model that leverages transcript colocalization relationships for joint noise-aware cell segmentation and molecular annotation in 2D and 3D spatial transcriptomics data. Graph embeddings for the cell annotation are transferred as a component of multi-modal input for cell segmentation, which is employed to enrich gene relationships throughout the process. To evaluate performance, we benchmarked Bering with state-of-the-art methods and observed significant improvement in cell segmentation accuracies and numbers of detected transcripts across various spatial technologies and tissues. To streamline segmentation processes, we constructed expansive pre-trained models, which yield high segmentation accuracy in new data through transfer learning and self-distillation, demonstrating the generalizability of Bering.
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Affiliation(s)
- Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Zuobai Zhang
- Mila - Québec AI Institute, Montréal, H2S 3H1, Québec, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, H3T 1J4, Québec, Canada
| | - Ke Zhang
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Francesca Viggiani
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Claire Callahan
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Jian Tang
- Mila - Québec AI Institute, Montréal, H2S 3H1, Québec, Canada
- Department of Decision Sciences, HEC Montréal, Montréal, H3T 2A7, Québec, Canada
- CIFAR AI Research Chair
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Jian Shu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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3
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Guo M, Morley MP, Jiang C, Wu Y, Li G, Du Y, Zhao S, Wagner A, Cakar AC, Kouril M, Jin K, Gaddis N, Kitzmiller JA, Stewart K, Basil MC, Lin SM, Ying Y, Babu A, Wikenheiser-Brokamp KA, Mun KS, Naren AP, Clair G, Adkins JN, Pryhuber GS, Misra RS, Aronow BJ, Tickle TL, Salomonis N, Sun X, Morrisey EE, Whitsett JA, Xu Y. Guided construction of single cell reference for human and mouse lung. Nat Commun 2023; 14:4566. [PMID: 37516747 PMCID: PMC10387117 DOI: 10.1038/s41467-023-40173-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 05/31/2022] [Accepted: 07/13/2023] [Indexed: 07/31/2023] Open
Abstract
Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive cell types, reproducible and functionally validated cell identities, and common nomenclatures are much needed by the research community for automated cell type annotation, data integration, and data sharing. Here, we develop a computational pipeline utilizing the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples to construct LungMAP single-cell reference (CellRef) for both normal human and mouse lungs. CellRefs define 48 human and 40 mouse lung cell types catalogued from diverse anatomic locations and developmental time points. We demonstrate the accuracy and stability of LungMAP CellRefs and their utility for automated cell type annotation of both normal and diseased lungs using multiple independent methods and testing data. We develop user-friendly web interfaces for easy access and maximal utilization of the LungMAP CellRefs.
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Affiliation(s)
- Minzhe Guo
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA.
| | - Michael P Morley
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Cheng Jiang
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Yixin Wu
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Yina Du
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Shuyang Zhao
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Andrew Wagner
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Adnan Cihan Cakar
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | | | - Joseph A Kitzmiller
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Kathleen Stewart
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria C Basil
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Susan M Lin
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yun Ying
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Apoorva Babu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn A Wikenheiser-Brokamp
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Kyu Shik Mun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Anjaparavanda P Naren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Gloria S Pryhuber
- Department of Pediatrics Division of Neonatology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Ravi S Misra
- Department of Pediatrics Division of Neonatology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Bruce J Aronow
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Timothy L Tickle
- Data Sciences Platform, The Broad Institute, Cambridge, MA, 02142, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Xin Sun
- Department of Pediatrics, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Department of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Edward E Morrisey
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jeffrey A Whitsett
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Yan Xu
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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4
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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] [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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5
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Ouyang X, Jessen WJ, Al-Ahmadie H, Serio AM, Lin Y, Shih WJ, Reuter VE, Scardino PT, Shen MM, Aronow BJ, Vickers AJ, Gerald WL, Abate-Shen C. Editor's Note: Activator Protein-1 Transcription Factors Are Associated with Progression and Recurrence of Prostate Cancer. Cancer Res 2023; 83:1161. [PMID: 37014042 DOI: 10.1158/0008-5472.can-23-0515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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6
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Tan ALM, Getzen EJ, Hutch MR, Strasser ZH, Gutiérrez-Sacristán A, Le TT, Dagliati A, Morris M, Hanauer DA, Moal B, Bonzel CL, Yuan W, Chiudinelli L, Das P, Zhang HG, Aronow BJ, Avillach P, Brat GA, Cai T, Hong C, La Cava WG, Hooi Will Loh H, Luo Y, Murphy SN, Yuan Hgiam K, Omenn GS, Patel LP, Jebathilagam Samayamuthu M, Shriver ER, Shakeri Hossein Abad Z, Tan BWL, Visweswaran S, Wang X, Weber GM, Xia Z, Verdy B, Long Q, Mowery DL, Holmes JH. Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record? J Biomed Inform 2023; 139:104306. [PMID: 36738870 PMCID: PMC10849195 DOI: 10.1016/j.jbi.2023.104306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/21/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND In electronic health records, patterns of missing laboratory test results could capture patients' course of disease as well as reflect clinician's concerns or worries for possible conditions. These patterns are often understudied and overlooked. This study aims to identify informative patterns of missingness among laboratory data collected across 15 healthcare system sites in three countries for COVID-19 inpatients. METHODS We collected and analyzed demographic, diagnosis, and laboratory data for 69,939 patients with positive COVID-19 PCR tests across three countries from 1 January 2020 through 30 September 2021. We analyzed missing laboratory measurements across sites, missingness stratification by demographic variables, temporal trends of missingness, correlations between labs based on missingness indicators over time, and clustering of groups of labs based on their missingness/ordering pattern. RESULTS With these analyses, we identified mapping issues faced in seven out of 15 sites. We also identified nuances in data collection and variable definition for the various sites. Temporal trend analyses may support the use of laboratory test result missingness patterns in identifying severe COVID-19 patients. Lastly, using missingness patterns, we determined relationships between various labs that reflect clinical behaviors. CONCLUSION In this work, we use computational approaches to relate missingness patterns to hospital treatment capacity and highlight the heterogeneity of looking at COVID-19 over time and at multiple sites, where there might be different phases, policies, etc. Changes in missingness could suggest a change in a patient's condition, and patterns of missingness among laboratory measurements could potentially identify clinical outcomes. This allows sites to consider missing data as informative to analyses and help researchers identify which sites are better poised to study particular questions.
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Affiliation(s)
| | - Emily J Getzen
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | - Trang T Le
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | - Priam Das
- Harvard Medical School, Cambridge, MA, USA
| | | | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Tianxi Cai
- Harvard Medical School, Cambridge, MA, USA
| | - Chuan Hong
- Harvard Medical School, Cambridge, MA, USA; Duke University, Durham, NC, USA
| | - William G La Cava
- Harvard Medical School, Cambridge, MA, USA; Boston Children's Hospital, Boston, MA, USA
| | | | - Yuan Luo
- Northwestern University, Chicago, IL, USA
| | | | | | | | - Lav P Patel
- University of Kansas Medical Center, United States
| | | | - Emily R Shriver
- University of Pennsylvania Health System, Philadelphia, PA, USA
| | | | | | | | - Xuan Wang
- Harvard Medical School, Cambridge, MA, USA
| | | | - Zongqi Xia
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Qi Long
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Danielle L Mowery
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - John H Holmes
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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7
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Gutiérrez-Sacristán A, Serret-Larmande A, Hutch MR, Sáez C, Aronow BJ, Bhatnagar S, Bonzel CL, Cai T, Devkota B, Hanauer DA, Loh NHW, Luo Y, Moal B, Ahooyi TM, Njoroge WFM, Omenn GS, Sanchez-Pinto LN, South AM, Sperotto F, Tan ALM, Taylor DM, Verdy G, Visweswaran S, Xia Z, Zahner J, Avillach P, Bourgeois FT. Hospitalizations Associated With Mental Health Conditions Among Adolescents in the US and France During the COVID-19 Pandemic. JAMA Netw Open 2022; 5:e2246548. [PMID: 36512353 PMCID: PMC9856226 DOI: 10.1001/jamanetworkopen.2022.46548] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/21/2022] [Indexed: 12/15/2022] Open
Abstract
Importance The COVID-19 pandemic has been associated with an increase in mental health diagnoses among adolescents, though the extent of the increase, particularly for severe cases requiring hospitalization, has not been well characterized. Large-scale federated informatics approaches provide the ability to efficiently and securely query health care data sets to assess and monitor hospitalization patterns for mental health conditions among adolescents. Objective To estimate changes in the proportion of hospitalizations associated with mental health conditions among adolescents following onset of the COVID-19 pandemic. Design, Setting, and Participants This retrospective, multisite cohort study of adolescents 11 to 17 years of age who were hospitalized with at least 1 mental health condition diagnosis between February 1, 2019, and April 30, 2021, used patient-level data from electronic health records of 8 children's hospitals in the US and France. Main Outcomes and Measures Change in the monthly proportion of mental health condition-associated hospitalizations between the prepandemic (February 1, 2019, to March 31, 2020) and pandemic (April 1, 2020, to April 30, 2021) periods using interrupted time series analysis. Results There were 9696 adolescents hospitalized with a mental health condition during the prepandemic period (5966 [61.5%] female) and 11 101 during the pandemic period (7603 [68.5%] female). The mean (SD) age in the prepandemic cohort was 14.6 (1.9) years and in the pandemic cohort, 14.7 (1.8) years. The most prevalent diagnoses during the pandemic were anxiety (6066 [57.4%]), depression (5065 [48.0%]), and suicidality or self-injury (4673 [44.2%]). There was an increase in the proportions of monthly hospitalizations during the pandemic for anxiety (0.55%; 95% CI, 0.26%-0.84%), depression (0.50%; 95% CI, 0.19%-0.79%), and suicidality or self-injury (0.38%; 95% CI, 0.08%-0.68%). There was an estimated 0.60% increase (95% CI, 0.31%-0.89%) overall in the monthly proportion of mental health-associated hospitalizations following onset of the pandemic compared with the prepandemic period. Conclusions and Relevance In this cohort study, onset of the COVID-19 pandemic was associated with increased hospitalizations with mental health diagnoses among adolescents. These findings support the need for greater resources within children's hospitals to care for adolescents with mental health conditions during the pandemic and beyond.
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Affiliation(s)
| | - Arnaud Serret-Larmande
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
- Department of Biostatistics and Biomedical Informatics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université Paris-Cité, Paris, France
| | - Meghan R Hutch
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Carlos Sáez
- Biomedical Data Science Lab, Instituto Universitario de Tecnologías de la Información y Comunicaciones, Universitat Politècnica de València, València, Spain
| | - Bruce J Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Surbhi Bhatnagar
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Batsal Devkota
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - David A Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor
| | - Ne Hooi Will Loh
- Department of Anaesthesia, National University Health System, Singapore
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Bertrand Moal
- Unité Informatique et Archivistique Médicale, Bordeaux University Hospital, Bordeaux, France
| | - Taha Mohseni Ahooyi
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Wanjiku F M Njoroge
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Gilbert S Omenn
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor
| | - L Nelson Sanchez-Pinto
- Department of Pediatrics (Critical Care), Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrew M South
- Department of Pediatrics-Section of Nephrology, Brenner Children's, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Francesca Sperotto
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amelia L M Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Guillaume Verdy
- Unité Informatique et Archivistique Médicale, Bordeaux University Hospital, Bordeaux, France
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Janet Zahner
- Department of Information Services, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Florence T Bourgeois
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
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8
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Jin K, Schnell D, Li G, Salomonis N, Prasath VBS, Szczesniak R, Aronow BJ. CellDrift: inferring perturbation responses in temporally sampled single-cell data. Brief Bioinform 2022; 23:6673850. [PMID: 35998893 PMCID: PMC9487655 DOI: 10.1093/bib/bbac324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/27/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Cells and tissues respond to perturbations in multiple ways that can be sensitively reflected in the alterations of gene expression. Current approaches to finding and quantifying the effects of perturbations on cell-level responses over time disregard the temporal consistency of identifiable gene programs. To leverage the occurrence of these patterns for perturbation analyses, we developed CellDrift (https://github.com/KANG-BIOINFO/CellDrift), a generalized linear model-based functional data analysis method that is capable of identifying covarying temporal patterns of various cell types in response to perturbations. As compared to several other approaches, CellDrift demonstrated superior performance in the identification of temporally varied perturbation patterns and the ability to impute missing time points. We applied CellDrift to multiple longitudinal datasets, including COVID-19 disease progression and gastrointestinal tract development, and demonstrated its ability to identify specific gene programs associated with sequential biological processes, trajectories and outcomes.
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Affiliation(s)
- Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Daniel Schnell
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45256, USA
| | - V B Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA.,Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45256, USA
| | - Rhonda Szczesniak
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, OH 45229, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45256, USA.,Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45256, USA
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9
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Zhang HG, Dagliati A, Shakeri Hossein Abad Z, Xiong X, Bonzel CL, Xia Z, Tan BWQ, Avillach P, Brat GA, Hong C, Morris M, Visweswaran S, Patel LP, Gutiérrez-Sacristán A, Hanauer DA, Holmes JH, Samayamuthu MJ, Bourgeois FT, L'Yi S, Maidlow SE, Moal B, Murphy SN, Strasser ZH, Neuraz A, Ngiam KY, Loh NHW, Omenn GS, Prunotto A, Dalvin LA, Klann JG, Schubert P, Vidorreta FJS, Benoit V, Verdy G, Kavuluru R, Estiri H, Luo Y, Malovini A, Tibollo V, Bellazzi R, Cho K, Ho YL, Tan ALM, Tan BWL, Gehlenborg N, Lozano-Zahonero S, Jouhet V, Chiovato L, Aronow BJ, Toh EMS, Wong WGS, Pizzimenti S, Wagholikar KB, Bucalo M, Cai T, South AM, Kohane IS, Weber GM. International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. NPJ Digit Med 2022; 5:81. [PMID: 35768548 PMCID: PMC9242995 DOI: 10.1038/s41746-022-00623-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/19/2022] [Indexed: 11/10/2022] Open
Abstract
The risk profiles of post-acute sequelae of COVID-19 (PASC) have not been well characterized in multi-national settings with appropriate controls. We leveraged electronic health record (EHR) data from 277 international hospitals representing 414,602 patients with COVID-19, 2.3 million control patients without COVID-19 in the inpatient and outpatient settings, and over 221 million diagnosis codes to systematically identify new-onset conditions enriched among patients with COVID-19 during the post-acute period. Compared to inpatient controls, inpatient COVID-19 cases were at significant risk for angina pectoris (RR 1.30, 95% CI 1.09–1.55), heart failure (RR 1.22, 95% CI 1.10–1.35), cognitive dysfunctions (RR 1.18, 95% CI 1.07–1.31), and fatigue (RR 1.18, 95% CI 1.07–1.30). Relative to outpatient controls, outpatient COVID-19 cases were at risk for pulmonary embolism (RR 2.10, 95% CI 1.58–2.76), venous embolism (RR 1.34, 95% CI 1.17–1.54), atrial fibrillation (RR 1.30, 95% CI 1.13–1.50), type 2 diabetes (RR 1.26, 95% CI 1.16–1.36) and vitamin D deficiency (RR 1.19, 95% CI 1.09–1.30). Outpatient COVID-19 cases were also at risk for loss of smell and taste (RR 2.42, 95% CI 1.90–3.06), inflammatory neuropathy (RR 1.66, 95% CI 1.21–2.27), and cognitive dysfunction (RR 1.18, 95% CI 1.04–1.33). The incidence of post-acute cardiovascular and pulmonary conditions decreased across time among inpatient cases while the incidence of cardiovascular, digestive, and metabolic conditions increased among outpatient cases. Our study, based on a federated international network, systematically identified robust conditions associated with PASC compared to control groups, underscoring the multifaceted cardiovascular and neurological phenotype profiles of PASC.
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Affiliation(s)
- Harrison G Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Arianna Dagliati
- Department of Electrical Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | | | - Xin Xiong
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryce W Q Tan
- Department of Medicine, National University Hospital, Singapore, Singapore
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Gabriel A Brat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lav P Patel
- Department of Internal Medicine, Division of Medical Informatics, University Of Kansas Medical Center, Kansas City, MO, USA
| | | | - David A Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John H Holmes
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sarah E Maidlow
- Michigan Institute for Clinical and Health Research (MICHR) Informatics, University of Michigan, Ann Arbor, MI, USA
| | - Bertrand Moal
- IAM unit, Bordeaux University Hospital, Bordeaux, France
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Antoine Neuraz
- Department of biomedical informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris (APHP), University of Paris, Paris, France
| | - Kee Yuan Ngiam
- Department of Biomedical informatics, WiSDM, National University Health Systems Singapore, Singapore, Singapore
| | - Ne Hooi Will Loh
- Department of Anaesthesia, National University Health Systems Singapore, Singapore, Singapore
| | - Gilbert S Omenn
- Department of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Prunotto
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Lauren A Dalvin
- Department of Ophthalmology, Mayo Clinic, Rochester, NY, USA
| | - Jeffrey G Klann
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Petra Schubert
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | | | - Vincent Benoit
- IT Department, Innovation & Data, APHP Greater Paris University Hospital, Paris, France
| | | | - Ramakanth Kavuluru
- Division of Biomedical Informatics (Department of Internal Medicine), University of Kentucky, Lexington, KY, USA
| | - Hossein Estiri
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Valentina Tibollo
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA.,Population Health and Data Science, VA Boston Healthcare System, Boston, MA, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Amelia L M Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Byorn W L Tan
- Department of Medicine, National University Hospital, Singapore, Singapore
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sara Lozano-Zahonero
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Vianney Jouhet
- IAM unit, INSERM Bordeaux Population Health ERIAS TEAM, Bordeaux University Hospital / ERIAS - Inserm, U1219 BPH, Bordeaux, France
| | - Luca Chiovato
- Unit of Internal Medicine and Endocrinology, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Bruce J Aronow
- Departments of Biomedical Informatics, Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Emma M S Toh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wei Gen Scott Wong
- Department of Medicine, National University Health Systems Singapore, Singapore, Singapore
| | - Sara Pizzimenti
- Scientific Direction, IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | | | - Mauro Bucalo
- BIOMERIS (BIOMedical Research Informatics Solutions), Pavia, Italy
| | | | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andrew M South
- Department of Pediatrics-Section of Nephrology, Brenner Children's, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Griffin M Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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10
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Weber GM, Hong C, Xia Z, Palmer NP, Avillach P, L'Yi S, Keller MS, Murphy SN, Gutiérrez-Sacristán A, Bonzel CL, Serret-Larmande A, Neuraz A, Omenn GS, Visweswaran S, Klann JG, South AM, Loh NHW, Cannataro M, Beaulieu-Jones BK, Bellazzi R, Agapito G, Alessiani M, Aronow BJ, Bell DS, Benoit V, Bourgeois FT, Chiovato L, Cho K, Dagliati A, DuVall SL, Barrio NG, Hanauer DA, Ho YL, Holmes JH, Issitt RW, Liu M, Luo Y, Lynch KE, Maidlow SE, Malovini A, Mandl KD, Mao C, Matheny ME, Moore JH, Morris JS, Morris M, Mowery DL, Ngiam KY, Patel LP, Pedrera-Jimenez M, Ramoni RB, Schriver ER, Schubert P, Balazote PS, Spiridou A, Tan ALM, Tan BWL, Tibollo V, Torti C, Trecarichi EM, Wang X, Kohane IS, Cai T, Brat GA. International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. NPJ Digit Med 2022; 5:74. [PMID: 35697747 PMCID: PMC9192605 DOI: 10.1038/s41746-022-00601-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/11/2022] [Indexed: 01/08/2023] Open
Abstract
Given the growing number of prediction algorithms developed to predict COVID-19 mortality, we evaluated the transportability of a mortality prediction algorithm using a multi-national network of healthcare systems. We predicted COVID-19 mortality using baseline commonly measured laboratory values and standard demographic and clinical covariates across healthcare systems, countries, and continents. Specifically, we trained a Cox regression model with nine measured laboratory test values, standard demographics at admission, and comorbidity burden pre-admission. These models were compared at site, country, and continent level. Of the 39,969 hospitalized patients with COVID-19 (68.6% male), 5717 (14.3%) died. In the Cox model, age, albumin, AST, creatine, CRP, and white blood cell count are most predictive of mortality. The baseline covariates are more predictive of mortality during the early days of COVID-19 hospitalization. Models trained at healthcare systems with larger cohort size largely retain good transportability performance when porting to different sites. The combination of routine laboratory test values at admission along with basic demographic features can predict mortality in patients hospitalized with COVID-19. Importantly, this potentially deployable model differs from prior work by demonstrating not only consistent performance but also reliable transportability across healthcare systems in the US and Europe, highlighting the generalizability of this model and the overall approach.
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Affiliation(s)
- Griffin M Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, USA
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, USA
| | - Nathan P Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Mark S Keller
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, USA
| | | | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Arnaud Serret-Larmande
- Department of biomedical informatics, Hôpital Européen Georges Pompidou, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Antoine Neuraz
- Department of biomedical informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris (APHP), University of Paris, Paris, France
| | - Gilbert S Omenn
- Department of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, USA
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA
| | - Jeffrey G Klann
- Department of Medicine, Massachusetts General Hospital, Boston, USA
| | - Andrew M South
- Department of Pediatrics-Section of Nephrology, Brenner Children's Hospital, Wake Forest School of Medicine, Winston Salem, USA
| | - Ne Hooi Will Loh
- Department of Anaesthesia, National University Health System, Singapore, Singapore, Singapore
| | - Mario Cannataro
- Department of Medical and Surgical Sciences, Data Analytics Research Center, University Magna Graecia of Catanzaro, Italy, Catanzaro, Italy
| | | | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Italy, Pavia, Italy
| | - Giuseppe Agapito
- Department of Legal, Economic and Social Sciences, University Magna Graecia of Catanzaro, Italy, Catanzaro, Italy
| | - Mario Alessiani
- Department of Surgery, ASST Pavia, Lombardia Region Health System, Pavia, Italy
| | - Bruce J Aronow
- Departments of Biomedical Informatics, Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, USA
| | - Douglas S Bell
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Vincent Benoit
- IT department, Innovation & Data, APHP Greater Paris University Hospital, Paris, France
| | | | - Luca Chiovato
- Unit of Internal Medicine and Endocrinology, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
| | - Arianna Dagliati
- Department of Electrical Computer and Biomedical Engineering, University of Pavia, Italy, Pavia, Italy
| | - Scott L DuVall
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, USA
| | | | - David A Hanauer
- Department of Learning Health Sciences, University of Michigan, Ann Arbor, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
| | - John H Holmes
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Richard W Issitt
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, UK, London, UK
| | - Molei Liu
- Department of Biostatistics, Harvard School of Public Health, Boston, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Chicago, USA
| | - Kristine E Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, USA
| | - Sarah E Maidlow
- Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor, USA
| | - Alberto Malovini
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, Boston, USA
| | - Chengsheng Mao
- Department of Preventive Medicine, Northwestern University, Chicago, USA
| | - Michael E Matheny
- VA Informatics and Computing Infrastructure, Tennessee Valley Healthcare System Veterans Affairs Medical Center, Nashville, USA
| | - Jason H Moore
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Jeffrey S Morris
- Department of Biostatistics, Epidemiology, and Biostatistics, University of Pennysylvania Perelman School of Medicine, Philadelphia, USA
| | - Michele Morris
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA
| | - Danielle L Mowery
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Kee Yuan Ngiam
- Department of Biomedical informatics, WiSDM, National University Health Systems Singapore, Singapore, Singapore
| | - Lav P Patel
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, Kansas City, USA
| | | | - Rachel B Ramoni
- Office of Research and Development, Department of Veterans Affairs, Washington, DC, USA
| | - Emily R Schriver
- Data Analytics Center, University of Pennsylvania Health System, Philadelphia, USA
| | - Petra Schubert
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
| | | | - Anastasia Spiridou
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, UK, London, UK
| | - Amelia L M Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Byorn W L Tan
- Department of Medicine, National University Hospital, Singapore, Singapore, Singapore
| | - Valentina Tibollo
- Laboratory of Informatics and Systems Engineering for Clinical Research, Istituti Clinici Scientifici Maugeri SpA SB IRCCS, Pavia, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, Infectious and Tropical Disease Unit, University Magna Graecia of Catanzaro, Italy, Catanzaro, Italy
| | - Enrico M Trecarichi
- Department of Medical and Surgical Sciences, Infectious and Tropical Disease Unit, University Magna Graecia of Catanzaro, Italy, Catanzaro, Italy
| | - Xuan Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA.
| | - Gabriel A Brat
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA.
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11
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Barrila J, Yang J, Franco Meléndez KP, Yang S, Buss K, Davis TJ, Aronow BJ, Bean HD, Davis RR, Forsyth RJ, Ott CM, Gangaraju S, Kang BY, Hanratty B, Nydam SD, Nauman EA, Kong W, Steel J, Nickerson CA. Spaceflight Analogue Culture Enhances the Host-Pathogen Interaction Between Salmonella and a 3-D Biomimetic Intestinal Co-Culture Model. Front Cell Infect Microbiol 2022; 12:705647. [PMID: 35711662 PMCID: PMC9195300 DOI: 10.3389/fcimb.2022.705647] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Physical forces associated with spaceflight and spaceflight analogue culture regulate a wide range of physiological responses by both bacterial and mammalian cells that can impact infection. However, our mechanistic understanding of how these environments regulate host-pathogen interactions in humans is poorly understood. Using a spaceflight analogue low fluid shear culture system, we investigated the effect of Low Shear Modeled Microgravity (LSMMG) culture on the colonization of Salmonella Typhimurium in a 3-D biomimetic model of human colonic epithelium containing macrophages. RNA-seq profiling of stationary phase wild type and Δhfq mutant bacteria alone indicated that LSMMG culture induced global changes in gene expression in both strains and that the RNA binding protein Hfq played a significant role in regulating the transcriptional response of the pathogen to LSMMG culture. However, a core set of genes important for adhesion, invasion, and motility were commonly induced in both strains. LSMMG culture enhanced the colonization (adherence, invasion and intracellular survival) of Salmonella in this advanced model of intestinal epithelium using a mechanism that was independent of Hfq. Although S. Typhimurium Δhfq mutants are normally defective for invasion when grown as conventional shaking cultures, LSMMG conditions unexpectedly enabled high levels of colonization by an isogenic Δhfq mutant. In response to infection with either the wild type or mutant, host cells upregulated transcripts involved in inflammation, tissue remodeling, and wound healing during intracellular survival. Interestingly, infection by the Δhfq mutant led to fewer transcriptional differences between LSMMG- and control-infected host cells relative to infection with the wild type strain. This is the first study to investigate the effect of LSMMG culture on the interaction between S. Typhimurium and a 3-D model of human intestinal tissue. These findings advance our understanding of how physical forces can impact the early stages of human enteric salmonellosis.
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Affiliation(s)
- Jennifer Barrila
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- *Correspondence: Jennifer Barrila, ; Cheryl A. Nickerson,
| | - Jiseon Yang
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Karla P. Franco Meléndez
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Gainesville, FL, United States
| | - Shanshan Yang
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, United States
| | - Kristina Buss
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, United States
| | - Trenton J. Davis
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Heather D. Bean
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Richard R. Davis
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Rebecca J. Forsyth
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - C. Mark Ott
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX, United States
| | - Sandhya Gangaraju
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Bianca Y. Kang
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Brian Hanratty
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, United States
| | - Seth D. Nydam
- Department of Animal Care & Technologies, Arizona State University, Tempe, AZ, United States
| | - Eric A. Nauman
- School of Mechanical Engineering, Weldon School of Biomedical Engineering and Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, United States
| | - Wei Kong
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, United States
| | - Jason Steel
- Bioinformatics Core Facility, Bioscience, Knowledge Enterprise, Arizona State University, Tempe, AZ, United States
| | - Cheryl A. Nickerson
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- *Correspondence: Jennifer Barrila, ; Cheryl A. Nickerson,
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12
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Katsuma D, Kawanaka H, Prasath VBS, Aronow BJ. Data Augmentation Using Generative Adversarial Networks for Multi-Class Segmentation of Lung Confocal IF Images. JACIII 2022. [DOI: 10.20965/jaciii.2022.p0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human lung is a complex organ with high cellular heterogeneity, and its development and maintenance require interactive gene networks and dynamic cross-talk among multiple cell types. We focus on the confocal immunofluorescent (IF) images of lung tissues from the LungMAP database to reveal lung development. Using the current state-of-the-art deep learning-based model, the authors consider obtaining accurate multi-class segmentation of lung confocal IF images. One of the primary bottlenecks in using deep Convolutional Neural Network (CNN) models is the lack of availability of large-scale training or ground-truth segmentation labels. Then, we implement the multi-class segmentation with Generative Adversarial Network (GAN) models to expand the training dataset, improve overall segmentation accuracy, and discuss the effectiveness of created synthetic images in the segmentation of IF images. Consequently, experimental results indicated that 15.1% increased the accuracy of six-class segmentation using Mask R-CNN. In particular, the accuracy of our few data was mainly improved by using our proposed method. Therefore, the synthetic dataset can moderate the imbalanced data and be used for expanding the dataset.
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13
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Locker KC, Kachapati K, Wu Y, Bednar KJ, Adams D, Patel C, Tsukamoto H, Heuer LS, Aronow BJ, Herr AB, Ridgway WM. Endosomal Sequestration of TLR4 Antibody Induces Myeloid-Derived Suppressor Cells and Reverses Acute Type 1 Diabetes. Diabetes 2022; 71:470-482. [PMID: 35040474 PMCID: PMC8893939 DOI: 10.2337/db21-0426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/08/2021] [Indexed: 11/13/2022]
Abstract
We previously showed that treating NOD mice with an agonistic monoclonal anti-TLR4/MD2 antibody (TLR4-Ab) reversed acute type 1 diabetes (T1D). Here, we show that TLR4-Ab reverses T1D by induction of myeloid-derived suppressor cells (MDSCs). Unbiased gene expression analysis after TLR4-Ab treatment demonstrated upregulation of genes associated with CD11b+Ly6G+ myeloid cells and downregulation of T-cell genes. Further RNA sequencing of purified, TLR4-Ab-treated CD11b+ cells showed significant upregulation of genes associated with bone marrow-derived CD11b+ cells and innate immune system genes. TLR4-Ab significantly increased percentages and numbers of CD11b+ cells. TLR4-Ab-induced CD11b+ cells, derived ex vivo from TLR4-Ab-treated mice, suppress T cells, and TLR4-Ab-conditioned bone marrow cells suppress acute T1D when transferred into acutely diabetic mice. Thus, the TLR4-Ab-induced CD11b+ cells, by the currently accepted definition, are MDSCs able to reverse T1D. To understand the TLR4-Ab mechanism, we compared TLR4-Ab with TLR4 agonist lipopolysaccharide (LPS), which cannot reverse T1D. TLR4-Ab remains sequestered at least 48 times longer than LPS within early endosomes, alters TLR4 signaling, and downregulates inflammatory genes and proteins, including nuclear factor-κB. TLR4-Ab in the endosome, therefore, induces a sustained, attenuated inflammatory response, providing an ideal "second signal" for the activation/maturation of MDSCs that can reverse acute T1D.
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Affiliation(s)
- Kathryn C.S. Locker
- Division of Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH
- Immunology Graduate Program, Cincinnati Children’s Hospital Medical Center, and University of Cincinnati College of Medicine, Cincinnati, OH
| | - Kritika Kachapati
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Yuehong Wu
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Kyle J. Bednar
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - David Adams
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Caroline Patel
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Hiroki Tsukamoto
- Department of Pharmaceutical Sciences, School of Pharmacy at Fukuoka International University of Health and Welfare, Okawa, Fukuoka, Japan
| | - Luke S. Heuer
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA
| | - Bruce J. Aronow
- Division of Bioinformatics, Cincinnati Children’s Hospital, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Infectious Diseases, Cincinnati Children’s Hospital, Cincinnati, OH
| | - William M. Ridgway
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA
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14
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Sun X, Perl AK, Li R, Bell SM, Sajti E, Kalinichenko VV, Kalin TV, Misra RS, Deshmukh H, Clair G, Kyle J, Crotty Alexander LE, Masso-Silva JA, Kitzmiller JA, Wikenheiser-Brokamp KA, Deutsch G, Guo M, Du Y, Morley MP, Valdez MJ, Yu HV, Jin K, Bardes EE, Zepp JA, Neithamer T, Basil MC, Zacharias WJ, Verheyden J, Young R, Bandyopadhyay G, Lin S, Ansong C, Adkins J, Salomonis N, Aronow BJ, Xu Y, Pryhuber G, Whitsett J, Morrisey EE. A census of the lung: CellCards from LungMAP. Dev Cell 2022; 57:112-145.e2. [PMID: 34936882 PMCID: PMC9202574 DOI: 10.1016/j.devcel.2021.11.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/19/2021] [Accepted: 11/05/2021] [Indexed: 01/07/2023]
Abstract
The human lung plays vital roles in respiration, host defense, and basic physiology. Recent technological advancements such as single-cell RNA sequencing and genetic lineage tracing have revealed novel cell types and enriched functional properties of existing cell types in lung. The time has come to take a new census. Initiated by members of the NHLBI-funded LungMAP Consortium and aided by experts in the lung biology community, we synthesized current data into a comprehensive and practical cellular census of the lung. Identities of cell types in the normal lung are captured in individual cell cards with delineation of function, markers, developmental lineages, heterogeneity, regenerative potential, disease links, and key experimental tools. This publication will serve as the starting point of a live, up-to-date guide for lung research at https://www.lungmap.net/cell-cards/. We hope that Lung CellCards will promote the community-wide effort to establish, maintain, and restore respiratory health.
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Affiliation(s)
- Xin Sun
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Anne-Karina Perl
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Rongbo Li
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sheila M Bell
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Eniko Sajti
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vladimir V Kalinichenko
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA; Center for Lung Regenerative Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Tanya V Kalin
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Ravi S Misra
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Hitesh Deshmukh
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Geremy Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer Kyle
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Laura E Crotty Alexander
- Deparment of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jorge A Masso-Silva
- Deparment of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph A Kitzmiller
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Kathryn A Wikenheiser-Brokamp
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Gail Deutsch
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA; Department of Laboratories, Seattle Children's Hospital, OC.8.720, 4800 Sand Point Way Northeast, Seattle, WA 98105, USA
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Yina Du
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Michael P Morley
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael J Valdez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haoze V Yu
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kang Jin
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Eric E Bardes
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jarod A Zepp
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Terren Neithamer
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria C Basil
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William J Zacharias
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Internal Medicine, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Jamie Verheyden
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Randee Young
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Gautam Bandyopadhyay
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sara Lin
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Ansong
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua Adkins
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce J Aronow
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Gloria Pryhuber
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeff Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Edward E Morrisey
- Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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15
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Jin K, Bardes EE, Mitelpunkt A, Wang JY, Bhatnagar S, Sengupta S, Krummel DP, Rothenberg ME, Aronow BJ. An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses. iScience 2021; 24:103115. [PMID: 34522848 PMCID: PMC8428985 DOI: 10.1016/j.isci.2021.103115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a data mine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to interacting with, exploring, and functional evaluating these modules via a new interactive web portal ToppCell (http://toppcell.cchmc.org/). As examples, we develop three hypotheses: (1) alternatively-differentiated monocyte-derived macrophages form a multicelllar signaling cascade that drives T cell recruitment and activation; (2) COVID-19-generated platelet subtypes exhibit dramatically altered potential to adhere, coagulate, and thrombose; and (3) extrafollicular B maturation is driven by a multilineage cell activation network that expresses an ensemble of genes strongly associated with risk for developing post-viral autoimmunity.
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Affiliation(s)
- Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Eric E Bardes
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Alexis Mitelpunkt
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Pediatric Rehabilitation, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, 6423906, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Jake Y Wang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Surbhi Bhatnagar
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Soma Sengupta
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Daniel Pomeranz Krummel
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45256, USA
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16
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Mo A, Nagpal S, Gettler K, Haritunians T, Giri M, Haberman Y, Karns R, Prince J, Arafat D, Hsu NY, Chuang LS, Argmann C, Kasarskis A, Suarez-Farinas M, Gotman N, Mengesha E, Venkateswaran S, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, LeLeiko NS, Heyman MB, Griffiths AM, Patel AS, Noe JD, Davis Thomas S, Aronow BJ, Walters TD, McGovern DPB, Hyams JS, Kugathasan S, Cho JH, Denson LA, Gibson G. Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. Am J Hum Genet 2021; 108:1765-1779. [PMID: 34450030 DOI: 10.1016/j.ajhg.2021.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of individuals with ulcerative colitis (UC) require colectomy within 5 years of diagnosis, but polygenic risk scores (PRSs) utilizing findings from genome-wide association studies (GWASs) are unable to provide meaningful prediction of this adverse status. By contrast, in Crohn disease, gene expression profiling of GWAS-significant genes does provide some stratification of risk of progression to complicated disease in the form of a transcriptional risk score (TRS). Here, we demonstrate that a measured TRS based on bulk rectal gene expression in the PROTECT inception cohort study has a positive predictive value approaching 50% for colectomy. Single-cell profiling demonstrates that the genes are active in multiple diverse cell types from both the epithelial and immune compartments. Expression quantitative trait locus (QTL) analysis identifies genes with differential effects at baseline and week 52 follow-up, but for the most part, differential expression associated with colectomy risk is independent of local genetic regulation. Nevertheless, a predicted polygenic transcriptional risk score (PPTRS) derived by summation of transcriptome-wide association study (TWAS) effects identifies UC-affected individuals at 5-fold elevated risk of colectomy with data from the UK Biobank population cohort studies, independently replicated in an NIDDK-IBDGC dataset. Prediction of gene expression from relatively small transcriptome datasets can thus be used in conjunction with TWASs for stratification of risk of disease complications.
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Affiliation(s)
- Angela Mo
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sini Nagpal
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kyle Gettler
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mamta Giri
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yael Haberman
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Sheba Medical Center, Tel Hashomer, Tel Aviv University, Tel Aviv 5265601, Israel
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dalia Arafat
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nai-Yun Hsu
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ling-Shiang Chuang
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Carmen Argmann
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Andrew Kasarskis
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Nathan Gotman
- University of North Carolina, Chapel Hill, NC 27516, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Paul A Rufo
- Harvard University-Children's Hospital Boston, Boston, MA 02115, USA
| | - Susan S Baker
- Women & Children's Hospital of Buffalo, Buffalo, NY 14222, USA
| | | | - James Markowitz
- Cohen Children's Medical Center of New York, New Hyde Park, NY 11040, USA
| | | | - Joel R Rosh
- Goryeb Children's Hospital-Atlantic Health, Morristown, NJ 07960, USA
| | | | - David R Mack
- Children's Hospital of East Ontario, Ottawa, ON K1P 1J1, Canada
| | | | - Sapana Shah
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Neal S LeLeiko
- Department of Pediatrics, Columbia University, New York City, NY 10032, USA
| | - Melvin B Heyman
- University of California at San Francisco, San Francisco, CA 94143, USA
| | | | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, CT 06106, USA
| | | | - Judy H Cho
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Greg Gibson
- Georgia Institute of Technology, Atlanta, GA 30332, USA.
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17
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Kerlavage AR, Kirchhoff AC, Guidry Auvil JM, Sharpless NE, Davis KL, Reilly K, Reaman G, Penberthy L, Deapen D, Hwang A, Durbin EB, Gallotto SL, Aplenc R, Volchenboum SL, Heath AP, Aronow BJ, Zhang J, Vaske O, Alonzo TA, Nathan PC, Poynter JN, Armstrong G, Hahn EE, Wernli KJ, Greene C, DiGiovanna J, Resnick AC, Shalley ER, Nadaf S, Kibbe WA. Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer. JCO Clin Cancer Inform 2021; 5:881-896. [PMID: 34428097 PMCID: PMC8763339 DOI: 10.1200/cci.21.00040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/11/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022] Open
Abstract
Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute-funded cancer centers. This consortium has regularly held topic-focused biannual face-to-face symposiums. These meetings are a place to review cancer informatics and data science priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues that we faced at our respective institutions and cancer centers. Here, we provide meeting highlights from the latest CI4CC Symposium, which was delayed from its original April 2020 schedule because of the COVID-19 pandemic and held virtually over three days (September 24, October 1, and October 8) in the fall of 2020. In addition to the content presented, we found that holding this event virtually once a week for 6 hours was a great way to keep the kind of deep engagement that a face-to-face meeting engenders. This is the second such publication of CI4CC Symposium highlights, the first covering the meeting that took place in Napa, California, from October 14-16, 2019. We conclude with some thoughts about using data science to learn from every child with cancer, focusing on emerging activities of the National Cancer Institute's Childhood Cancer Data Initiative.
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Affiliation(s)
- Anthony R Kerlavage
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | - Anne C Kirchhoff
- Huntsman Cancer Institute and University of Utah, School of Medicine, Salt Lake City, UT
| | - Jaime M Guidry Auvil
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | | | - Kara L Davis
- Maternal and Child Health Research Institute, Stanford School of Medicine, Stanford, CA
| | - Karlyne Reilly
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Gregory Reaman
- Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, MD
| | - Lynne Penberthy
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD
| | - Dennis Deapen
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Amie Hwang
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Eric B Durbin
- University of Kentucky, Markey Cancer Center, Lexington, KY
| | | | | | | | | | | | | | - Olena Vaske
- University of California, Santa Cruz, Santa Cruz, CA
| | - Todd A Alonzo
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | | | - Jenny N Poynter
- University of Minnesota, Masonic Cancer Center, Minneapolis, MN
| | | | - Erin E Hahn
- Kaiser Permanente Southern California, Los Angeles, CA
| | - Karen J Wernli
- Kaiser Permanente Washington Health Research Institute, Seattle, WA
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18
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Lewis CS, Karve A, Matiash K, Stone T, Li J, Wang JK, Versteeg HH, Aronow BJ, Ahmad SA, Desai PB, Bogdanov VY. A First-In-Class, Humanized Antibody Targeting Alternatively Spliced Tissue Factor: Preclinical Evaluation in an Orthotopic Model of Pancreatic Ductal Adenocarcinoma. Front Oncol 2021; 11:691685. [PMID: 34395257 PMCID: PMC8358774 DOI: 10.3389/fonc.2021.691685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/28/2021] [Indexed: 01/22/2023] Open
Abstract
In 2021, pancreatic ductal adenocarcinoma (PDAC) is the 3rd leading cause of cancer deaths in the United States. This is largely due to a lack of symptoms and limited treatment options, which extend survival by only a few weeks. There is thus an urgent need to develop new therapies effective against PDAC. Previously, we have shown that the growth of PDAC cells is suppressed when they are co-implanted with RabMab1, a rabbit monoclonal antibody specific for human alternatively spliced tissue factor (asTF). Here, we report on humanization of RabMab1, evaluation of its binding characteristics, and assessment of its in vivo properties. hRabMab1 binds asTF with a KD in the picomolar range; suppresses the migration of high-grade Pt45.P1 cells in Boyden chamber assays; has a long half-life in circulation (~ 5 weeks); and significantly slows the growth of pre-formed orthotopic Pt45.P1 tumors in athymic nude mice when administered intravenously. Immunohistochemical analysis of tumor tissue demonstrates the suppression of i) PDAC cell proliferation, ii) macrophage infiltration, and iii) neovascularization, whereas RNAseq analysis of tumor tissue reveals the suppression of pathways that promote cell division and focal adhesion. This is the first proof-of-concept study whereby a novel biologic targeting asTF has been investigated as a systemically administered single agent, with encouraging results. Given that hRabMab1 has a favorable PK profile and is able to suppress the growth of human PDAC cells in vivo, it comprises a promising candidate for further clinical development.
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Affiliation(s)
- Clayton S Lewis
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Aniruddha Karve
- Division of Pharmaceutical Sciences, University of Cincinnati College of Pharmacy, Cincinnati, OH, United States
| | - Kateryna Matiash
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Timothy Stone
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Jingxing Li
- Technology Development, LakePharma, Inc., Belmont, CA, United States
| | - Jordon K Wang
- Technology Development, LakePharma, Inc., Belmont, CA, United States
| | - Henri H Versteeg
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Bruce J Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital and Medical Center, Cincinnati, OH, United States
| | - Syed A Ahmad
- Division of Surgical Oncology, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Pankaj B Desai
- Division of Pharmaceutical Sciences, University of Cincinnati College of Pharmacy, Cincinnati, OH, United States
| | - Vladimir Y Bogdanov
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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19
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Jin K, Bardes EE, Mitelpunkt A, Wang JY, Bhatnagar S, Sengupta S, Krummel DP, Rothenberg ME, Aronow BJ. Implicating Gene and Cell Networks Responsible for Differential COVID-19 Host Responses via an Interactive Single Cell Web Portal. bioRxiv 2021:2021.06.07.447287. [PMID: 34127975 PMCID: PMC8202427 DOI: 10.1101/2021.06.07.447287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a datamine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to probe these via a new interactive web portal (http://toppcell.cchmc.org/COVID-19). As examples, we develop three hypotheses: (1) a multicellular signaling cascade among alternatively differentiated monocyte-derived macrophages whose tasks include T cell recruitment and activation; (2) novel platelet subtypes with drastically modulated expression of genes responsible for adhesion, coagulation and thrombosis; and (3) a multilineage cell activator network able to drive extrafollicular B maturation via an ensemble of genes strongly associated with risk for developing post-viral autoimmunity.
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Affiliation(s)
- Kang Jin
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Eric E. Bardes
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Alexis Mitelpunkt
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Pediatric Rehabilitation, Dana-Dwek Children’s Hospital, Tel Aviv Medical Center, Tel Aviv, 6423906, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Jake Y. Wang
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Surbhi Bhatnagar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Soma Sengupta
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Daniel Pomeranz Krummel
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Marc E. Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, 45256, USA
- Lead contact
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20
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Bourgeois FT, Gutiérrez-Sacristán A, Keller MS, Liu M, Hong C, Bonzel CL, Tan ALM, Aronow BJ, Boeker M, Booth J, Cruz Rojo J, Devkota B, García Barrio N, Gehlenborg N, Geva A, Hanauer DA, Hutch MR, Issitt RW, Klann JG, Luo Y, Mandl KD, Mao C, Moal B, Moshal KL, Murphy SN, Neuraz A, Ngiam KY, Omenn GS, Patel LP, Jiménez MP, Sebire NJ, Balazote PS, Serret-Larmande A, South AM, Spiridou A, Taylor DM, Tippmann P, Visweswaran S, Weber GM, Kohane IS, Cai T, Avillach P. International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries. JAMA Netw Open 2021; 4:e2112596. [PMID: 34115127 PMCID: PMC8196345 DOI: 10.1001/jamanetworkopen.2021.12596] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IMPORTANCE Additional sources of pediatric epidemiological and clinical data are needed to efficiently study COVID-19 in children and youth and inform infection prevention and clinical treatment of pediatric patients. OBJECTIVE To describe international hospitalization trends and key epidemiological and clinical features of children and youth with COVID-19. DESIGN, SETTING, AND PARTICIPANTS This retrospective cohort study included pediatric patients hospitalized between February 2 and October 10, 2020. Patient-level electronic health record (EHR) data were collected across 27 hospitals in France, Germany, Spain, Singapore, the UK, and the US. Patients younger than 21 years who tested positive for COVID-19 and were hospitalized at an institution participating in the Consortium for Clinical Characterization of COVID-19 by EHR were included in the study. MAIN OUTCOMES AND MEASURES Patient characteristics, clinical features, and medication use. RESULTS There were 347 males (52%; 95% CI, 48.5-55.3) and 324 females (48%; 95% CI, 44.4-51.3) in this study's cohort. There was a bimodal age distribution, with the greatest proportion of patients in the 0- to 2-year (199 patients [30%]) and 12- to 17-year (170 patients [25%]) age range. Trends in hospitalizations for 671 children and youth found discrete surges with variable timing across 6 countries. Data from this cohort mirrored national-level pediatric hospitalization trends for most countries with available data, with peaks in hospitalizations during the initial spring surge occurring within 23 days in the national-level and 4CE data. A total of 27 364 laboratory values for 16 laboratory tests were analyzed, with mean values indicating elevations in markers of inflammation (C-reactive protein, 83 mg/L; 95% CI, 53-112 mg/L; ferritin, 417 ng/mL; 95% CI, 228-607 ng/mL; and procalcitonin, 1.45 ng/mL; 95% CI, 0.13-2.77 ng/mL). Abnormalities in coagulation were also evident (D-dimer, 0.78 ug/mL; 95% CI, 0.35-1.21 ug/mL; and fibrinogen, 477 mg/dL; 95% CI, 385-569 mg/dL). Cardiac troponin, when checked (n = 59), was elevated (0.032 ng/mL; 95% CI, 0.000-0.080 ng/mL). Common complications included cardiac arrhythmias (15.0%; 95% CI, 8.1%-21.7%), viral pneumonia (13.3%; 95% CI, 6.5%-20.1%), and respiratory failure (10.5%; 95% CI, 5.8%-15.3%). Few children were treated with COVID-19-directed medications. CONCLUSIONS AND RELEVANCE This study of EHRs of children and youth hospitalized for COVID-19 in 6 countries demonstrated variability in hospitalization trends across countries and identified common complications and laboratory abnormalities in children and youth with COVID-19 infection. Large-scale informatics-based approaches to integrate and analyze data across health care systems complement methods of disease surveillance and advance understanding of epidemiological and clinical features associated with COVID-19 in children and youth.
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Affiliation(s)
- Florence T. Bourgeois
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts
| | | | - Mark S. Keller
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Molei Liu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Clara-Lea Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Amelia L. M. Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Bruce J. Aronow
- Departments of Biomedical Informatics, Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Ohio
| | - Martin Boeker
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| | - John Booth
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, London, United Kingdom
| | - Jaime Cruz Rojo
- Department of Health Informatics, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Batsal Devkota
- Department of Biomedical Health Informatics and the Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Noelia García Barrio
- Department of Health Informatics, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Alon Geva
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts
| | - David A. Hanauer
- Department of Learning Health Sciences, University of Michigan, Ann Arbor
| | - Meghan R. Hutch
- Department of Preventive Medicine, Northwestern University, Evanston, Illinois
| | - Richard W. Issitt
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, London, United Kingdom
| | | | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Evanston, Illinois
| | - Kenneth D. Mandl
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts
| | - Chengsheng Mao
- Department of Preventive Medicine, Northwestern University, Evanston, Illinois
| | - Bertrand Moal
- IAM Unit, Bordeaux University Hospital, Bordeaux, France
| | - Karyn L. Moshal
- Department of Infectious Diseases, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Shawn N. Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Antoine Neuraz
- Department of Biomedical Informatics, Hôpital Necker-Enfants Malade, Assistance Publique Hôpitaux de Paris, University of Paris, Paris, France
| | - Kee Yuan Ngiam
- Department of Biomedical informatics, WiSDM, National University Health Systems Singapore, Singapore
| | - Gilbert S Omenn
- Department of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, & School of Public Health, University of Michigan, Ann Arbor
| | - Lav P. Patel
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, Kansas City
| | | | - Neil J. Sebire
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, London, United Kingdom
| | | | | | - Andrew M. South
- Department of Pediatrics-Section of Nephrology, Brenner Children's Hospital, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Anastasia Spiridou
- Digital Research, Informatics and Virtual Environments (DRIVE), Great Ormond Street Hospital for Children, London, United Kingdom
| | - Deanne M. Taylor
- Department of Biomedical Health Informatics and the Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman Medical School at the University of Pennsylvania, Philadelphia
| | - Patric Tippmann
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany
| | - Shyam Visweswaran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Griffin M. Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Paul Avillach
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
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21
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Kohane IS, Aronow BJ, Avillach P, Beaulieu-Jones BK, Bellazzi R, Bradford RL, Brat GA, Cannataro M, Cimino JJ, García-Barrio N, Gehlenborg N, Ghassemi M, Gutiérrez-Sacristán A, Hanauer DA, Holmes JH, Hong C, Klann JG, Loh NHW, Luo Y, Mandl KD, Daniar M, Moore JH, Murphy SN, Neuraz A, Ngiam KY, Omenn GS, Palmer N, Patel LP, Pedrera-Jiménez M, Sliz P, South AM, Tan ALM, Taylor DM, Taylor BW, Torti C, Vallejos AK, Wagholikar KB, Weber GM, Cai T. What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask. J Med Internet Res 2021; 23:e22219. [PMID: 33600347 PMCID: PMC7927948 DOI: 10.2196/22219] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/14/2020] [Accepted: 01/10/2021] [Indexed: 12/13/2022] Open
Abstract
Coincident with the tsunami of COVID-19–related publications, there has been a surge of studies using real-world data, including those obtained from the electronic health record (EHR). Unfortunately, several of these high-profile publications were retracted because of concerns regarding the soundness and quality of the studies and the EHR data they purported to analyze. These retractions highlight that although a small community of EHR informatics experts can readily identify strengths and flaws in EHR-derived studies, many medical editorial teams and otherwise sophisticated medical readers lack the framework to fully critically appraise these studies. In addition, conventional statistical analyses cannot overcome the need for an understanding of the opportunities and limitations of EHR-derived studies. We distill here from the broader informatics literature six key considerations that are crucial for appraising studies utilizing EHR data: data completeness, data collection and handling (eg, transformation), data type (ie, codified, textual), robustness of methods against EHR variability (within and across institutions, countries, and time), transparency of data and analytic code, and the multidisciplinary approach. These considerations will inform researchers, clinicians, and other stakeholders as to the recommended best practices in reviewing manuscripts, grants, and other outputs from EHR-data derived studies, and thereby promote and foster rigor, quality, and reliability of this rapidly growing field.
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Affiliation(s)
- Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Bruce J Aronow
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | | | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.,ICS Maugeri, Pavia, Italy
| | - Robert L Bradford
- North Carolina Translational and Clinical Sciences Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gabriel A Brat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Mario Cannataro
- Data Analytics Research Center, University Magna Graecia of Catanzaro, Catanzaro, Italy.,Department of Medical and Surgical Sciences, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - James J Cimino
- Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Marzyeh Ghassemi
- Department of Computer Science and Medicine, University of Toronto, Toronto, ON, Canada
| | | | - David A Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI, United States
| | - John H Holmes
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Chuan Hong
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Jeffrey G Klann
- Department of Medicine, Harvard Medical School, Boston, MA, United States.,Laboratory of Computer Science, Massachusetts General Hospital, Boston, MA, United States
| | | | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Chicago, IL, United States
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
| | - Mohamad Daniar
- Clinical Research Informatics, Boston Children's Hospital, Boston, MA, United States
| | - Jason H Moore
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, United States
| | - Shawn N Murphy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.,Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Antoine Neuraz
- Department of Biomedical Informatics, Necker-Enfant Malades Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France.,Centre de Recherche des Cordeliers, INSERM UMRS 1138 Team 22, Université de Paris, Paris, France
| | - Kee Yuan Ngiam
- National University Health Systems, Singapore, Singapore
| | - Gilbert S Omenn
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Nathan Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Lav P Patel
- Department of Internal Medicine, Division of Medical Informatics, University of Kansas Medical Center, Kansas City, KS, United States
| | | | - Piotr Sliz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, United States
| | - Andrew M South
- Section of Nephrology, Department of Pediatrics, Brenner Children's Hospital, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Amelia Li Min Tan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.,Department of Biomedical Informatics, National University of Singapore, Singapore, Singapore
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, United States
| | - Bradley W Taylor
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Carlo Torti
- Department of Medical and Surgical Sciences, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Andrew K Vallejos
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Kavishwar B Wagholikar
- Department of Medicine, Harvard Medical School, Boston, MA, United States.,Laboratory of Computer Science, Massachusetts General Hospital, Boston, MA, United States
| | | | - Griffin M Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
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22
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Weber GM, Hong C, Palmer NP, Avillach P, Murphy SN, Gutiérrez-Sacristán A, Xia Z, Serret-Larmande A, Neuraz A, Omenn GS, Visweswaran S, Klann JG, South AM, Loh NHW, Cannataro M, Beaulieu-Jones BK, Bellazzi R, Agapito G, Alessiani M, Aronow BJ, Bell DS, Bellasi A, Benoit V, Beraghi M, Boeker M, Booth J, Bosari S, Bourgeois FT, Brown NW, Bucalo M, Chiovato L, Chiudinelli L, Dagliati A, Devkota B, DuVall SL, Follett RW, Ganslandt T, García Barrio N, Gradinger T, Griffier R, Hanauer DA, Holmes JH, Horki P, Huling KM, Issitt RW, Jouhet V, Keller MS, Kraska D, Liu M, Luo Y, Lynch KE, Malovini A, Mandl KD, Mao C, Maram A, Matheny ME, Maulhardt T, Mazzitelli M, Milano M, Moore JH, Morris JS, Morris M, Mowery DL, Naughton TP, Ngiam KY, Norman JB, Patel LP, Pedrera Jimenez M, Ramoni RB, Schriver ER, Scudeller L, Sebire NJ, Serrano Balazote P, Spiridou A, Tan AL, Tan BW, Tibollo V, Torti C, Trecarichi EM, Vitacca M, Zambelli A, Zucco C, Kohane IS, Cai T, Brat GA. International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe COVID-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study. medRxiv 2021:2020.12.16.20247684. [PMID: 33564777 PMCID: PMC7872369 DOI: 10.1101/2020.12.16.20247684] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Objectives To perform an international comparison of the trajectory of laboratory values among hospitalized patients with COVID-19 who develop severe disease and identify optimal timing of laboratory value collection to predict severity across hospitals and regions. Design Retrospective cohort study. Setting The Consortium for Clinical Characterization of COVID-19 by EHR (4CE), an international multi-site data-sharing collaborative of 342 hospitals in the US and in Europe. Participants Patients hospitalized with COVID-19, admitted before or after PCR-confirmed result for SARS-CoV-2. Primary and secondary outcome measures Patients were categorized as "ever-severe" or "never-severe" using the validated 4CE severity criteria. Eighteen laboratory tests associated with poor COVID-19-related outcomes were evaluated for predictive accuracy by area under the curve (AUC), compared between the severity categories. Subgroup analysis was performed to validate a subset of laboratory values as predictive of severity against a published algorithm. A subset of laboratory values (CRP, albumin, LDH, neutrophil count, D-dimer, and procalcitonin) was compared between North American and European sites for severity prediction. Results Of 36,447 patients with COVID-19, 19,953 (43.7%) were categorized as ever-severe. Most patients (78.7%) were 50 years of age or older and male (60.5%). Longitudinal trajectories of CRP, albumin, LDH, neutrophil count, D-dimer, and procalcitonin showed association with disease severity. Significant differences of laboratory values at admission were found between the two groups. With the exception of D-dimer, predictive discrimination of laboratory values did not improve after admission. Sub-group analysis using age, D-dimer, CRP, and lymphocyte count as predictive of severity at admission showed similar discrimination to a published algorithm (AUC=0.88 and 0.91, respectively). Both models deteriorated in predictive accuracy as the disease progressed. On average, no difference in severity prediction was found between North American and European sites. Conclusions Laboratory test values at admission can be used to predict severity in patients with COVID-19. Prediction models show consistency across international sites highlighting the potential generalizability of these models.
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Affiliation(s)
- Griffin M Weber
- Harvard Medical School, Department of Biomedical Informatics
| | - Chuan Hong
- Harvard Medical School, Department of Biomedical Informatics
| | - Nathan P Palmer
- Harvard Medical School, Department of Biomedical Informatics
| | - Paul Avillach
- Harvard Medical School, Department of Biomedical Informatics
| | | | | | | | - Arnaud Serret-Larmande
- Ho pital Européen Georges Pompidou, Assistance Publique - Ho pitaux de Paris, Department of biomedical informatics
| | | | - Gilbert S Omenn
- University of Michigan, Dept of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John Booth
- Great Ormond Street Hospital for Children
| | - Silvano Bosari
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico
| | | | | | - Mauro Bucalo
- BIOMERIS (BIOMedical Research Informatics Solutions)
| | | | | | | | | | | | | | - Thomas Ganslandt
- Ruprecht Karls University Heidelberg Faculty of Medicine Mannheim
| | | | - Tobias Gradinger
- Ruprecht Karls University Heidelberg Faculty of Medicine Mannheim
| | | | - David A Hanauer
- University of Michigan Institute for Healthcare Policy & Innovation
| | - John H Holmes
- University of Pennsylvania Perelman School of Medicine
| | | | | | | | | | - Mark S Keller
- Harvard Medical School, Department of Biomedical Informatics
| | | | - Molei Liu
- Harvard University T H Chan School of Public Health
| | | | | | | | - Kenneth D Mandl
- Boston Children's Hospital, Computational Health Informatics Program
| | | | | | | | | | | | | | - Jason H Moore
- University of Pennsylvania Perelman School of Medicine
| | | | | | | | | | | | - James B Norman
- Harvard Medical School, Department of Biomedical Informatics
| | | | | | | | | | | | | | | | | | - Amelia Lm Tan
- Harvard Medical School, Department of Biomedical Informatics
| | | | | | | | | | | | | | | | - Isaac S Kohane
- Harvard Medical School, Department of Biomedical Informatics
| | - Tianxi Cai
- Harvard Medical School, Department of Biomedical Informatics
| | - Gabriel A Brat
- Beth Israel Deaconess Medical Center, Surgery
- Harvard Medical School, Department of Biomedical Informatics
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23
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Sarangdhar M, Yacyshyn MB, Gruenzel AR, Engevik MA, Harris NL, Aronow BJ, Yacyshyn BR. Therapeutic Opportunities for Intestinal Angioectasia- Targeting PPARγ and Oxidative Stress. Clin Transl Sci 2020; 14:518-528. [PMID: 33048460 PMCID: PMC7993272 DOI: 10.1111/cts.12899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/30/2020] [Indexed: 01/22/2023] Open
Abstract
Recurrent and acute bleeding from intestinal tract angioectasia (AEC) presents a major challenge for clinical intervention. Current treatments are empiric, with frequent poor clinical outcomes. Improvements in understanding the pathophysiology of these lesions will help guide treatment. Using data from the US Food and Drug Administration (FDA)'s Adverse Event Reporting System (FAERS), we analyzed 12 million patient reports to identify drugs inversely correlated with gastrointestinal bleeding and potentially limiting AEC severity. FAERS analysis revealed that drugs used in patients with diabetes and those targeting PPARγ-related mechanisms were associated with decreased AEC phenotypes (P < 0.0001). Electronic health records (EHRs) at University of Cincinnati Hospital were analyzed to validate FAERS analysis. EHR data showed a 5.6% decrease in risk of AEC and associated phenotypes in patients on PPARγ agonists. Murine knockout models of AEC phenotypes were used to construct a gene-regulatory network of candidate drug targets and pathways, which revealed that wound healing, vasculature development and regulation of oxidative stress were impacted in AEC pathophysiology. Human colonic tissue was examined for expression differences across key pathway proteins, PPARγ, HIF1α, VEGF, and TGFβ1. In vitro analysis of human AEC tissues showed lower expression of PPARγ and TGFβ1 compared with controls (0.55 ± 0.07 and 0.49 ± 0.05). National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) RNA-Seq data was analyzed to substantiate human tissue findings. This integrative discovery approach showing altered expression of key genes involved in oxidative stress and injury repair mechanisms presents novel insight into AEC etiology, which will improve targeted mechanistic studies and more optimal medical therapy for AEC.
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Affiliation(s)
- Mayur Sarangdhar
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mary B Yacyshyn
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio, USA
| | - Andrew R Gruenzel
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Department of Anesthesiology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Melinda A Engevik
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio, USA.,Department of Pathology, Baylor College of Medicine, Houston, Texas, USA
| | - Nathaniel L Harris
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Bruce J Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Bruce R Yacyshyn
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio, USA.,Division of Gastroenterology, Hepatology and Nutrition, University of Louisville, Louisville, Kentucky, USA
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24
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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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25
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Khalil H, Jones SM, Alam P, Aronow BJ, Molkentin JD, Kanisicak O. Abstract 837: Different Disease States in Heart Have Distinct Cardiac Interstitial Cells Contributing to Fibrosis. Circ Res 2019. [DOI: 10.1161/res.125.suppl_1.837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cardiac fibrosis is a grim consequence for almost all myocardial injuries. In myocardial infarction (MI), what starts as a protective scarring process to prevent ventricular wall rupture becomes a pathological remodeling of the tissue with the accumulation of excess extracellular matrix (ECM) proteins. Eventually, this adaptation impedes the mechanical and electrical properties of the myocardium resulting in heart failure. Recently, we showed that periostin (Postn) expressing resident cardiac fibroblasts (CFs) are a potential therapeutic target since they differentiate into the scar associated, matrix-producing myofibroblasts (MFs) after injury. In fact, deletion of these cells after an acute injury eliminates interstitial fibrosis but results in ventricular rupture which is a hallmark outcome of impaired ECM deposition during the acute phase of MI. On the other hand, ablation of these cells during a chronic injury such as pressure overload-induced cardiac fibrosis model, we observe sustained perivascular fibrosis. Previous studies report heterogeneity of origin and function for ECM producing cells associated with different cardiac diseases. Here we utilized several novel mouse models that permit lineage tracing of all activated MFs as well as perivascular mural cells in the heart to elucidate the role and fate of these distinct cardiac interstitial cells during fibrogenesis. Cells were lineage traced with a tamoxifen-inducible cre recombinase cDNA knock-in alleles (PostnMCM and Gli1CreER) in combination with a Rosa26-eGFP cre-dependent reporter. Hearts subjected to MI, TAC or Angiotensin injury were processed for extensive histological and RNAseq analyses. Results show that interstitial fibrosis in acute MI injury is a result of Postn+ MFs activity, whereas a subset of Gli1+ mural cells are responsible for the perivascular fibrosis observed after pressure overload models. Therefore, we concluded that pathological ECM deposition resulting in fibrosis comes from disease-specific specialized sub-populations of interstitial cells of the heart with distinct gene expressions and require manipulation of alternative cell- and state-specific therapeutic targets.
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Affiliation(s)
- Hadi Khalil
- Cincinnati Children's Hosp Med Cntr, Cincinnati, OH
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26
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Wen T, Aronow BJ, Rochman Y, Rochman M, Kc K, Dexheimer PJ, Putnam P, Mukkada V, Foote H, Rehn K, Darko S, Douek D, Rothenberg ME. Single-cell RNA sequencing identifies inflammatory tissue T cells in eosinophilic esophagitis. J Clin Invest 2019; 129:2014-2028. [PMID: 30958799 DOI: 10.1172/jci125917] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/21/2019] [Indexed: 12/26/2022] Open
Abstract
T cell heterogeneity is highly relevant to allergic disorders. We resolved the heterogeneity of human tissue CD3+ T cells during allergic inflammation, focusing on a tissue-specific allergic disease, eosinophilic esophagitis (EoE). We investigated 1088 single T cells derived from patients with a spectrum of disease activity. Eight disparate tissue T cell subtypes (designated T1-T8) were identified, with T7 and T8 enriched in the diseased tissue. The phenotypes of T7 and T8 resemble putative Treg (FOXP3+) and effector Th2-like (GATA3+) cells, respectively. Prodigious levels of IL-5 and IL-13 were confined to HPGDS+ CRTH2+IL-17RB+FFAR3+CD4+ T8 effector Th2 cells. EoE severity closely paralleled a lipid/fatty acid-induced activation node highlighted by the expression of the short-chain fatty acid receptor FFAR3. Ligands for FFAR3 induced Th2 cytokine production from human and murine T cells, including in an in vivo allergy model. Therefore, we elucidated the defining characteristics of tissue-residing CD3+ T cells in EoE, a specific enrichment of CD4+ Treg and effector Th2 cells, confinement of type 2 cytokine production to the CD4+ effector population, a highly likely role for FFAR3 in amplifying local Th2 responses in EoE, and a resource to further dissect tissue lymphocytes and allergic responses.
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Affiliation(s)
- Ting Wen
- Division of Allergy and Immunology
| | | | | | | | - Kiran Kc
- Division of Allergy and Immunology
| | | | - Philip Putnam
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Vincent Mukkada
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
| | | | | | - Sam Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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27
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Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, Bönnemann CG, Mandl KD, White PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Dev Cell 2019; 49:10-29. [PMID: 30930166 PMCID: PMC6616346 DOI: 10.1016/j.devcel.2019.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/11/2019] [Accepted: 03/01/2019] [Indexed: 12/15/2022]
Abstract
Single-cell gene expression analyses of mammalian tissues have uncovered profound stage-specific molecular regulatory phenomena that have changed the understanding of unique cell types and signaling pathways critical for lineage determination, morphogenesis, and growth. We discuss here the case for a Pediatric Cell Atlas as part of the Human Cell Atlas consortium to provide single-cell profiles and spatial characterization of gene expression across human tissues and organs. Such data will complement adult and developmentally focused HCA projects to provide a rich cytogenomic framework for understanding not only pediatric health and disease but also environmental and genetic impacts across the human lifespan.
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Affiliation(s)
- Deanne M Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, and the Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Bruce J Aronow
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA.
| | - Kai Tan
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, and the Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Kathrin Bernt
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan Salomonis
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA
| | - Casey S Greene
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA 19102, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alina Frolova
- Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Kyiv 03143, Ukraine
| | - Sarah E Henrickson
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia and the Institute for Immunology, the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Andrew Wells
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Liming Pei
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jyoti K Jaiswal
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA; Center for Genetic Medicine Research, Children's National Medical Center, NW, Washington, DC, 20010-2970, USA
| | - Jeffrey Whitsett
- Cincinnati Children's Hospital Medical Center, Section of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati, OH 45229, USA
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sonya A MacParland
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Departments of Laboratory Medicine and Pathobiology and Immunology, University of Toronto, Toronto, ON, Canada
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert O Heuckeroth
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - S Steven Potter
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Laura A Vella
- Division of Infectious Diseases, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Natalie A Terry
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Louis R Ghanem
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Benjamin C Kennedy
- Division of Neurosurgery, Department of Surgery, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia and the Institute for Immunology, the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Leslie Castelo-Soccio
- Department of Pediatrics, Section of Dermatology, The Children's Hospital of Philadelphia and University of Pennsylvania Perleman School of Medicine, Philadelphia, PA 19104, USA
| | - Arnold Kreigstein
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Florian Herse
- Experimental and Clinical Research Center, A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Department of Pediatric Pulmonology and Pediatric Allergology, and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Melissa Haendel
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA; Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jo Lynne Rokita
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yuanchao Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Koch Institure of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer E Rood
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy L Tickle
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, South Cambridgeshire CB10 1SA, UK
| | - Saif Alimohamed
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA
| | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Jessica C Mar
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Kathleen M Loomes
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David M Barrett
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Prech Uapinyoying
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Center for Genetic Medicine Research, Children's National Medical Center, NW, Washington, DC, 20010-2970, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- The Manton Center for Orphan Disease Research, Divisions of Newborn Medicine and of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yi-Wen Chen
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA; Center for Genetic Medicine Research, Children's National Medical Center, NW, Washington, DC, 20010-2970, USA
| | - Amanda B Muir
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Lana X Garmire
- Department of Computational Medicine & Bioinformatics, The University of Michigan Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Javad Nazarian
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA; Center for Genetic Medicine Research, Children's National Medical Center, NW, Washington, DC, 20010-2970, USA
| | - Steven H Seeholzer
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hossein Fazelinia
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Pichai Raman
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Noor Dawany
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hongbo Michael Xie
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Batsal Devkota
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sharon J Diskin
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A Anderson
- Department of Psychiatry, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric F Rappaport
- Nucleic Acid PCR Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - William Peranteau
- Department of Surgery, Division of General, Thoracic, and Fetal Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kathryn A Wikenheiser-Brokamp
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Divisions of Pathology & Laboratory Medicine and Pulmonary Biology in the Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sarah Teichmann
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, South Cambridgeshire CB10 1SA, UK; European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, South Cambridgeshire CB10 1SA, UK; Cavendish Laboratory, Theory of Condensed Matter, 19 JJ Thomson Ave, Cambridge CB3 1SA, UK
| | - Douglas Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Tao Peng
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, and the Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yang-Yang Ding
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Man S Kim
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yi Xing
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, Departments of Biomedical Informatics and Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, Departments of Biomedical Informatics and Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter S White
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA
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Denson LA, Jurickova I, Karns R, Shaw KA, Cutler DJ, Okou D, Valencia CA, Dodd A, Mondal K, Aronow BJ, Haberman Y, Linn A, Price A, Bezold R, Lake K, Jackson K, Walters TD, Griffiths A, Baldassano RN, Noe JD, Hyams JS, Crandall WV, Kirschner BS, Heyman MB, Snapper S, Guthery SL, Dubinsky MC, Leleiko NS, Otley AR, Xavier RJ, Stevens C, Daly MJ, Zwick ME, Kugathasan S. Genetic and Transcriptomic Variation Linked to Neutrophil Granulocyte-Macrophage Colony-Stimulating Factor Signaling in Pediatric Crohn's Disease. Inflamm Bowel Dis 2019; 25:547-560. [PMID: 30124884 PMCID: PMC6391846 DOI: 10.1093/ibd/izy265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Granulocyte-macrophage colony-stimulating factor auto-antibodies (GMAbs) suppress neutrophil-extrinsic GM-CSF signaling and increase risk for stricturing behavior in Crohn's disease (CD). We aimed to define clinical, genomic, and functional associations with neutrophil-intrinsic GM-CSF signaling. METHODS Missense mutations in CSF2RA, CSF2RB, JAK2, STAT5A, and STAT5B were identified using whole-exome sequencing in 543 pediatric inflammatory bowel disease (IBD) patients. Neutrophil-intrinsic GM-CSF signaling was defined using the GM-CSF-induced STAT5 stimulation index (GMSI) in 180 pediatric IBD patients and 26 non-IBD controls. Reduced GM-CSF signaling (GMSI-Lo) was defined as the 20th percentile within the control group. Variation in neutrophil phospho-protein abundance, bacterial killing, and the global pattern of gene expression with the GMSI was determined. RESULTS We validated 18 potentially damaging missense mutations in CSF2RA and CSF2RB. CSF2RA A17G carriage increased from 10% in those with intact neutrophil GMSI to 32% in those with low GMSI (P = 0.02). The frequency of reduced Staphylococcus aureus killing increased from 17% in those with intact neutrophil GMSI to 35% in GMSI-Lo neutrophils (P = 0.043). Crohn's disease neutrophils with low GMSI exhibited specific alterations in phospho-protein networks and genes regulating cytokine production, wound healing, and cell survival and proliferation. Stricturing behavior increased from 7% in patients with both low GMAb and intact GMSI to 64% in patients with both elevated GMAb and low GMSI (P < 0.0001). CONCLUSIONS Low/normal neutrophil-intrinsic GM-CSF signaling is associated with CSF2RA missense mutations, alterations in gene expression networks, and higher rates of disease complications in pediatric CD.
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Affiliation(s)
- Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Address correspondence to: Lee A. Denson, MD, MLC 2010, 3333 Burnet Avenue, Cincinnati, OH ()
| | - Ingrid Jurickova
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Rebekah Karns
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kelly A Shaw
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - David Okou
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - C Alexander Valencia
- Program and Division of Human Genetics, Molecular Genetics Laboratory, Cincinnati, Ohio
| | - Anne Dodd
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Kajari Mondal
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Yael Haberman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Aaron Linn
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Adam Price
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Ramona Bezold
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kathleen Lake
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kimberly Jackson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Robert N Baldassano
- Department of Pediatrics, University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, Connecticut
| | - Wallace V Crandall
- Department of Pediatric Gastroenterology, Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, Ohio
| | | | - Melvin B Heyman
- Department of Pediatrics, University of California at San Francisco, San Francisco, California
| | - Scott Snapper
- Department of Gastroenterology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | | | - Marla C Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, New York
| | - Neal S Leleiko
- Department of Pediatrics, Hasbro Children’s Hospital, Providence, Rhode Island
| | - Anthony R Otley
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Mark J Daly
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michael E Zwick
- Department of Human Genetics, Emory University, Atlanta, Georgia
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29
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Ljungberg MC, Sadi M, Wang Y, Aronow BJ, Xu Y, Kao RJ, Liu Y, Gaddis N, Ardini-Poleske ME, Umrod T, Ambalavanan N, Nicola T, Kaminski N, Ahangari F, Sontag R, Corley RA, Ansong C, Carson JP. Spatial distribution of marker gene activity in the mouse lung during alveolarization. Data Brief 2019; 22:365-372. [PMID: 30596133 PMCID: PMC6307338 DOI: 10.1016/j.dib.2018.10.150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 11/28/2022] Open
Abstract
This data is a curated collection of visual images of gene expression patterns from the pre- and post-natal mouse lung, accompanied by associated mRNA probe sequences and RNA-Seq expression profiles. Mammalian lungs undergo significant growth and cellular differentiation before and after the transition to breathing air. Documenting normal lung development is an important step in understanding abnormal lung development, as well as the challenges faced during a preterm birth. Images in this dataset indicate the spatial distribution of mRNA transcripts for over 500 different genes that are active during lung development, as initially determined via RNA-Seq. Images were systematically acquired using high-throughput in situ hybridization with non-radioactive digoxigenin-labeled mRNA probes across mouse lungs from developmental time points E16.5, E18.5, P7, and P28. The dataset was produced as part of The Molecular Atlas of Lung Development Program (LungMAP) and is hosted at https://lungmap.net. This manuscript describes the nature of the data and the protocols for generating the dataset.
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Affiliation(s)
- M. Cecilia Ljungberg
- Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children׳s Hospital, Houston, TX, USA
| | - Mayce Sadi
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA
| | | | - Bruce J. Aronow
- Cincinnati Children׳s Hospital Medical Center, Cincinnati, OH, USA
| | - Yan Xu
- Cincinnati Children׳s Hospital Medical Center, Cincinnati, OH, USA
| | - Rong J. Kao
- Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children׳s Hospital, Houston, TX, USA
| | - Ying Liu
- Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children׳s Hospital, Houston, TX, USA
| | | | | | - Tipparat Umrod
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA
| | | | - Teodora Nicola
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Ryan Sontag
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Charles Ansong
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - James P. Carson
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA
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30
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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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31
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Lewis CS, Thomas HE, Orr-Asman M, Green LC, Boody RE, Matiash K, Karve A, Hisada YM, Davis HW, Qi X, Mercer C, Lucas FV, Aronow BJ, Mackman N, Versteeg HH, Bogdanov VY. mTOR kinase inhibition reduces tissue factor expression and growth of pancreatic neuroendocrine tumors. J Thromb Haemost 2019; 17:169-182. [PMID: 30472780 PMCID: PMC6345540 DOI: 10.1111/jth.14342] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Indexed: 12/22/2022]
Abstract
Essentials Tissue factor (TF) isoforms are expressed in pancreatic neuroendocrine tumors (pNET). TF knockdown inhibits proliferation of human pNET cells in vitro. mTOR kinase inhibitor sapanisertib/MLN0128 suppresses TF expression in human pNET cells. Sapanisertib suppresses TF expression and activity and reduces the growth of pNET tumors in vivo. SUMMARY: Background Full-length tissue factor (flTF) and alternatively spliced TF (asTF) contribute to growth and spread of pancreatic ductal adenocarcinoma. It is unknown, however, if flTF and/or asTF contribute to the pathobiology of pancreatic neuroendocrine tumors (pNETs). Objective To assess TF expression in pNETs and the effects of mTOR complex 1/2 (mTORC1/2) inhibition on pNET growth. Methods Human pNET specimens were immunostained for TF. Human pNET cell lines QGP1 and BON were evaluated for TF expression and responsiveness to mTOR inhibition. shRNA were used to knock down TF in BON. TF cofactor activity was assessed using a two-step FXa generation assay. TF promoter activity was assessed using transient transfection of human TF promoter-driven reporter constructs into cells. Mice bearing orthotopic BON tumors were treated with the mTORC1/2 ATP site competitive inhibitor sapanisertib/MLN0128 (3 mg kg-1 , oral gavage) for 34 days. Results Immunostaining of pNET tissue revealed flTF and asTF expression. BON and QGP1 expressed both TF isoforms, with BON exhibiting higher levels. shRNA directed against TF suppressed BON proliferation in vitro. Treatment of BON with sapanisertib inhibited mTOR signaling and suppressed TF levels. BON tumors grown in mice treated with sapanisertib had significantly less TF protein and cofactor activity, and were smaller compared with tumors grown in control mice. Conclusions TF isoforms are expressed in pNETs. Sapanisertib suppresses TF mRNA and protein expression as well as TF cofactor activity in vitro and in vivo. Thus, further studies are warranted to evaluate the clinical utility of TF-suppressing mTORC1/2 inhibitor sapanisertib in pNET management.
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Affiliation(s)
- Clayton S Lewis
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Hala Elnakat Thomas
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Melissa Orr-Asman
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Lisa C Green
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Rachel E Boody
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Kateryna Matiash
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Aniruddha Karve
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Yohei M. Hisada
- Division of Hematology/Oncology, Department of Medicine, University of North Carolina at Chapel Hill
| | - Harold W Davis
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Xiaoyang Qi
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Carol Mercer
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Fred V Lucas
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine
| | - Bruce J. Aronow
- Computational Medicine and Division of Biomedical Informatics, Cincinnati Children’s Hospital and Medical Center
| | - Nigel Mackman
- Division of Hematology/Oncology, Department of Medicine, University of North Carolina at Chapel Hill
| | - Henri H Versteeg
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Internal Medicine, Leiden University Medical Center
| | - Vladimir Y Bogdanov
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine
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32
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Higashi AY, Aronow BJ, Dressler GR. Expression Profiling of Fibroblasts in Chronic and Acute Disease Models Reveals Novel Pathways in Kidney Fibrosis. J Am Soc Nephrol 2018; 30:80-94. [PMID: 30545984 DOI: 10.1681/asn.2018060644] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 06/22/2018] [Accepted: 11/07/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Renal interstitial fibrosis results from activation and proliferation of fibroblasts to myofibroblasts, secretion and accumulation of extracellular matrix, and displacement of normal renal tubules. In contrast to chronic renal disease, acute injury may be repaired, a process that includes a decrease in the number of myofibroblasts in the interstitium and degradation of the accumulated extracellular matrix, leaving little evidence of prior injury. METHODS To investigate whether activated fibroblasts demonstrate changes in gene expression that correspond with regression after acute injury but are not observed in chronic models of fibrosis, we used microarrays to analyze gene expression patterns among fibroblast populations at different stages of injury or repair. We then mined the data for signaling pathways in fibroblasts corresponding to the acute proliferative, regression, and chronic phases of renal injury. RESULTS We identified multiple gene clusters with changes that correlate with the three phases of renal injury, including changes in levels of receptors for the antifibrotic factor PGE2. In adult renal fibroblast cultures, PGE2 was able to upregulate many genes that are suppressed by the profibrotic cytokine TGF-β, whereas many PGE2-downregulated genes were activated by TGF-β. High levels of TGF-β suppressed expression of a subset of PG receptors in fibroblast cultures, making these cells resistant to any effects of PGE2. CONCLUSIONS Inherent gene expression changes in activated fibroblasts accompany the transition from AKI to repair and regeneration. In chronic models, however, activated fibroblasts are resistant to the antifibrotic effects of PGE2 due to suppression of a subset of PGE receptors.
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Affiliation(s)
- Atsuko Y Higashi
- Department of Pathology, University of Michigan, Ann Arbor, Michigan; and
| | - Bruce J Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Gregory R Dressler
- Department of Pathology, University of Michigan, Ann Arbor, Michigan; and
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33
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Rowbotham SP, Li F, Dost AFM, Louie SM, Marsh BP, Pessina P, Anbarasu CR, Brainson CF, Tuminello SJ, Lieberman A, Ryeom S, Schlaeger TM, Aronow BJ, Watanabe H, Wong KK, Kim CF. H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression. Nat Commun 2018; 9:4559. [PMID: 30455465 PMCID: PMC6242814 DOI: 10.1038/s41467-018-07077-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/10/2018] [Indexed: 12/25/2022] Open
Abstract
Epigenetic regulators are attractive anticancer targets, but the promise of therapeutic strategies inhibiting some of these factors has not been proven in vivo or taken into account tumor cell heterogeneity. Here we show that the histone methyltransferase G9a, reported to be a therapeutic target in many cancers, is a suppressor of aggressive lung tumor-propagating cells (TPCs). Inhibition of G9a drives lung adenocarcinoma cells towards the TPC phenotype by de-repressing genes which regulate the extracellular matrix. Depletion of G9a during tumorigenesis enriches tumors in TPCs and accelerates disease progression metastasis. Depleting histone demethylases represses G9a-regulated genes and TPC phenotypes. Demethylase inhibition impairs lung adenocarcinoma progression in vivo. Therefore, inhibition of G9a is dangerous in certain cancer contexts, and targeting the histone demethylases is a more suitable approach for lung cancer treatment. Understanding cellular context and specific tumor populations is critical when targeting epigenetic regulators in cancer for future therapeutic development.
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Affiliation(s)
- S P Rowbotham
- Stem Cell Program, Division of Hematology/Oncology and Pulmonary and Respiratory Diseases, Children's Hospital Boston, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - F Li
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016, USA
| | - A F M Dost
- Stem Cell Program, Division of Hematology/Oncology and Pulmonary and Respiratory Diseases, Children's Hospital Boston, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - S M Louie
- Stem Cell Program, Division of Hematology/Oncology and Pulmonary and Respiratory Diseases, Children's Hospital Boston, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - B P Marsh
- Stem Cell Program, Division of Hematology/Oncology and Pulmonary and Respiratory Diseases, Children's Hospital Boston, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - P Pessina
- Stem Cell Program, Division of Hematology/Oncology and Pulmonary and Respiratory Diseases, Children's Hospital Boston, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - C R Anbarasu
- Stem Cell Program, Division of Hematology/Oncology and Pulmonary and Respiratory Diseases, Children's Hospital Boston, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - C F Brainson
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, 40536, USA
| | - S J Tuminello
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - A Lieberman
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Abramson Cancer Center, Philadelphia, PA, 19104, USA
| | - S Ryeom
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Abramson Cancer Center, Philadelphia, PA, 19104, USA
| | - T M Schlaeger
- Stem Cell Program, Division of Hematology/Oncology and Pulmonary and Respiratory Diseases, Children's Hospital Boston, Boston, MA, 02115, USA
| | - B J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - H Watanabe
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - K K Wong
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016, USA
| | - C F Kim
- Stem Cell Program, Division of Hematology/Oncology and Pulmonary and Respiratory Diseases, Children's Hospital Boston, Boston, MA, 02115, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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Kelly D, Kotliar M, Woo V, Jagannathan S, Whitt J, Moncivaiz J, Aronow BJ, Dubinsky MC, Hyams JS, Markowitz JF, Baldassano RN, Stephens MC, Walters TD, Kugathasan S, Haberman Y, Sundaram N, Rosen MJ, Helmrath M, Karns R, Barski A, Denson LA, Alenghat T. Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease. JCI Insight 2018; 3:122104. [PMID: 30232290 PMCID: PMC6237229 DOI: 10.1172/jci.insight.122104] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/07/2018] [Indexed: 12/19/2022] Open
Abstract
Altered response to the intestinal microbiota strongly associates with inflammatory bowel disease (IBD); however, how commensal microbial cues are integrated by the host during the pathogenesis of IBD is not understood. Epigenetics represents a potential mechanism that could enable intestinal microbes to modulate transcriptional output during the development of IBD. Here, we reveal a histone methylation signature of intestinal epithelial cells isolated from the terminal ilea of newly diagnosed pediatric IBD patients. Genes characterized by significant alterations in histone H3-lysine 4 trimethylation (H3K4me3) showed differential enrichment in pathways involving immunoregulation, cell survival and signaling, and metabolism. Interestingly, a large subset of these genes was epigenetically regulated by microbiota in mice and several microbiota-sensitive epigenetic targets demonstrated altered expression in IBD patients. Remarkably though, a substantial proportion of these genes exhibited H3K4me3 levels that correlated with the severity of intestinal inflammation in IBD, despite lacking significant differential expression. Collectively, these data uncover a previously unrecognized epigenetic profile of IBD that can be primed by commensal microbes and indicate sensitive targets in the epithelium that may underlie how microbiota predispose to subsequent intestinal inflammation and disease.
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Affiliation(s)
- Daniel Kelly
- Division of Immunobiology, Center for Inflammation and Tolerance
- Division of Gastroenterology, Hepatology, and Nutrition
| | | | - Vivienne Woo
- Division of Immunobiology, Center for Inflammation and Tolerance
| | | | - Jordan Whitt
- Division of Immunobiology, Center for Inflammation and Tolerance
| | | | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center (CCHMC) and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Marla C. Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey S. Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, Connecticut, USA
| | | | - Robert N. Baldassano
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael C. Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas D. Walters
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yael Haberman
- Division of Gastroenterology, Hepatology, and Nutrition
- Sheba Medical Center, Tel Hashomer, affiliated with the Tel-Aviv University, Israel
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, CCHMC and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Michael Helmrath
- Division of Pediatric General and Thoracic Surgery, CCHMC and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology, and Nutrition
| | - Artem Barski
- Divisions of Allergy and Immunology and Human Genetics, and
| | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition
| | - Theresa Alenghat
- Division of Immunobiology, Center for Inflammation and Tolerance
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35
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Meyer SE, Muench DE, Rogers AM, Newkold TJ, Orr E, O'Brien E, Perentesis JP, Doench JG, Lal A, Morris PJ, Thomas CJ, Lieberman J, McGlinn E, Aronow BJ, Salomonis N, Grimes HL. miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. J Exp Med 2018; 215:2115-2136. [PMID: 29997117 PMCID: PMC6080909 DOI: 10.1084/jem.20171312] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 04/30/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023] Open
Abstract
We have shown that antagomiR inhibition of miRNA miR-21 and miR-196b activity is sufficient to ablate MLL-AF9 leukemia stem cells (LSC) in vivo. Here, we used an shRNA screening approach to mimic miRNA activity on experimentally verified miR-196b targets to identify functionally important and therapeutically relevant pathways downstream of oncogenic miRNA in MLL-r AML. We found Cdkn1b (p27Kip1) is a direct miR-196b target whose repression enhanced an embryonic stem cell-like signature associated with decreased leukemia latency and increased numbers of leukemia stem cells in vivo. Conversely, elevation of p27Kip1 significantly reduced MLL-r leukemia self-renewal, promoted monocytic differentiation of leukemic blasts, and induced cell death. Antagonism of miR-196b activity or pharmacologic inhibition of the Cks1-Skp2-containing SCF E3-ubiquitin ligase complex increased p27Kip1 and inhibited human AML growth. This work illustrates that understanding oncogenic miRNA target pathways can identify actionable targets in leukemia.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Cell Differentiation/genetics
- Cell Line, Tumor
- Cell Proliferation/genetics
- Cell Survival/genetics
- Chromosomes, Human, Pair 11/genetics
- Cyclin-Dependent Kinase Inhibitor p27/metabolism
- Cyclin-Dependent Kinases/metabolism
- Cyclins/metabolism
- Embryonic Stem Cells/metabolism
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Mice, Inbred C57BL
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogenes
- RNA, Small Interfering/metabolism
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Affiliation(s)
- Sara E Meyer
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - David E Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Andrew M Rogers
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Tess J Newkold
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emily Orr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Eric O'Brien
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - John P Perentesis
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Patrick J Morris
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Edwina McGlinn
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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36
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Yonekura A, Kawanaka H, Prasath VBS, Aronow BJ, Takase H. Automatic disease stage classification of glioblastoma multiforme histopathological images using deep convolutional neural network. Biomed Eng Lett 2018; 8:321-327. [PMID: 30603216 PMCID: PMC6208537 DOI: 10.1007/s13534-018-0077-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/28/2018] [Accepted: 06/17/2018] [Indexed: 02/07/2023] Open
Abstract
In the field of computational histopathology, computer-assisted diagnosis systems are important in obtaining patient-specific diagnosis for various diseases and help precision medicine. Therefore, many studies on automatic analysis methods for digital pathology images have been reported. In this work, we discuss an automatic feature extraction and disease stage classification method for glioblastoma multiforme (GBM) histopathological images. In this paper, we use deep convolutional neural networks (Deep CNNs) to acquire feature descriptors and a classification scheme simultaneously. Further, comparisons with other popular CNNs objectively as well as quantitatively in this challenging classification problem is undertaken. The experiments using Glioma images from The Cancer Genome Atlas shows that we obtain 96.5 % average classification accuracy for our network and for higher cross validation folds other networks perform similarly with a higher accuracy of 98.0 % . Deep CNNs could extract significant features from the GBM histopathology images with high accuracy. Overall, the disease stage classification of GBM from histopathological images with deep CNNs is very promising and with the availability of large scale histopathological image data the deep CNNs are well suited in tackling this challenging problem.
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Affiliation(s)
- Asami Yonekura
- Graduate School of Engineering, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507 Japan
| | - Hiroharu Kawanaka
- Graduate School of Engineering, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507 Japan
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267 USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267 USA
| | - Haruhiko Takase
- Graduate School of Engineering, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507 Japan
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37
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Hankey W, Chen Z, Bergman MJ, Fernandez MO, Hancioglu B, Lan X, Jegga AG, Zhang J, Jin VX, Aronow BJ, Wang Q, Groden J. Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1. Oncotarget 2018; 9:31214-31230. [PMID: 30131849 PMCID: PMC6101278 DOI: 10.18632/oncotarget.25781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 02/06/2018] [Accepted: 07/05/2018] [Indexed: 11/25/2022] Open
Abstract
Mutation of the APC gene occurs in a high percentage of colorectal tumors and is a central event driving tumor initiation in the large intestine. The APC protein performs multiple tumor suppressor functions including negative regulation of the canonical WNT signaling pathway by both cytoplasmic and nuclear mechanisms. Published reports that APC interacts with β-catenin in the chromatin fraction to repress WNT-activated targets have raised the possibility that chromatin-associated APC participates more broadly in mechanisms of transcriptional control. This screening study has used chromatin immunoprecipitation and next-generation sequencing to identify APC-associated genomic regions in colon cancer cell lines. Initial target selection was performed by comparison and statistical analysis of 3,985 genomic regions associated with the APC protein to whole transcriptome sequencing data from APC-deficient and APC-wild-type colon cancer cells, and two types of murine colon adenomas characterized by activated Wnt signaling. 289 transcripts altered in expression following APC loss in human cells were linked to APC-associated genomic regions. High-confidence targets additionally validated in mouse adenomas included 16 increased and 9 decreased in expression following APC loss, indicating that chromatin-associated APC may antagonize canonical WNT signaling at both WNT-activated and WNT-repressed targets. Motif analysis and comparison to ChIP-seq datasets for other transcription factors identified a prevalence of binding sites for the TCF7L2 and AP-1 transcription factors in APC-associated genomic regions. Our results indicate that canonical WNT signaling can collaborate with or antagonize the AP-1 transcription factor to fine-tune the expression of shared target genes in the colorectal epithelium. Future therapeutic strategies for APC-deficient colorectal cancers might be expanded to include agents targeting the AP-1 pathway.
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Affiliation(s)
- William Hankey
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Zhong Chen
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Maxwell J Bergman
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Max O Fernandez
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Baris Hancioglu
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, Ohio, United States of America
| | - Xun Lan
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, China
| | - Anil G Jegga
- Division of Bioinformatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Bruce J Aronow
- Division of Bioinformatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Qianben Wang
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Joanna Groden
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
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Denson LA, Jurickova I, Karns R, Shaw KA, Cutler DJ, Okou D, Dodd A, Quinn K, Mondal K, Aronow BJ, Haberman Y, Linn A, Price A, Bezold R, Lake K, Jackson K, Walters TD, Griffiths A, Baldassano RN, Noe JD, Hyams JS, Crandall WV, Kirschner BS, Heyman MB, Snapper S, Guthery SL, Dubinsky MC, Leleiko NS, Otley AR, Xavier RJ, Stevens C, Daly MJ, Zwick ME, Kugathasan S. Clinical and Genomic Correlates of Neutrophil Reactive Oxygen Species Production in Pediatric Patients With Crohn's Disease. Gastroenterology 2018; 154:2097-2110. [PMID: 29454792 PMCID: PMC5985211 DOI: 10.1053/j.gastro.2018.02.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Individuals with monogenic disorders of phagocyte function develop chronic colitis that resembles Crohn's disease (CD). We tested for associations between mutations in genes encoding reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidases, neutrophil function, and phenotypes of CD in pediatric patients. METHODS We performed whole-exome sequence analysis to identify mutations in genes encoding NADPH oxidases (such as CYBA, CYBB, NCF1, NCF2, NCF4, RAC1, and RAC2) using DNA from 543 pediatric patients with inflammatory bowel diseases. Blood samples were collected from an additional 129 pediatric patients with CD and 26 children without IBD (controls); we performed assays for neutrophil activation, reactive oxygen species (ROS) production, and bacteria uptake and killing. Whole-exome sequence analysis was performed using DNA from 46 of the children with CD to examine associations with NADPH gene mutations; RNA sequence analyses were performed using blood cells from 46 children with CD to test for variations in neutrophil gene expression associated with ROS production. RESULTS We identified 26 missense mutations in CYBA, CYBB, NCF1, NCF2, and NCF4. Patients with CD who carried mutations in these genes were 3-fold more likely to have perianal disease (P = .0008) and stricturing complications (P = .002) than children with CD without these mutations. Among patients with CD with none of these mutations, 9% had undergone abdominal surgery; among patients with mutations in these NADPH oxidase genes, 31% had undergone abdominal surgery (P = .0004). A higher proportion of neutrophils from children with CD had low ROS production (47%) than from controls (15%) among the 129 patients tested for ROS (P = .002). Minor alleles of the NADPH genes were detected in 7% of children with CD whose neutrophils produced normal levels of ROS vs 38% of children whose neutrophils produced low levels of ROS (P = .009). Neutrophils that produced low levels of ROS had specific alterations in genes that regulate glucose metabolism and antimicrobial responses. CONCLUSIONS We identified missense mutations in genes that encode NADPH oxidases in children with CD; these were associated with a more aggressive disease course and reduced ROS production by neutrophils from the patients.
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Affiliation(s)
- Lee A. Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA,to whom correspondence should be addressed: MLC 2010, 3333 Burnet Avenue, Cincinnati, OH 45229, Tel: 513-636-7575, Fax: 513-636-5581,
| | - Ingrid Jurickova
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Rebekah Karns
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kelly A. Shaw
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Okou
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Anne Dodd
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Kathryn Quinn
- Cancer and Blood Disease Institute, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kajari Mondal
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yael Haberman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Aaron Linn
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Adam Price
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ramona Bezold
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kathleen Lake
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kimberly Jackson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Thomas D. Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Robert N. Baldassano
- Department of Pediatrics, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua D. Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeffrey S. Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, CT, USA
| | - Wallace V. Crandall
- Department of Pediatric Gastroenterology, Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Melvin B. Heyman
- Department of Pediatrics, University of California at San Francisco, San Francisco, CA, USA
| | - Scott Snapper
- Department of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Neal S. Leleiko
- Department of Pediatrics, Hasbro Children’s Hospital, Providence, RI, USA
| | - Anthony R. Otley
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | - Mark J. Daly
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E. Zwick
- Department of Human Genetics, Emory University, Atlanta, GA, USA
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39
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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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40
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Shaw KA, Cutler DJ, Okou D, Dodd A, Aronow BJ, Haberman Y, Stevens C, Walters TD, Griffiths A, Baldassano RN, Noe JD, Hyams JS, Crandall WV, Kirschner BS, Heyman MB, Snapper S, Guthery S, Dubinsky MC, Shapiro JM, Otley AR, Daly M, Denson LA, Kugathasan S, Zwick ME. Genetic variants and pathways implicated in a pediatric inflammatory bowel disease cohort. Genes Immun 2018; 20:131-142. [PMID: 29593342 PMCID: PMC6162182 DOI: 10.1038/s41435-018-0015-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/28/2017] [Accepted: 09/11/2017] [Indexed: 12/13/2022]
Abstract
In the United States, approximately 5% of individuals with inflammatory bowel disease (IBD) are younger than 20 years old. Studies of pediatric cohorts can provide unique insights into genetic architecture of IBD, which includes Crohn's disease (CD) and ulcerative colitis (UC). Large genome-wide association studies have found more than 200 IBD-associated loci but explain a minority of disease variance for CD and UC. We sought to characterize the contribution of rare variants to disease development, comparing exome sequencing of 368 pediatric IBD patients to publicly available exome sequencing (dbGaP) and aggregate frequency data (ExAC). Using dbGaP data, we performed logistic regression for common variants and optimal unified association tests (SKAT-O) for rare, likely-deleterious variants. We further compared rare variants to ExAC counts with Fisher's exact tests. We did pathway enrichment analysis on the most significant genes from each comparison. Many variants overlapped with known IBD-associated genes (e.g. NOD2). Rare variants were enriched in CD-associated loci (p = 0.009) and showed suggestive enrichment in neutrophil function genes (p = 0.05). Pathway enrichment implicated immune-related pathways, especially cell killing and apoptosis. Variants in extracellular matrix genes also emerged as an important theme in our analysis.
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Affiliation(s)
- Kelly A Shaw
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Okou
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Anne Dodd
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yael Haberman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Robert N Baldassano
- Department of Pediatrics, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Wallace V Crandall
- Department of Pediatric Gastroenterology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Barbara S Kirschner
- Department of Pediatrics, The University of Chicago Comer Children's Hospital, Chicago, IL, USA
| | - Melvin B Heyman
- Department of Pediatrics, University of California at San Francisco, San Francisco, CA, USA
| | - Scott Snapper
- Department of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Stephen Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, NY, USA
| | - Jason M Shapiro
- Department of Pediatrics, Hasbro Children's Hospital, Providence, RI, USA
| | - Anthony R Otley
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Michael E Zwick
- Department of Human Genetics, Emory University, Atlanta, GA, USA.
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41
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Moreno-Fernandez ME, Giles DA, Stankiewicz TE, Sheridan R, Karns R, Cappelletti M, Lampe K, Mukherjee R, Sina C, Sallese A, Bridges JP, Hogan SP, Aronow BJ, Hoebe K, Divanovic S. Peroxisomal β-oxidation regulates whole body metabolism, inflammatory vigor, and pathogenesis of nonalcoholic fatty liver disease. JCI Insight 2018; 3:93626. [PMID: 29563328 DOI: 10.1172/jci.insight.93626] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 02/08/2018] [Indexed: 12/14/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), a metabolic predisposition for development of hepatocellular carcinoma (HCC), represents a disease spectrum ranging from steatosis to steatohepatitis to cirrhosis. Acox1, a rate-limiting enzyme in peroxisomal fatty acid β-oxidation, regulates metabolism, spontaneous hepatic steatosis, and hepatocellular damage over time. However, it is unknown whether Acox1 modulates inflammation relevant to NAFLD pathogenesis or if Acox1-associated metabolic and inflammatory derangements uncover and accelerate potential for NAFLD progression. Here, we show that mice with a point mutation in Acox1 (Acox1Lampe1) exhibited altered cellular metabolism, modified T cell polarization, and exacerbated immune cell inflammatory potential. Further, in context of a brief obesogenic diet stress, NAFLD progression associated with Acox1 mutation resulted in significantly accelerated and exacerbated hepatocellular damage via induction of profound histological changes in hepatocytes, hepatic inflammation, and robust upregulation of gene expression associated with HCC development. Collectively, these data demonstrate that β-oxidation links metabolism and immune responsiveness and that a better understanding of peroxisomal β-oxidation may allow for discovery of mechanisms central for NAFLD progression.
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Affiliation(s)
- Maria E Moreno-Fernandez
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
| | - Daniel A Giles
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA.,Immunology Graduate Program, CCHMC, and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Traci E Stankiewicz
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
| | - Rachel Sheridan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Pathology, CCHMC, Cincinnati, Ohio, USA
| | - Rebekah Karns
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Gastroenterology, Hepatology, and Nutrition, CCHMC, Cincinnati, Ohio, USA
| | - Monica Cappelletti
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
| | - Kristin Lampe
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
| | - Rajib Mukherjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
| | - Christian Sina
- Molecular Gastroenterology, University Hospital Schleswig-Holstein, Campus Lübeck, Germany
| | - Anthony Sallese
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Neonatology and Pulmonary Biology
| | - James P Bridges
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Neonatology and Pulmonary Biology
| | - Simon P Hogan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Allergy and Immunology, and
| | - Bruce J Aronow
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Biomedical Informatics, CCHMC, Cincinnati, Ohio, USA
| | - Kasper Hoebe
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
| | - Senad Divanovic
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
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42
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Sarangdhar M, Tabar S, Schmidt C, Kushwaha A, Shah K, Dahlquist JE, Jegga AG, Aronow BJ. Data mining differential clinical outcomes associated with drug regimens using adverse event reporting data. Nat Biotechnol 2018; 34:697-700. [PMID: 27404875 DOI: 10.1038/nbt.3623] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mayur Sarangdhar
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Scott Tabar
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Charles Schmidt
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Akash Kushwaha
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Krish Shah
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jeanine E Dahlquist
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Anil G Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Clinical and Translational Sciences Program, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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43
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Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Res 2018; 28:gr.225979.117. [PMID: 29317474 PMCID: PMC5848617 DOI: 10.1101/gr.225979.117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 12/21/2017] [Indexed: 12/26/2022]
Abstract
Generating detailed and accurate organogenesis models using single-cell RNA-seq data remains a major challenge. Current methods have relied primarily on the assumption that descendant cells are similar to their parents in terms of gene expression levels. These assumptions do not always hold for in vivo studies, which often include infrequently sampled, unsynchronized, and diverse cell populations. Thus, additional information may be needed to determine the correct ordering and branching of progenitor cells and the set of transcription factors (TFs) that are active during advancing stages of organogenesis. To enable such modeling, we have developed a method that learns a probabilistic model that integrates expression similarity with regulatory information to reconstruct the dynamic developmental cell trajectories. When applied to mouse lung developmental data, the method accurately distinguished different cell types and lineages. Existing and new experimental data validated the ability of the method to identify key regulators of cell fate.
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Affiliation(s)
- Jun Ding
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Joseph Kitzmiller
- Section of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Jeffrey A Whitsett
- Section of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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44
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Giles DA, Moreno-Fernandez ME, Stankiewicz TE, Graspeuntner S, Cappelletti M, Wu D, Mukherjee R, Chan CC, Lawson MJ, Klarquist J, Sünderhauf A, Softic S, Kahn CR, Stemmer K, Iwakura Y, Aronow BJ, Karns R, Steinbrecher KA, Karp CL, Sheridan R, Shanmukhappa SK, Reynaud D, Haslam DB, Sina C, Rupp J, Hogan SP, Divanovic S. Erratum: Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling. Nat Med 2017; 23:1241. [DOI: 10.1038/nm1017-1241c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Marigorta UM, Denson LA, Hyams JS, Mondal K, Prince J, Walters TD, Griffiths A, Noe JD, Crandall WV, Rosh JR, Mack DR, Kellermayer R, Heyman MB, Baker SS, Stephens MC, Baldassano RN, Markowitz JF, Kim MO, Dubinsky MC, Cho J, Aronow BJ, Kugathasan S, Gibson G. Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease. Nat Genet 2017; 49:1517-1521. [PMID: 28805827 PMCID: PMC5745037 DOI: 10.1038/ng.3936] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 07/21/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Urko M Marigorta
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology and Nutrition, Connecticut Children's Medical Center, Hartford, Connecticut, USA
| | - Kajari Mondal
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jarod Prince
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Wallace V Crandall
- Department of Pediatric Gastroenterology, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Joel R Rosh
- Department of Pediatrics, Goryeb Children's Hospital, Morristown, New Jersey, USA
| | - David R Mack
- Department of Pediatrics, Children's Hospital of Eastern Ontario IBD Centre and University of Ottawa, Ottawa, Ontario, Canada
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Melvin B Heyman
- Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Susan S Baker
- Department of Digestive Diseases and Nutrition Center, University at Buffalo, Buffalo, New York, USA
| | - Michael C Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert N Baldassano
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Mi-Ok Kim
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, New York, USA
| | - Judy Cho
- Department of Pediatrics, Mount Sinai Hospital, New York, New York, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA
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46
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Giles DA, Moreno-Fernandez ME, Stankiewicz TE, Graspeuntner S, Cappelletti M, Wu D, Mukherjee R, Chan CC, Lawson MJ, Klarquist J, Sünderhauf A, Softic S, Kahn CR, Stemmer K, Iwakura Y, Aronow BJ, Karns R, Steinbrecher KA, Karp CL, Sheridan R, Shanmukhappa SK, Reynaud D, Haslam DB, Sina C, Rupp J, Hogan SP, Divanovic S. Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling. Nat Med 2017; 23:829-838. [PMID: 28604704 PMCID: PMC5596511 DOI: 10.1038/nm.4346] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [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: 01/06/2017] [Accepted: 04/22/2017] [Indexed: 02/08/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD), a common prelude to cirrhosis and hepatocellular carcinoma, is the most common chronic liver disease worldwide. Defining the molecular mechanisms underlying the pathogenesis of NAFLD has been hampered by a lack of animal models that closely recapitulate the severe end of the disease spectrum in humans, including bridging hepatic fibrosis. Here we demonstrate that a novel experimental model employing thermoneutral housing, as opposed to standard housing, resulted in lower stress-driven production of corticosterone, augmented mouse proinflammatory immune responses and markedly exacerbated high-fat diet (HFD)-induced NAFLD pathogenesis. Disease exacerbation at thermoneutrality was conserved across multiple mouse strains and was associated with augmented intestinal permeability, an altered microbiome and activation of inflammatory pathways that are associated with the disease in humans. Depletion of Gram-negative microbiota, hematopoietic cell deletion of Toll-like receptor 4 (TLR4) and inactivation of the IL-17 axis resulted in altered immune responsiveness and protection from thermoneutral-housing-driven NAFLD amplification. Finally, female mice, typically resistant to HFD-induced obesity and NAFLD, develop full disease characteristics at thermoneutrality. Thus, thermoneutral housing provides a sex-independent model of exacerbated NAFLD in mice and represents a novel approach for interrogation of the cellular and molecular mechanisms underlying disease pathogenesis.
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Affiliation(s)
- Daniel A Giles
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Maria E Moreno-Fernandez
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Traci E Stankiewicz
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Monica Cappelletti
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - David Wu
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rajib Mukherjee
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Calvin C Chan
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Matthew J Lawson
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jared Klarquist
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Annika Sünderhauf
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Samir Softic
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Boston, Massachusetts, USA
| | - C Ronald Kahn
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Boston, Massachusetts, USA
| | - Kerstin Stemmer
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center and German Center for Diabetes Research (DZD), Helmholtz Zentrum München, Neuherberg, Germany
| | - Yoichiro Iwakura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Bruce J Aronow
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kris A Steinbrecher
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Rachel Sheridan
- Division of Pathology and Laboratory Medicine, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Shiva K Shanmukhappa
- Division of Pathology and Laboratory Medicine, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Damien Reynaud
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - David B Haslam
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Christian Sina
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Simon P Hogan
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Senad Divanovic
- Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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47
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Kugathasan S, Denson LA, Walters TD, Kim MO, Marigorta UM, Schirmer M, Mondal K, Liu C, Griffiths A, Noe JD, Crandall WV, Snapper S, Rabizadeh S, Rosh JR, Shapiro JM, Guthery S, Mack DR, Kellermayer R, Kappelman MD, Steiner S, Moulton DE, Keljo D, Cohen S, Oliva-Hemker M, Heyman MB, Otley AR, Baker SS, Evans JS, Kirschner BS, Patel AS, Ziring D, Trapnell BC, Sylvester FA, Stephens MC, Baldassano RN, Markowitz JF, Cho J, Xavier RJ, Huttenhower C, Aronow BJ, Gibson G, Hyams JS, Dubinsky MC. Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study. Lancet 2017; 389:1710-1718. [PMID: 28259484 PMCID: PMC5719489 DOI: 10.1016/s0140-6736(17)30317-3] [Citation(s) in RCA: 407] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/18/2016] [Accepted: 11/26/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Stricturing and penetrating complications account for substantial morbidity and health-care costs in paediatric and adult onset Crohn's disease. Validated models to predict risk for complications are not available, and the effect of treatment on risk is unknown. METHODS We did a prospective inception cohort study of paediatric patients with newly diagnosed Crohn's disease at 28 sites in the USA and Canada. Genotypes, antimicrobial serologies, ileal gene expression, and ileal, rectal, and faecal microbiota were assessed. A competing-risk model for disease complications was derived and validated in independent groups. Propensity-score matching tested the effect of anti-tumour necrosis factor α (TNFα) therapy exposure within 90 days of diagnosis on complication risk. FINDINGS Between Nov 1, 2008, and June 30, 2012, we enrolled 913 patients, 78 (9%) of whom experienced Crohn's disease complications. The validated competing-risk model included age, race, disease location, and antimicrobial serologies and provided a sensitivity of 66% (95% CI 51-82) and specificity of 63% (55-71), with a negative predictive value of 95% (94-97). Patients who received early anti-TNFα therapy were less likely to have penetrating complications (hazard ratio [HR] 0·30, 95% CI 0·10-0·89; p=0·0296) but not stricturing complication (1·13, 0·51-2·51; 0·76) than were those who did not receive early anti-TNFα therapy. Ruminococcus was implicated in stricturing complications and Veillonella in penetrating complications. Ileal genes controlling extracellular matrix production were upregulated at diagnosis, and this gene signature was associated with stricturing in the risk model (HR 1·70, 95% CI 1·12-2·57; p=0·0120). When this gene signature was included, the model's specificity improved to 71%. INTERPRETATION Our findings support the usefulness of risk stratification of paediatric patients with Crohn's disease at diagnosis, and selection of anti-TNFα therapy. FUNDING Crohn's and Colitis Foundation of America, Cincinnati Children's Hospital Research Foundation Digestive Health Center.
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Affiliation(s)
- Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA; Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Mi-Ok Kim
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Urko M Marigorta
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Kajari Mondal
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
| | - Chunyan Liu
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wallace V Crandall
- Department of Pediatric Gastroenterology, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, OH, USA
| | - Scott Snapper
- Department of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Shervin Rabizadeh
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joel R Rosh
- Department of Pediatrics, Goryeb Children's Hospital, Morristown, NJ, USA
| | - Jason M Shapiro
- Department of Pediatrics, Hasbro Children's Hospital, Providence, RI, USA
| | - Stephen Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - David R Mack
- Department of Pediatrics, Children's Hospital of Eastern Ontario IBD Centre and University of Ottawa, ON, Canada
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Michael D Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steven Steiner
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dedrick E Moulton
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Keljo
- Department of Gastroenterology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Stanley Cohen
- Children's Healthcare of Atlanta, Atlanta, GA, USA; Children's Center for Digestive Health Care, Atlanta, GA, USA
| | - Maria Oliva-Hemker
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melvin B Heyman
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Anthony R Otley
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Susan S Baker
- Department of Digestive Diseases and Nutrition Center, University at Buffalo, Buffalo, NY, USA
| | - Jonathan S Evans
- Department of Pediatrics, Nemours Children's Specialty Care, Jacksonville, FL, USA
| | | | - Ashish S Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David Ziring
- Department of Pediatrics, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Bruce C Trapnell
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Francisco A Sylvester
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael C Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Judy Cho
- Department of Pediatrics, Mount Sinai Hospital, New York, NY, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, NY, USA
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48
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Rochman M, Travers J, Miracle CE, Bedard MC, Wen T, Azouz NP, Caldwell JM, Kc K, Sherrill JD, Davis BP, Rymer JK, Kaufman KM, Aronow BJ, Rothenberg ME. Profound loss of esophageal tissue differentiation in patients with eosinophilic esophagitis. J Allergy Clin Immunol 2017; 140:738-749.e3. [PMID: 28104354 DOI: 10.1016/j.jaci.2016.11.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 05/09/2016] [Revised: 09/16/2016] [Accepted: 11/16/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND A key question in the allergy field is to understand how tissue-specific disease is manifested. Eosinophilic esophagitis (EoE) is an emerging tissue-specific allergic disease with an unclear pathogenesis. OBJECTIVE Herein we tested the hypothesis that a defect in tissue-specific esophageal genes is an integral part of EoE pathogenesis. METHODS We interrogated the pattern of expression of esophagus-specific signature genes derived from the Human Protein Atlas in the EoE transcriptome and in EPC2 esophageal epithelial cells. Western blotting and immunofluorescence were used for evaluating expression of esophageal proteins in biopsy specimens from control subjects and patients with active EoE. Whole-exome sequencing was performed to identify mutations in esophagus-specific genes. RESULTS We found that approximately 39% of the esophagus-specific transcripts were altered in patients with EoE, with approximately 90% being downregulated. The majority of transcriptional changes observed in esophagus-specific genes were reproduced in vitro in esophageal epithelial cells differentiated in the presence of IL-13. Functional enrichment analysis revealed keratinization and differentiation as the most affected biological processes and identified IL-1 cytokines and serine peptidase inhibitors as the most dysregulated esophagus-specific protein families in patients with EoE. Accordingly, biopsy specimens from patients with EoE evidenced a profound loss of tissue differentiation, decreased expression of keratin 4 (KRT4) and cornulin (CRNN), and increased expression of KRT5 and KRT14. Whole-exome sequencing of 33 unrelated patients with EoE revealed 39 rare mutations in 18 esophagus-specific differentially expressed genes. CONCLUSIONS A tissue-centered analysis has revealed a profound loss of esophageal tissue differentiation (identity) as an integral and specific part of the pathophysiology of EoE and implicated protease- and IL-1-related activities as putative central pathways in disease pathogenesis.
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Affiliation(s)
- Mark Rochman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jared Travers
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Cora E Miracle
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Mary C Bedard
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ting Wen
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Nurit P Azouz
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Julie M Caldwell
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kiran Kc
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joseph D Sherrill
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Benjamin P Davis
- Department of Internal Medicine, Division of Immunology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Jeffrey K Rymer
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Division of Rheumatology, Cincinnati Children's Hospital Medical Center, University of Cincinnati, and the Cincinnati VA Medical Center, Research Department, Cincinnati, Ohio
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
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49
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Morgan AA, Crawford DC, Denny JC, Mooney SD, Aronow BJ, Brenner SE. PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY. Pac Symp Biocomput 2016; 22:348-355. [PMID: 27896988 DOI: 10.1142/9789813207813_0033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The major goal of precision medicine is to improve human health. A feature that unites much research in the field is the use of large datasets such as genomic data and electronic health records. Research in this field includes examination of variation in the core bases of DNA and their methylation status, through variations in metabolic and signaling molecules, all the way up to broader systems level changes in physiology and disease presentation. Intermediate goals include understanding the individual drivers of disease that differentiate the cause of disease in each individual. To match this development of approaches to physical and activitybased measurements, computational approaches to using these new streams of data to better understand improve human health are being rapidly developed by the thriving biomedical informatics research community. This session of the 2017 Pacific Symposium of Biocomputing presents some of the latest advances in the capture, analysis and use of diverse biomedical data in precision medicine.
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50
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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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