A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions
Post-Acute Sequelae of SARS-CoV-2 infection (PASC or “Long COVID”), includes numerous chronic conditions associated with widespread morbidity and rising healthcare costs. PASC has highly variable clinical presentations, and likely includes multiple molecular subtypes, but it remains poorly understoo...
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2025-01-01
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| author | Jun Sun Masanori Aikawa Hassan Ashktorab Noam D. Beckmann Noam D. Beckmann Michael L. Enger Joaquin M. Espinosa Xiaowu Gai Xiaowu Gai Benjamin D. Horne Benjamin D. Horne Paul Keim Paul Keim Paul Keim Jessica Lasky-Su Rebecca Letts Cheryl L. Maier Meisha Mandal Lauren Nichols Nadia R. Roan Nadia R. Roan Mark W. Russell Jacqueline Rutter George R. Saade George R. Saade Kumar Sharma Kumar Sharma Stephanie Shiau Stephen N. Thibodeau Samuel Yang Lucio Miele NIH Researching COVID to Enhance Recovery (RECOVER) Consortium |
| author_facet | Jun Sun Masanori Aikawa Hassan Ashktorab Noam D. Beckmann Noam D. Beckmann Michael L. Enger Joaquin M. Espinosa Xiaowu Gai Xiaowu Gai Benjamin D. Horne Benjamin D. Horne Paul Keim Paul Keim Paul Keim Jessica Lasky-Su Rebecca Letts Cheryl L. Maier Meisha Mandal Lauren Nichols Nadia R. Roan Nadia R. Roan Mark W. Russell Jacqueline Rutter George R. Saade George R. Saade Kumar Sharma Kumar Sharma Stephanie Shiau Stephen N. Thibodeau Samuel Yang Lucio Miele NIH Researching COVID to Enhance Recovery (RECOVER) Consortium |
| author_sort | Jun Sun |
| collection | DOAJ |
| description | Post-Acute Sequelae of SARS-CoV-2 infection (PASC or “Long COVID”), includes numerous chronic conditions associated with widespread morbidity and rising healthcare costs. PASC has highly variable clinical presentations, and likely includes multiple molecular subtypes, but it remains poorly understood from a molecular and mechanistic standpoint. This hampers the development of rationally targeted therapeutic strategies. The NIH-sponsored “Researching COVID to Enhance Recovery” (RECOVER) initiative includes several retrospective/prospective observational cohort studies enrolling adult, pregnant adult and pediatric patients respectively. RECOVER formed an “OMICS” multidisciplinary task force, including clinicians, pathologists, laboratory scientists and data scientists, charged with developing recommendations to apply cutting-edge system biology technologies to achieve the goals of RECOVER. The task force met biweekly over 14 months, to evaluate published evidence, examine the possible contribution of each “omics” technique to the study of PASC and develop study design recommendations. The OMICS task force recommended an integrated, longitudinal, simultaneous systems biology study of participant biospecimens on the entire RECOVER cohorts through centralized laboratories, as opposed to multiple smaller studies using one or few analytical techniques. The resulting multi-dimensional molecular dataset should be correlated with the deep clinical phenotyping performed through RECOVER, as well as with information on demographics, comorbidities, social determinants of health, the exposome and lifestyle factors that may contribute to the clinical presentations of PASC. This approach will minimize lab-to-lab technical variability, maximize sample size for class discovery, and enable the incorporation of as many relevant variables as possible into statistical models. Many of our recommendations have already been considered by the NIH through the peer-review process, resulting in the creation of a systems biology panel that is currently designing the studies we proposed. This system biology strategy, coupled with modern data science approaches, will dramatically improve our prospects for accurate disease subtype identification, biomarker discovery and therapeutic target identification for precision treatment. The resulting dataset should be made available to the scientific community for secondary analyses. Analogous system biology approaches should be built into the study designs of large observational studies whenever possible. |
| format | Article |
| id | doaj-art-f8c2915946d34a63840b852e40c87977 |
| institution | Kabale University |
| issn | 2674-0702 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Systems Biology |
| spelling | doaj-art-f8c2915946d34a63840b852e40c879772025-01-07T04:12:25ZengFrontiers Media S.A.Frontiers in Systems Biology2674-07022025-01-01410.3389/fsysb.2024.14223841422384A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditionsJun Sun0Masanori Aikawa1Hassan Ashktorab2Noam D. Beckmann3Noam D. Beckmann4Michael L. Enger5Joaquin M. Espinosa6Xiaowu Gai7Xiaowu Gai8Benjamin D. Horne9Benjamin D. Horne10Paul Keim11Paul Keim12Paul Keim13Jessica Lasky-Su14Rebecca Letts15Cheryl L. Maier16Meisha Mandal17Lauren Nichols18Nadia R. Roan19Nadia R. Roan20Mark W. Russell21Jacqueline Rutter22George R. Saade23George R. Saade24Kumar Sharma25Kumar Sharma26Stephanie Shiau27Stephen N. Thibodeau28Samuel Yang29Lucio Miele30NIH Researching COVID to Enhance Recovery (RECOVER) ConsortiumDepartment of Medicine, Division of Gastroenterology and Hepatology, University of Illinois Chicago, Chicago, IL, United StatesCardiovascular Division and Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United StatesDepartment of Medicine, Howard University, Washington, DC, United StatesDepartment of Medicine, Division of Data Driven and Digital Medicine (D3M), New York, NY, United StatesCharles Bronfman Institute for Personalized Medicine, Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, United StatesRTI International, Durham, NC, United StatesLinda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, United StatesDepartment of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United StatesDepartment of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States0Intermountain Medical Center Heart Institute, Murray, UT, United States1Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, United States2Department of Biology, Northern Arizona University, Flagstaff, AZ, United States3Pathogens Genomics Program, Translational Genomics Institute (TGen), Phoenix, AZ, United States4Department of Biology, University of Oxford, Oxford, United Kingdom5Channing Department of Network Medicine, Brigham and Women’s Hospital, Harvard University, Boston, MA, United States6RECOVER patient representative, Durham, NC, United States7Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United StatesRTI International, Durham, NC, United States6RECOVER patient representative, Durham, NC, United States8Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, United States9Department of Urology, University of California San Francisco, San Francisco, CA, United States0Department of Pediatrics, Division of Pediatric Cardiology, University of Michigan, Ann Arbor, MI, United States6RECOVER patient representative, Durham, NC, United States1Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX, United States2Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, VA, United States3Center for Precision Medicine, University of Texas San Antonio Health Sciences Center, San Antonio, TX, United States4Department of Medicine, Division of Nephrology, University of Texas San Antonio Health Sciences Center, San Antonio, TX, United States5Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, United States6Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States7Department of Emergency Medicine, Stanford University, Stanford, CA, United States8Department of Genetics, School of Medicine, Louisiana State University Health Sciences, Center New Orleans, New Orleans, LA, United StatesPost-Acute Sequelae of SARS-CoV-2 infection (PASC or “Long COVID”), includes numerous chronic conditions associated with widespread morbidity and rising healthcare costs. PASC has highly variable clinical presentations, and likely includes multiple molecular subtypes, but it remains poorly understood from a molecular and mechanistic standpoint. This hampers the development of rationally targeted therapeutic strategies. The NIH-sponsored “Researching COVID to Enhance Recovery” (RECOVER) initiative includes several retrospective/prospective observational cohort studies enrolling adult, pregnant adult and pediatric patients respectively. RECOVER formed an “OMICS” multidisciplinary task force, including clinicians, pathologists, laboratory scientists and data scientists, charged with developing recommendations to apply cutting-edge system biology technologies to achieve the goals of RECOVER. The task force met biweekly over 14 months, to evaluate published evidence, examine the possible contribution of each “omics” technique to the study of PASC and develop study design recommendations. The OMICS task force recommended an integrated, longitudinal, simultaneous systems biology study of participant biospecimens on the entire RECOVER cohorts through centralized laboratories, as opposed to multiple smaller studies using one or few analytical techniques. The resulting multi-dimensional molecular dataset should be correlated with the deep clinical phenotyping performed through RECOVER, as well as with information on demographics, comorbidities, social determinants of health, the exposome and lifestyle factors that may contribute to the clinical presentations of PASC. This approach will minimize lab-to-lab technical variability, maximize sample size for class discovery, and enable the incorporation of as many relevant variables as possible into statistical models. Many of our recommendations have already been considered by the NIH through the peer-review process, resulting in the creation of a systems biology panel that is currently designing the studies we proposed. This system biology strategy, coupled with modern data science approaches, will dramatically improve our prospects for accurate disease subtype identification, biomarker discovery and therapeutic target identification for precision treatment. The resulting dataset should be made available to the scientific community for secondary analyses. Analogous system biology approaches should be built into the study designs of large observational studies whenever possible.https://www.frontiersin.org/articles/10.3389/fsysb.2024.1422384/fullCOVID-19PASCRECOVERsystems biologymulti-omics |
| spellingShingle | Jun Sun Masanori Aikawa Hassan Ashktorab Noam D. Beckmann Noam D. Beckmann Michael L. Enger Joaquin M. Espinosa Xiaowu Gai Xiaowu Gai Benjamin D. Horne Benjamin D. Horne Paul Keim Paul Keim Paul Keim Jessica Lasky-Su Rebecca Letts Cheryl L. Maier Meisha Mandal Lauren Nichols Nadia R. Roan Nadia R. Roan Mark W. Russell Jacqueline Rutter George R. Saade George R. Saade Kumar Sharma Kumar Sharma Stephanie Shiau Stephen N. Thibodeau Samuel Yang Lucio Miele NIH Researching COVID to Enhance Recovery (RECOVER) Consortium A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions Frontiers in Systems Biology COVID-19 PASC RECOVER systems biology multi-omics |
| title | A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions |
| title_full | A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions |
| title_fullStr | A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions |
| title_full_unstemmed | A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions |
| title_short | A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions |
| title_sort | multi omics strategy to understand pasc through the recover cohorts a paradigm for a systems biology approach to the study of chronic conditions |
| topic | COVID-19 PASC RECOVER systems biology multi-omics |
| url | https://www.frontiersin.org/articles/10.3389/fsysb.2024.1422384/full |
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