1
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Hafezqorani S, Nip KM, Birol I. ntEmbd: Deep learning embedding for nucleotide sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591806. [PMID: 38746190 PMCID: PMC11092672 DOI: 10.1101/2024.04.30.591806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Enabled by the explosion of data and substantial increase in computational power, deep learning has transformed fields such as computer vision and natural language processing (NLP) and it has become a successful method to be applied to many transcriptomic analysis tasks. A core advantage of deep learning is its inherent capability to incorporate feature computation within the machine learning models. This results in a comprehensive and machine-readable representation of sequences, facilitating the downstream classification and clustering tasks. Compared to machine translation problems in NLP, feature embedding is particularly challenging for transcriptomic studies as the sequences are string of thousands of nucleotides in length, which make the long-term dependencies between features from different parts of the sequence even more difficult to capture. This highlights the need for nucleotide sequence embedding methods that are capable of learning input sequence features implicitly. Here we introduce ntEmbd, a deep learning embedding tool that captures dependencies between different features of the sequences and learns a latent representation for given nucleotide sequences. We further provide two sample use cases, describing how learned RNA features can be used in downstream analysis. The first use case demonstrates ntEmbd's utility in classifying coding and noncoding RNA benchmarked against existing tools, and the second one explores the utility of learned representations in identifying adapter sequences in nanopore RNA-seq reads. The tool as well as the trained models are freely available on GitHub at https://github.com/bcgsc/ntEmbd.
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Affiliation(s)
- Saber Hafezqorani
- 570 W 7 Ave, Michael Smith Genome Sciences Centre, BC Cancer, V5Z 4S6, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Ka Ming Nip
- 570 W 7 Ave, Michael Smith Genome Sciences Centre, BC Cancer, V5Z 4S6, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Inanc Birol
- 570 W 7 Ave, Michael Smith Genome Sciences Centre, BC Cancer, V5Z 4S6, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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2
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Das AS, Sherry EC, Vaughan RM, Henderson ML, Zieba J, Uhl KL, Koehn O, Bupp CP, Rajasekaran S, Li X, Chhetri SB, Nissim S, Williams CL, Prokop JW. The complex, dynamic SpliceOme of the small GTPase transcripts altered by technique, sex, genetics, tissue specificity, and RNA base editing. Front Cell Dev Biol 2022; 10:1033695. [PMID: 36467401 PMCID: PMC9714508 DOI: 10.3389/fcell.2022.1033695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/01/2022] [Indexed: 04/04/2024] Open
Abstract
The small GTPase family is well-studied in cancer and cellular physiology. With 162 annotated human genes, the family has a broad expression throughout cells of the body. Members of the family have multiple exons that require splicing. Yet, the role of splicing within the family has been underexplored. We have studied the splicing dynamics of small GTPases throughout 41,671 samples by integrating Nanopore and Illumina sequencing techniques. Within this work, we have made several discoveries. 1). Using the GTEx long read data of 92 samples, each small GTPase gene averages two transcripts, with 83 genes (51%) expressing two or more isoforms. 2). Cross-tissue analysis of GTEx from 17,382 samples shows 41 genes (25%) expressing two or more protein-coding isoforms. These include protein-changing transcripts in genes such as RHOA, RAB37, RAB40C, RAB4B, RAB5C, RHOC, RAB1A, RAN, RHEB, RAC1, and KRAS. 3). The isolation and library technique of the RNAseq influences the abundance of non-sense-mediated decay and retained intron transcripts of small GTPases, which are observed more often in genes than appreciated. 4). Analysis of 16,243 samples of "Blood PAXgene" identified seven genes (3.7%; RHOA, RAB40C, RAB4B, RAB37, RAB5B, RAB5C, RHOC) with two or more transcripts expressed as the major isoform (75% of the total gene), suggesting a role of genetics in altering splicing. 5). Rare (ARL6, RAB23, ARL13B, HRAS, NRAS) and common variants (GEM, RHOC, MRAS, RAB5B, RERG, ARL16) can influence splicing and have an impact on phenotypes and diseases. 6). Multiple genes (RAB9A, RAP2C, ARL4A, RAB3A, RAB26, RAB3C, RASL10A, RAB40B, and HRAS) have sex differences in transcript expression. 7). Several exons are included or excluded for small GTPase genes (RASEF, KRAS, RAC1, RHEB, ARL4A, RHOA, RAB30, RHOBTB1, ARL16, RAP1A) in one or more forms of cancer. 8). Ten transcripts are altered in hypoxia (SAR1B, IFT27, ARL14, RAB11A, RAB10, RAB38, RAN, RIT1, RAB9A) with RHOA identified to have a transient 3'UTR RNA base editing at a conserved site found in all of its transcripts. Overall, we show a remarkable and dynamic role of splicing within the small GTPase family that requires future explorations.
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Affiliation(s)
- Akansha S. Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Biology, Washington and Jefferson College, Washington, PA, United States
| | - Emily C. Sherry
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, United States
| | - Robert M. Vaughan
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Marian L. Henderson
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- The Department of Biology, Calvin University, Grand Rapids, MI, United States
| | - Jacob Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI, United States
| | - Katie L. Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Olivia Koehn
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Medical Genetics, Spectrum Health and Helen DeVos Children’s Hospital, Grand Rapids, MI, United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Pediatric Critical Care Medicine, Helen DeVos Children’s Hospital Spectrum Health, Grand Rapids, MI, United States
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Surya B. Chhetri
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MA, United States
| | - Sahar Nissim
- Genetics and Gastroenterology Divisions, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, United States
| | - Carol L. Williams
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
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3
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Mark PR, Murray SA, Yang T, Eby A, Lai A, Lu D, Zieba J, Rajasekaran S, VanSickle EA, Rossetti LZ, Guidugli L, Watkins K, Wright MS, Bupp CP, Prokop JW. Autosomal recessive LRP1-related syndrome featuring cardiopulmonary dysfunction, bone dysmorphology, and corneal clouding. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006169. [PMID: 36307211 PMCID: PMC9632358 DOI: 10.1101/mcs.a006169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 08/22/2022] [Indexed: 01/25/2023] Open
Abstract
We provide the first study of two siblings with a novel autosomal recessive LRP1-related syndrome identified by rapid genome sequencing and overlapping multiple genetic models. The patients presented with respiratory distress, congenital heart defects, hypotonia, dysmorphology, and unique findings, including corneal clouding and ascites. Both siblings had compound heterozygous damaging variants, c.11420G > C (p.Cys3807Ser) and c.12407T > G (p.Val4136Gly) in LRP1, in which segregation analysis helped dismiss additional variants of interest. LRP1 analysis using multiple human/mouse data sets reveals a correlation to patient phenotypes of Peters plus syndrome with additional severe cardiomyopathy and blood vessel development complications linked to neural crest cells.
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Affiliation(s)
- Paul R. Mark
- Division of Medical Genetics, Spectrum Health, Grand Rapids, Michigan 49503, USA;,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | | | - Tao Yang
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, USA
| | - Alexandra Eby
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA;,Department of Science, Davenport University, Grand Rapids, Michigan 49512, USA
| | - Angela Lai
- Neonatal Intensive Care Unit, Bronson Methodist Hospital, Kalamazoo, Michigan 49007, USA
| | - Di Lu
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, USA
| | - Jacob Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA;,Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA;,Office of Research, Spectrum Health, Grand Rapids, Michigan 49503, USA
| | | | - Linda Z. Rossetti
- Division of Medical Genetics, Spectrum Health, Grand Rapids, Michigan 49503, USA;,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Kelly Watkins
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Meredith S. Wright
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Caleb P. Bupp
- Division of Medical Genetics, Spectrum Health, Grand Rapids, Michigan 49503, USA;,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA;,Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan 48824, USA;,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, USA
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4
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Bupp CP, English BK, Rajasekaran S, Prokop JW. Introduction to Personalized Medicine in Pediatrics. Pediatr Ann 2022; 51:e381-e386. [PMID: 36215089 DOI: 10.3928/19382359-20220803-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Exciting new developments in biomedical and computational sciences provide an extraordinary and unparalleled opportunity to compile, connect, and analyze multiple types of "big data," driving the development of personalized medicine. These insights must begin in early life (ie, pregnancy, neonatal, and infancy) and focus on early prevention, diagnosis, and intervention-areas of medicine where pediatricians are poised to lead the way to a personalized medicine future. The rapid growth of genomics (including pharmacogenomics), transcriptomics, and related "omics" has revolutionized the diagnosis of rare monogenic disorders. It is now clarifying the pathogenesis of complex conditions ranging from autism spectrum disorder to asthma. Collaborations between clinicians and basic scientists integrating multiomics approaches in evaluating children with severe illness are transforming the fields of perinatal, neonatal, and pediatric critical care medicine. Improvements in rapid diagnostic and prognostic information suggest that pediatric personalized medicine is under way and has an exciting future. [Pediatr Ann. 2022;51(10):e381-e386.].
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5
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Prokop JW, Jdanov V, Savage L, Morris M, Lamb N, VanSickle E, Stenger CL, Rajasekaran S, Bupp CP. Computational and Experimental Analysis of Genetic Variants. Compr Physiol 2022; 12:3303-3336. [PMID: 35578967 DOI: 10.1002/cphy.c210012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics has grown exponentially over the last decade. Common variants are associated with physiological changes through statistical strategies such as Genome-Wide Association Studies (GWAS) and quantitative trail loci (QTL). Rare variants are associated with diseases through extensive filtering tools, including population genomics and trio-based sequencing (parents and probands). However, the genomic associations require follow-up analyses to narrow causal variants, identify genes that are influenced, and to determine the physiological changes. Large quantities of data exist that can be used to connect variants to gene changes, cell types, protein pathways, clinical phenotypes, and animal models that establish physiological genomics. This data combined with bioinformatics including evolutionary analysis, structural insights, and gene regulation can yield testable hypotheses for mechanisms of genomic variants. Molecular biology, biochemistry, cell culture, CRISPR editing, and animal models can test the hypotheses to give molecular variant mechanisms. Variant characterizations can be a significant component of educating future professionals at the undergraduate, graduate, or medical training programs through teaching the basic concepts and terminology of genetics while learning independent research hypothesis design. This article goes through the computational and experimental analysis strategies of variant characterization and provides examples of these tools applied in publications. © 2022 American Physiological Society. Compr Physiol 12:3303-3336, 2022.
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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, USA.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Vladislav Jdanov
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Lane Savage
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA.,Office of Research, Spectrum Health, Grand Rapids, Michigan, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Medical Genetics, Spectrum Health, Grand Rapids, Michigan, USA
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6
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Bauss J, Morris M, Shankar R, Olivero R, Buck LN, Stenger CL, Hinds D, Mills J, Eby A, Zagorski JW, Smith C, Cline S, Hartog NL, Chen B, Huss J, Carcillo JA, Rajasekaran S, Bupp CP, Prokop JW. CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications. Front Immunol 2021; 12:790041. [PMID: 34925370 PMCID: PMC8674737 DOI: 10.3389/fimmu.2021.790041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/18/2021] [Indexed: 01/02/2023] Open
Abstract
In the age of genomics, public understanding of complex scientific knowledge is critical. To combat reductionistic views, it is necessary to generate and organize educational material and data that keep pace with advances in genomics. The view that CCR5 is solely the receptor for HIV gave rise to demand to remove the gene in patients to create host HIV resistance, underestimating the broader roles and complex genetic inheritance of CCR5. A program aimed at providing research projects to undergraduates, known as CODE, has been expanded to build educational material for genes such as CCR5 in a rapid approach, exposing students and trainees to large bioinformatics databases and previous experiments for broader data to challenge commitment to biological reductionism. Our students organize expression databases, query environmental responses, assess genetic factors, generate protein models/dynamics, and profile evolutionary insights into a protein such as CCR5. The knowledgebase generated in the initiative opens the door for public educational information and tools (molecular videos, 3D printed models, and handouts), classroom materials, and strategy for future genetic ideas that can be distributed in formal, semiformal, and informal educational environments. This work highlights that many factors are missing from the reductionist view of CCR5, including the role of missense variants or expression of CCR5 with neurological phenotypes and the role of CCR5 and the delta32 variant in complex critical care patients with sepsis. When connected to genomic stories in the news, these tools offer critically needed Ethical, Legal, and Social Implication (ELSI) education to combat biological reductionism.
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Affiliation(s)
- Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Rama Shankar
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Rosemary Olivero
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Infectious Disease, Helen DeVos Children's Hospital, Grand Rapids, MI, United States
| | - Leah N Buck
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Mathematics, University of North Alabama, Florence, AL, United States
| | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, AL, United States
| | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Joshua Mills
- Department of Biology, Grand Valley State University, Allendale, MI, United States
| | - Alexandra Eby
- Department of Science, Davenport University, Grand Rapids, MI, United States
| | - Joseph W Zagorski
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | - Caitlin Smith
- Department of Biology, Athens State University, Athens, AL, United States
| | - Sara Cline
- Department of Biology, Athens State University, Athens, AL, United States
| | - Nicholas L Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Allergy & Immunology, Spectrum Health, Grand Rapids, MI, United States
| | - Bin Chen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - John Huss
- Department of Philosophy, The University of Akron, Akron, OH, United States
| | - Joseph A Carcillo
- Department of Critical Care Medicine and Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Office of Research, Spectrum Health, Grand Rapids, MI, United States.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, MI, United States
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Medical Genetics, Spectrum Health, Grand Rapids, MI, United States
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
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7
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Okada D, Zheng C, Cheng JH, Yamada R. Cell population-based framework of genetic epidemiology in the single-cell omics era. Bioessays 2021; 44:e2100118. [PMID: 34821401 DOI: 10.1002/bies.202100118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/18/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022]
Abstract
Genetic epidemiology is a rapidly advancing field due to the recent availability of large amounts of omics data. In recent years, it has become possible to obtain omics information at the single-cell level, so genetic epidemiological models need to be updated to integrate with single-cell expression data. In this perspective paper, we propose a cell population-based framework for genetic epidemiology in the single-cell era. In this framework, genetic diversity influences phenotypic diversity through the diversity of cell population profiles, which are defined as high-dimensional probability distributions of the state spaces of biomolecules of each omics layer. We discuss how biomolecular experimental measurement data can capture the different properties of this distribution. In particular, single-cell data constitute a sample from this population distribution where only some coordinate values are observable. From a data analysis standpoint, we introduce methodology for feature extraction from cell population profiles. Finally, we discuss how this framework can be applied not only to genetic epidemiology but also to systems biology.
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Affiliation(s)
- Daigo Okada
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Cheng Zheng
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Jian Hao Cheng
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Ryo Yamada
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
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8
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Prokop JW, Hartog NL, Chesla D, Faber W, Love CP, Karam R, Abualkheir N, Feldmann B, Teng L, McBride T, Leimanis ML, English BK, Holsworth A, Frisch A, Bauss J, Kalpage N, Derbedrossian A, Pinti RM, Hale N, Mills J, Eby A, VanSickle EA, Pageau SC, Shankar R, Chen B, Carcillo JA, Sanfilippo D, Olivero R, Bupp CP, Rajasekaran S. High-Density Blood Transcriptomics Reveals Precision Immune Signatures of SARS-CoV-2 Infection in Hospitalized Individuals. Front Immunol 2021; 12:694243. [PMID: 34335605 PMCID: PMC8322982 DOI: 10.3389/fimmu.2021.694243] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/30/2021] [Indexed: 12/27/2022] Open
Abstract
The immune response to COVID-19 infection is variable. How COVID-19 influences clinical outcomes in hospitalized patients needs to be understood through readily obtainable biological materials, such as blood. We hypothesized that a high-density analysis of host (and pathogen) blood RNA in hospitalized patients with SARS-CoV-2 would provide mechanistic insights into the heterogeneity of response amongst COVID-19 patients when combined with advanced multidimensional bioinformatics for RNA. We enrolled 36 hospitalized COVID-19 patients (11 died) and 15 controls, collecting 74 blood PAXgene RNA tubes at multiple timepoints, one early and in 23 patients after treatment with various therapies. Total RNAseq was performed at high-density, with >160 million paired-end, 150 base pair reads per sample, representing the most sequenced bases per sample for any publicly deposited blood PAXgene tube study. There are 770 genes significantly altered in the blood of COVID-19 patients associated with antiviral defense, mitotic cell cycle, type I interferon signaling, and severe viral infections. Immune genes activated include those associated with neutrophil mechanisms, secretory granules, and neutrophil extracellular traps (NETs), along with decreased gene expression in lymphocytes and clonal expansion of the acquired immune response. Therapies such as convalescent serum and dexamethasone reduced many of the blood expression signatures of COVID-19. Severely ill or deceased patients are marked by various secondary infections, unique gene patterns, dysregulated innate response, and peripheral organ damage not otherwise found in the cohort. High-density transcriptomic data offers shared gene expression signatures, providing unique insights into the immune system and individualized signatures of patients that could be used to understand the patient's clinical condition. Whole blood transcriptomics provides patient-level insights for immune activation, immune repertoire, and secondary infections that can further guide precision treatment.
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Affiliation(s)
- Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - Nicholas L. Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Allergy & Immunology, Spectrum Health, Grand Rapids, MI, United States
| | - Dave Chesla
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - William Faber
- Physical Sciences, Grand Rapids Community College, Grand Rapids, MI, United States
| | - Chanise P. Love
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | | | | | | | - Li Teng
- Ambry Genetics, Aliso Viejo, CA, United States
| | | | - Mara L. Leimanis
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI, United States
| | - B. Keith English
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Amanda Holsworth
- Allergy & Immunology, Spectrum Health, Grand Rapids, MI, United States
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Nathisha Kalpage
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Aram Derbedrossian
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Ryan M. Pinti
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Nicole Hale
- The Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI, United States
| | - Joshua Mills
- Department of Biology, Grand Valley State University, Allendale, MI, United States
| | - Alexandra Eby
- Department of Science, Davenport University, Grand Rapids, MI, United States
| | | | - Spencer C. Pageau
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | - Rama Shankar
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - Bin Chen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - Joseph A. Carcillo
- Department of Critical Care Medicine and Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Dominic Sanfilippo
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI, United States
| | - Rosemary Olivero
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Infectious Disease, Helen DeVos Children’s Hospital, Grand Rapids, MI, United States
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Medical Genetics, Spectrum Health Medical Genetics, Grand Rapids, MI, United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI, United States
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9
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Leimanis-Laurens M, Wolfrum E, Ferguson K, Grunwell JR, Sanfilippo D, Prokop JW, Lydic TA, Rajasekaran S. Hexosylceramides and Glycerophosphatidylcholine GPC(36:1) Increase in Multi-Organ Dysfunction Syndrome Patients with Pediatric Intensive Care Unit Admission over 8-Day Hospitalization. J Pers Med 2021; 11:339. [PMID: 33923179 PMCID: PMC8145972 DOI: 10.3390/jpm11050339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/21/2022] Open
Abstract
Glycero- and sphingo-lipids are important in plasma membrane structure, caloric storage and signaling. An un-targeted lipidomics approach for a cohort of critically ill pediatric intensive care unit (PICU) patients undergoing multi-organ dysfunction syndrome (MODS) was compared to sedation controls. After IRB approval, patients meeting the criteria for MODS were screened, consented (n = 24), and blood samples were collected from the PICU at HDVCH, Michigan; eight patients needed veno-arterial extracorporeal membrane oxygenation (VA ECMO). Sedation controls were presenting for routine sedation (n = 4). Plasma lipid profiles were determined by nano-electrospray (nESI) direct infusion high resolution/accurate mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Biostatistics analysis was performed using R v 3.6.0. Sixty-one patient samples over three time points revealed a ceramide metabolite, hexosylceramide (Hex-Cer) was high across all time points (mean 1.63-3.19%; vs. controls 0.22%). Fourteen species statistically differentiated from sedation controls (p-value ≤ 0.05); sphingomyelin (SM) [SM(d18:1/23:0), SM(d18:1/22:0), SM(d18:1/23:1), SM(d18:1/21:0), SM(d18:1/24:0)]; and glycerophosphotidylcholine (GPC) [GPC(36:01), GPC(18:00), GPC(O:34:02), GPC(18:02), GPC(38:05), GPC(O:34:03), GPC(16:00), GPC(40:05), GPC(O:36:03)]. Hex-Cer has been shown to be involved in viral infection and may be at play during acute illness. GPC(36:01) was elevated in all MODS patients at all time points and is associated with inflammation and brain injury.
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Affiliation(s)
- Mara Leimanis-Laurens
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA; (K.F.); (D.S.); (S.R.)
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg., 1355 Bogue Street, East Lansing, MI 48824, USA;
| | - Emily Wolfrum
- Bioinformatics & Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA;
| | - Karen Ferguson
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA; (K.F.); (D.S.); (S.R.)
| | - Jocelyn R. Grunwell
- Pediatric Critical Care Medicine, Emory University & Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA;
| | - Dominic Sanfilippo
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA; (K.F.); (D.S.); (S.R.)
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg., 1355 Bogue Street, East Lansing, MI 48824, USA;
| | - Jeremy W. Prokop
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg., 1355 Bogue Street, East Lansing, MI 48824, USA;
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Todd A. Lydic
- Collaborative Mass Spectrometry Core, Department of Physiology, Michigan State University, East Lansing, MI 48824, USA;
| | - Surender Rajasekaran
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA; (K.F.); (D.S.); (S.R.)
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg., 1355 Bogue Street, East Lansing, MI 48824, USA;
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
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10
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Gupta R, Leimanis ML, Adams M, Bachmann AS, Uhl KL, Bupp CP, Hartog NL, Kort EJ, Olivero R, Comstock SS, Sanfilippo DJ, Lunt SY, Prokop JW, Rajasekaran S. Balancing precision versus cohort transcriptomic analysis of acute and recovery phase of viral bronchiolitis. Am J Physiol Lung Cell Mol Physiol 2021; 320:L1147-L1157. [PMID: 33851876 DOI: 10.1152/ajplung.00440.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Viral infections affecting the lower respiratory tract place enormous burdens on hospitals. As neither vaccines nor antiviral agents exist for many viruses, understanding risk factors and outcomes in each patient using minimally invasive analysis, such as blood, can lead to improved health care delivery. A cohort of PAXgene RNA sequencing of infants admitted with moderate or severe acute bronchiolitis and respiratory syncytial virus were compared with case-control statistical analysis and cohort-based outlier mapping for precision transcriptomics. Patients with severe bronchiolitis had signatures connected to the immune system, interferon signaling, and cytokine signaling, with marked sex differences in XIST, RPS4Y1, KDM5D, and LINC00278 for severity. Several patients had unique secondary infections, cytokine activation, immune responses, biological pathways, and immune cell activation, highlighting the need for defining patient-level transcriptomic signatures. Balancing relative contributions of cohort-based biomarker discoveries with patient's biological responses is needed to understand the totality of mechanisms of adverse outcomes in viral bronchiolitis.
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Affiliation(s)
- 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
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - André S Bachmann
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | - Katie L 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
| | - Caleb P Bupp
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | | | - Eric J Kort
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,DeVos Cardiovascular Research Program, Spectrum Health and Van Andel Institute, Grand Rapids, Michigan
| | - Rosemary Olivero
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Infectious Disease, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, 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
| | - Sophia Y Lunt
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.,Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - 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
| | - 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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11
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Leimanis-Laurens ML, Ferguson K, Wolfrum E, Boville B, Sanfilippo D, Lydic TA, Prokop JW, Rajasekaran S. Pediatric Multi-Organ Dysfunction Syndrome: Analysis by an Untargeted "Shotgun" Lipidomic Approach Reveals Low-Abundance Plasma Phospholipids and Dynamic Recovery over 8-Day Period, a Single-Center Observational Study. Nutrients 2021; 13:774. [PMID: 33673500 PMCID: PMC7997359 DOI: 10.3390/nu13030774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/23/2021] [Indexed: 12/30/2022] Open
Abstract
Lipids are molecules involved in metabolism and inflammation. This study investigates the plasma lipidome for markers of severity and nutritional status in critically ill children. Children with multi-organ dysfunction syndrome (MODS) (n = 24) are analyzed at three time-points and cross-referenced to sedation controls (n = 4) for a total of N = 28. Eight of the patients with MODS, needed veno-arterial extracorporeal membrane oxygenation (VA ECMO) support to survive. Blood plasma lipid profiles are quantified by nano-electrospray (nESI), direct infusion high resolution/accurate mass spectrometry (MS), and tandem mass spectrometry (MS/MS), and compared to nutritional profiles and pediatric logistic organ dysfunction (PELOD) scores. Our results show that PELOD scores were not significantly different between MODS and ECMO cases across time-points (p = 0.66). Lipid profiling provides stratification between sedation controls and all MODS patients for total lysophosphatidylserine (lysoPS) (p-value = 0.004), total phosphatidylserine (PS) (p-value = 0.015), and total ether-linked phosphatidylethanolamine (ether-PE) (p-value = 0.03) after adjusting for sex and age. Nutrition intake over time did not correlate with changes in lipid profiles, as measured by caloric and protein intake. Lipid measurement in the intensive care environment shows dynamic changes over an 8-day pediatric intensive care unit (PICU) course, suggesting novel metabolic indicators for defining critically ill children.
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Affiliation(s)
- Mara L. Leimanis-Laurens
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, 100 Michigan Street NE, Grand Rapids, MI 49503, USA; (K.F.); (B.B.); (D.S.); (S.R.)
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg. 1355 Bogue Street, East Lansing, MI 48824, USA;
| | - Karen Ferguson
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, 100 Michigan Street NE, Grand Rapids, MI 49503, USA; (K.F.); (B.B.); (D.S.); (S.R.)
| | - Emily Wolfrum
- Van Andel Institute, Bioinformatics & Biostatistics Core, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA;
| | - Brian Boville
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, 100 Michigan Street NE, Grand Rapids, MI 49503, USA; (K.F.); (B.B.); (D.S.); (S.R.)
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg. 1355 Bogue Street, East Lansing, MI 48824, USA;
| | - Dominic Sanfilippo
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, 100 Michigan Street NE, Grand Rapids, MI 49503, USA; (K.F.); (B.B.); (D.S.); (S.R.)
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg. 1355 Bogue Street, East Lansing, MI 48824, USA;
| | - Todd A. Lydic
- Department of Physiology, Collaborative Mass Spectrometry Core, 567 Wilson Road, East Lansing, MI 48824, USA;
| | - Jeremy W. Prokop
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg. 1355 Bogue Street, East Lansing, MI 48824, USA;
- Department of Pharmacology and Toxicology, Michigan State University, 1355 Bogue Street, East Lansing, MI 48824, USA
| | - Surender Rajasekaran
- Pediatric Critical Care Unit, Helen DeVos Children’s Hospital, 100 Michigan Street NE, Grand Rapids, MI 49503, USA; (K.F.); (B.B.); (D.S.); (S.R.)
- Department of Pediatric and Human Development, College of Human Medicine, Michigan State University, Life Sciences Bldg. 1355 Bogue Street, East Lansing, MI 48824, USA;
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12
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López-Cortés A, Guevara-Ramírez P, Kyriakidis NC, Barba-Ostria C, León Cáceres Á, Guerrero S, Ortiz-Prado E, Munteanu CR, Tejera E, Cevallos-Robalino D, Gómez-Jaramillo AM, Simbaña-Rivera K, Granizo-Martínez A, Pérez-M G, Moreno S, García-Cárdenas JM, Zambrano AK, Pérez-Castillo Y, Cabrera-Andrade A, Puig San Andrés L, Proaño-Castro C, Bautista J, Quevedo A, Varela N, Quiñones LA, Paz-y-Miño C. In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19. Front Pharmacol 2021; 12:598925. [PMID: 33716737 PMCID: PMC7952300 DOI: 10.3389/fphar.2021.598925] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
Background: There is pressing urgency to identify therapeutic targets and drugs that allow treating COVID-19 patients effectively. Methods: We performed in silico analyses of immune system protein interactome network, single-cell RNA sequencing of human tissues, and artificial neural networks to reveal potential therapeutic targets for drug repurposing against COVID-19. Results: We screened 1,584 high-confidence immune system proteins in ACE2 and TMPRSS2 co-expressing cells, finding 25 potential therapeutic targets significantly overexpressed in nasal goblet secretory cells, lung type II pneumocytes, and ileal absorptive enterocytes of patients with several immunopathologies. Then, we performed fully connected deep neural networks to find the best multitask classification model to predict the activity of 10,672 drugs, obtaining several approved drugs, compounds under investigation, and experimental compounds with the highest area under the receiver operating characteristics. Conclusion: After being effectively analyzed in clinical trials, these drugs can be considered for treatment of severe COVID-19 patients. Scripts can be downloaded at https://github.com/muntisa/immuno-drug-repurposing-COVID-19.
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Affiliation(s)
- Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, A Coruña, Spain
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Nikolaos C. Kyriakidis
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Carlos Barba-Ostria
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Ángela León Cáceres
- Heidelberg Institute of Global Health, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Instituto de Salud Pública, Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Tropical Herping, Quito, Ecuador
| | - Santiago Guerrero
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Esteban Ortiz-Prado
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Cristian R. Munteanu
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, A Coruña, Spain
- Biomedical Research Institute of A Coruna (INIBIC), University Hospital Complex of A Coruna (CHUAC), A Coruña, Spain
- Centro de Información en Tecnologías de la Información y las Comunicaciones (CITIC), A Coruña, Spain
| | - Eduardo Tejera
- Grupo de Bio-Quimioinformática, Universidad de Las Américas (UDLA), Quito, Ecuador
| | | | | | - Katherine Simbaña-Rivera
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Adriana Granizo-Martínez
- Carrera de Medicina, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Gabriela Pérez-M
- Centro Clínico Quirúrgico Ambulatorio Hospital del Día El Batán, Instituto Ecuatoriano de Seguridad Social, Quito, Ecuador
| | - Silvana Moreno
- Department of Plant Biology, Faculty of Natural Resources and Agricultural Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jennyfer M. García-Cárdenas
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
- Biomedical Research Institute of A Coruna (INIBIC), University Hospital Complex of A Coruna (CHUAC), A Coruña, Spain
| | | | - Alejandro Cabrera-Andrade
- RNASA-IMEDIR, Computer Science Faculty, University of A Coruna, A Coruña, Spain
- Grupo de Bio-Quimioinformática, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Lourdes Puig San Andrés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | | | - Jhommara Bautista
- Facultad de Ingeniería y Ciencias Aplicadas-Biotecnología, Universidad de Las Américas, Quito, Ecuador
| | - Andreina Quevedo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Nelson Varela
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Luis Abel Quiñones
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - César Paz-y-Miño
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
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13
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The Feasibility of Studying Metabolites in PICU Multi-Organ Dysfunction Syndrome Patients over an 8-Day Course Using an Untargeted Approach. CHILDREN-BASEL 2021; 8:children8020151. [PMID: 33670443 PMCID: PMC7922853 DOI: 10.3390/children8020151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/07/2021] [Accepted: 02/11/2021] [Indexed: 12/14/2022]
Abstract
Metabolites are generated from critical biological functions and metabolism. This pediatric study reviewed plasma metabolites in patients suffering from multi-organ dysfunction syndrome (MODS) in the pediatric intensive care unit (PICU) using an untargeted metabolomics approach. Patients meeting the criteria for MODS were screened for eligibility and consented (n = 24), and blood samples were collected at baseline, 72 h, and 8 days; control patients (n = 4) presented for routine sedation in an outpatient setting. A subset of MODS patients (n = 8) required additional support with veno-atrial extracorporeal membrane oxygenation (VA-ECMO) therapy. Metabolites from thawed blood plasma were determined from ion pairing reversed-phase liquid chromatography–mass spectrometry (LC-MS) analysis. Chromatographic peak alignment, identification, relative quantitation, and statistical and bioinformatics evaluation were performed using MAVEN and MetaboAnalyst 4.0. Metabolite analysis revealed 115 peaks per sample. From the partial least squares-discriminant analysis (PLS-DA) with variance of importance (VIP) scores above ≥2.0, 7 dynamic metabolites emerged over the three time points: tauro-chenodeoxycholic acid (TCDCA), hexose, p-hydroxybenzoate, hydroxyphenylacetic acid (HPLA), 2_3-dihydroxybenzoic acid, 2-keto-isovalerate, and deoxyribose phosphate. After Bonferroni adjustment for repeated measures, hexose and p-hydroxybenzoate were significant at one time point or more. Kendall’s tau-b test was used for internal validation of creatinine. Metabolites may be benign or significant in describing a patient’s pathophysiology and require operator interpretation.
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14
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Traversi D, Pulliero A, Izzotti A, Franchitti E, Iacoviello L, Gianfagna F, Gialluisi A, Izzi B, Agodi A, Barchitta M, Calabrò GE, Hoxhaj I, Sassano M, Sbrogiò LG, Del Sole A, Marchiori F, Pitini E, Migliara G, Marzuillo C, De Vito C, Tamburro M, Sammarco ML, Ripabelli G, Villari P, Boccia S. Precision Medicine and Public Health: New Challenges for Effective and Sustainable Health. J Pers Med 2021; 11:135. [PMID: 33669364 PMCID: PMC7920275 DOI: 10.3390/jpm11020135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 02/06/2023] Open
Abstract
The development of high-throughput omics technologies represents an unmissable opportunity for evidence-based prevention of adverse effects on human health. However, the applicability and access to multi-omics tests are limited. In Italy, this is due to the rapid increase of knowledge and the high levels of skill and economic investment initially necessary. The fields of human genetics and public health have highlighted the relevance of an implementation strategy at a national level in Italy, including integration in sanitary regulations and governance instruments. In this review, the emerging field of public health genomics is discussed, including the polygenic scores approach, epigenetic modulation, nutrigenomics, and microbiomes implications. Moreover, the Italian state of implementation is presented. The omics sciences have important implications for the prevention of both communicable and noncommunicable diseases, especially because they can be used to assess the health status during the whole course of life. An effective population health gain is possible if omics tools are implemented for each person after a preliminary assessment of effectiveness in the medium to long term.
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Affiliation(s)
- Deborah Traversi
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Alessandra Pulliero
- Department of Health Sciences School of Medicine, University of Genoa, 16132 Genova, Italy;
| | - Alberto Izzotti
- Department of Experimental Medicine, University of Genoa, 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 161632 Genova, Italy
| | - Elena Franchitti
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Licia Iacoviello
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Francesco Gianfagna
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Mediterranea Cardiocentro, 80122 Napoli, Italy
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Martina Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Giovanna Elisa Calabrò
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Ilda Hoxhaj
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Michele Sassano
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Luca Gino Sbrogiò
- Dipartimento di Prevenzione, Az. ULSS3 Serenissima, 30174 Venezia, Italy;
| | | | | | - Erica Pitini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Manuela Tamburro
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Michela Lucia Sammarco
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Giancarlo Ripabelli
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
- Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
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15
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Hartog N, Faber W, Frisch A, Bauss J, Bupp CP, Rajasekaran S, Prokop JW. SARS-CoV-2 infection: molecular mechanisms of severe outcomes to suggest therapeutics. Expert Rev Proteomics 2021; 18:105-118. [PMID: 33779460 PMCID: PMC8022340 DOI: 10.1080/14789450.2021.1908894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Introduction:The year 2020 was defined by the 29,903 base pairs of RNA that codes for the SARS-CoV-2 genome. SARS-CoV-2 infects humans to cause COVID-19, spreading from patient-to-patient yet impacts patients very divergently.Areas covered: Within this review, we address the known molecular mechanisms and supporting data for COVID-19 clinical course and pathology, clinical risk factors and molecular signatures, therapeutics of severe COVID-19, and reinfection/vaccination. Literature and published datasets were reviewed using PubMed, Google Scholar, and NCBI SRA tools. The combination of exaggerated cytokine signaling, pneumonia, NETosis, pyroptosis, thrombocytopathy, endotheliopathy, multiple organ dysfunction syndrome (MODS), and acute respiratory distress syndrome (ARDS) create a positive feedback loop of severe damage in patients with COVID-19 that impacts the entire body and may persist for months following infection. Understanding the molecular pathways of severe COVID-19 opens the door for novel therapeutic design. We summarize the current insights into pathology, risk factors, secondary infections, genetics, omics, and drugs being tested to treat severe COVID-19.Expert opinion: A growing level of support suggests the need for stronger integration of biomarkers and precision medicine to guide treatment strategies of severe COVID-19, where each patient has unique outcomes and thus require guided treatment.
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Affiliation(s)
- Nicholas Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Allergy & Immunology, Spectrum Health, Grand Rapids, MI, USA
| | - William Faber
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Chemistry, Grand Rapids Community College, Grand Rapids, MI, USA
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI, USA
- Office of Research, Office of Research, Spectrum Health, Grand Rapids, MI, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
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16
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Chen Z, Wu A. Progress and challenge for computational quantification of tissue immune cells. Brief Bioinform 2021; 22:6065002. [PMID: 33401306 DOI: 10.1093/bib/bbaa358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 12/28/2022] Open
Abstract
Tissue immune cells have long been recognized as important regulators for the maintenance of balance in the body system. Quantification of the abundance of different immune cells will provide enhanced understanding of the correlation between immune cells and normal or abnormal situations. Currently, computational methods to predict tissue immune cell compositions from bulk transcriptomes have been largely developed. Therefore, summarizing the advantages and disadvantages is appropriate. In addition, an examination of the challenges and possible solutions for these computational models will assist the development of this field. The common hypothesis of these models is that the expression of signature genes for immune cell types might represent the proportion of immune cells that contribute to the tissue transcriptome. In general, we grouped all reported tools into three groups, including reference-free, reference-based scoring and reference-based deconvolution methods. In this review, a summary of all the currently reported computational immune cell quantification tools and their applications, limitations, and perspectives are presented. Furthermore, some critical problems are found that have limited the performance and application of these models, including inadequate immune cell type, the collinearity problem, the impact of the tissue environment on the immune cell expression level, and the deficiency of standard datasets for model validation. To address these issues, tissue specific training datasets that include all known immune cells, a hierarchical computational framework, and benchmark datasets including both tissue expression profiles and the abundances of all the immune cells are proposed to further promote the development of this field.
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Affiliation(s)
- Ziyi Chen
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
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17
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Sirpilla O, Bauss J, Gupta R, Underwood A, Qutob D, Freeland T, Bupp C, Carcillo J, Hartog N, Rajasekaran S, Prokop JW. SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes. J Proteome Res 2020; 19:4275-4290. [PMID: 32686937 PMCID: PMC7418564 DOI: 10.1021/acs.jproteome.0c00421] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics.
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Affiliation(s)
- Olivia Sirpilla
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Jacob Bauss
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
| | - Ruchir Gupta
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Adam Underwood
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Dinah Qutob
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Tom Freeland
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Caleb Bupp
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Spectrum Health Medical
Genetics, Grand Rapids, Michigan 49503,
United States
| | - Joseph Carcillo
- Department of Critical Care Medicine
and Pediatrics, Children’s Hospital of Pittsburgh,
University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania 15421,
United States
| | - Nicholas Hartog
- Allergy & Immunology,
Spectrum Health, Grand Rapids, Michigan 49503,
United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Pediatric Intensive Care
Unit, Helen DeVos Children’s Hospital,
Grand Rapids, Michigan 49503, United States
- Office of Research,
Spectrum Health, Grand Rapids, Michigan 49503,
United States
| | - Jeremy W. Prokop
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
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18
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Hartog N, Holsworth A, Rajasekaran S. Controlled trials needed to prove efficacy and safety of convalescent plasma therapy in coronavirus disease 2019. Ann Allergy Asthma Immunol 2020; 126:122-123. [PMID: 33161152 PMCID: PMC7642751 DOI: 10.1016/j.anai.2020.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 11/17/2022]
Affiliation(s)
- Nicholas Hartog
- Spectrum Health Allergy and Clinical Immunology, Grand Rapids, Michigan; Michigan State University College of Human Medicine, East Lansing, Michigan.
| | - Amanda Holsworth
- Spectrum Health Allergy and Clinical Immunology, Grand Rapids, Michigan; Michigan State University College of Human Medicine, East Lansing, Michigan
| | - Surender Rajasekaran
- Michigan State University College of Human Medicine, East Lansing, Michigan; Helen DeVos Children's Hospital Pediatric Critical Care Medicine, Grand Rapids, Michigan
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