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Prokop JW, Shankar R, Gupta R, Leimanis ML, Nedveck D, Uhl K, Chen B, Hartog NL, Van Veen J, Sisco JS, Sirpilla O, Lydic T, Boville B, Hernandez A, Braunreiter C, Kuk CC, Singh V, Mills J, Wegener M, Adams M, Rhodes M, Bachmann AS, Pan W, Byrne-Steele ML, Smith DC, Depinet M, Brown BE, Eisenhower M, Han J, Haw M, Madura C, Sanfilippo DJ, Seaver LH, Bupp C, Rajasekaran S. Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19. Physiol Genomics 2020; 52:255-268. [PMID: 32437232 PMCID: PMC7303726 DOI: 10.1152/physiolgenomics.00045.2020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Precision medicine requires the translation of basic biological understanding to medical insights, mainly applied to characterization of each unique patient. In many clinical settings, this requires tools that can be broadly used to identify pathology and risks. Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Etiology and outcomes are unique to individuals, making it difficult to cohort patients with MODS, but presenting a prime target for testing/developing tools for precision medicine. Using multitime point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology versus environmental response, and unique biological insights in each patient using a single platform measurement. Integration of a transcriptome workflow yielded unexpected insights into the complex interplay between host genetics and viral/bacterial specific mechanisms, highlighted by a unique case of virally induced genetics (VIG) within one of these 27 patients. The power of RNA-Seq to study unique patient biology while investigating environmental contributions can be a critical tool moving forward for translational sciences applied to precision medicine.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Rama Shankar
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Ruchir Gupta
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Mara L Leimanis
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Derek Nedveck
- Office of Research, Spectrum Health, Grand Rapids, Michigan
| | - Katie Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Bin Chen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Nicholas L Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Allergy and Immunology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
- Adult Allergy and Immunology, Spectrum Health, Grand Rapids, Michigan
| | - Jason Van Veen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Joshua S Sisco
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Olivia Sirpilla
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Walsh University, North Canton, Ohio
| | - Todd Lydic
- Department of Physiology, Michigan State University, East Lansing, Michigan
| | - Brian Boville
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Angel Hernandez
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Chi Braunreiter
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Hematology-Oncology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - ChiuYing Cynthia Kuk
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | - Varinder Singh
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan
| | - Joshua Mills
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Marc Wegener
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Mary Rhodes
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Andre S Bachmann
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | | | | | | | | | | | | | - Jian Han
- iRepertoire Inc., Huntsville, Alabama
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Marcus Haw
- Congenital Heart Center, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Casey Madura
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Dominic J Sanfilippo
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Laurie H Seaver
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | - Caleb Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
- Office of Research, Spectrum Health, Grand Rapids, Michigan
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