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Maleknia S, Tavassolifar MJ, Mottaghitalab F, Zali MR, Meyfour A. Identifying novel host-based diagnostic biomarker panels for COVID-19: a whole-blood/nasopharyngeal transcriptome meta-analysis. Mol Med 2022; 28:86. [PMID: 35922752 PMCID: PMC9347150 DOI: 10.1186/s10020-022-00513-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Regardless of improvements in controlling the COVID-19 pandemic, the lack of comprehensive insight into SARS-COV-2 pathogenesis is still a sophisticated challenge. In order to deal with this challenge, we utilized advanced bioinformatics and machine learning algorithms to reveal more characteristics of SARS-COV-2 pathogenesis and introduce novel host response-based diagnostic biomarker panels. METHODS In the present study, eight published RNA-Seq datasets related to whole-blood (WB) and nasopharyngeal (NP) swab samples of patients with COVID-19, other viral and non-viral acute respiratory illnesses (ARIs), and healthy controls (HCs) were integrated. To define COVID-19 meta-signatures, Gene Ontology and pathway enrichment analyses were applied to compare COVID-19 with other similar diseases. Additionally, CIBERSORTx was executed in WB samples to detect the immune cell landscape. Furthermore, the optimum WB- and NP-based diagnostic biomarkers were identified via all the combinations of 3 to 9 selected features and the 2-phases machine learning (ML) method which implemented k-fold cross validation and independent test set validation. RESULTS The host gene meta-signatures obtained for SARS-COV-2 infection were different in the WB and NP samples. The gene ontology and enrichment results of the WB dataset represented the enhancement in inflammatory host response, cell cycle, and interferon signature in COVID-19 patients. Furthermore, NP samples of COVID-19 in comparison with HC and non-viral ARIs showed the significant upregulation of genes associated with cytokine production and defense response to the virus. In contrast, these pathways in COVID-19 compared to other viral ARIs were strikingly attenuated. Notably, immune cell proportions of WB samples altered in COVID-19 versus HC. Moreover, the optimum WB- and NP-based diagnostic panels after two phases of ML-based validation included 6 and 8 markers with an accuracy of 97% and 88%, respectively. CONCLUSIONS Based on the distinct gene expression profiles of WB and NP, our results indicated that SARS-COV-2 function is body-site-specific, although according to the common signature in WB and NP COVID-19 samples versus controls, this virus also induces a global and systematic host response to some extent. We also introduced and validated WB- and NP-based diagnostic biomarkers using ML methods which can be applied as a complementary tool to diagnose the COVID-19 infection from non-COVID cases.
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Affiliation(s)
- Samaneh Maleknia
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Tavassolifar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Faezeh Mottaghitalab
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Delaveris C, Wilk AJ, Riley NM, Stark JC, Yang SS, Rogers AJ, Ranganath T, Nadeau KC, Blish CA, Bertozzi CR. Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19. ACS CENTRAL SCIENCE 2021; 7:650-657. [PMID: 34056095 PMCID: PMC8009098 DOI: 10.1021/acscentsci.0c01669] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 05/02/2023]
Abstract
Severe cases of coronavirus disease 2019 (COVID-19), caused by infection with SARS-CoV-2, are characterized by a hyperinflammatory immune response that leads to numerous complications. Production of proinflammatory neutrophil extracellular traps (NETs) has been suggested to be a key factor in inducing a hyperinflammatory signaling cascade, allegedly causing both pulmonary tissue damage and peripheral inflammation. Accordingly, therapeutic blockage of neutrophil activation and NETosis, the cell death pathway accompanying NET formation, could limit respiratory damage and death from severe COVID-19. Here, we demonstrate that synthetic glycopolymers that activate signaling of the neutrophil checkpoint receptor Siglec-9 suppress NETosis induced by agonists of viral toll-like receptors (TLRs) and plasma from patients with severe COVID-19. Thus, Siglec-9 agonism is a promising therapeutic strategy to curb neutrophilic hyperinflammation in COVID-19.
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Affiliation(s)
- Corleone
S. Delaveris
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Aaron J. Wilk
- Stanford
Medical Scientist Training Program, Stanford
University, Stanford, California 94305, United States
- Stanford
Immunology Program, Stanford University, Stanford, California 94305, United States
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
| | - Nicholas M. Riley
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jessica C. Stark
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Samuel S. Yang
- Department
of Emergency Medicine, Stanford University, Stanford, California 94305, United States
| | - Angela J. Rogers
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
| | - Thanmayi Ranganath
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
| | - Kari C. Nadeau
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
- Sean
N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, California 94305, United States
| | | | - Catherine A. Blish
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Carolyn R. Bertozzi
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- ChEM-H, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford, California 94305, United States
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3
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Andreoletti G, Lanata CM, Trupin L, Paranjpe I, Jain TS, Nititham J, Taylor KE, Combes AJ, Maliskova L, Ye CJ, Katz P, Dall'Era M, Yazdany J, Criswell LA, Sirota M. Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures. Commun Biol 2021; 4:488. [PMID: 33883687 PMCID: PMC8060402 DOI: 10.1038/s42003-021-02000-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease in which outcomes vary among different racial groups. We leverage cell-sorted RNA-seq data (CD14+ monocytes, B cells, CD4+ T cells, and NK cells) from 120 SLE patients (63 Asian and 57 White individuals) and apply a four-tier approach including unsupervised clustering, differential expression analyses, gene co-expression analyses, and machine learning to identify SLE subgroups within this multiethnic cohort. K-means clustering on each cell-type resulted in three clusters for CD4 and CD14, and two for B and NK cells. To understand the identified clusters, correlation analysis revealed significant positive associations between the clusters and clinical parameters including disease activity as well as ethnicity. We then explored differentially expressed genes between Asian and White groups for each cell-type. The shared differentially expressed genes across cells were involved in SLE or other autoimmune-related pathways. Co-expression analysis identified similarly regulated genes across samples and grouped these genes into modules. Finally, random forest classification of disease activity in the White and Asian cohorts showed the best classification in CD4+ T cells in White individuals. The results from these analyses will help stratify patients based on their gene expression signatures to enable SLE precision medicine.
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Affiliation(s)
- Gaia Andreoletti
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Cristina M Lanata
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura Trupin
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ishan Paranjpe
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Tia S Jain
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Joanne Nititham
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kimberly E Taylor
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alexis J Combes
- Department of Pathology, University of California San Francisco, San Francisco, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Lenka Maliskova
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Patricia Katz
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Maria Dall'Era
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jinoos Yazdany
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lindsey A Criswell
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
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4
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Daamen AR, Bachali P, Owen KA, Kingsmore KM, Hubbard EL, Labonte AC, Robl R, Shrotri S, Grammer AC, Lipsky PE. Comprehensive transcriptomic analysis of COVID-19 blood, lung, and airway. Sci Rep 2021; 11:7052. [PMID: 33782412 PMCID: PMC8007747 DOI: 10.1038/s41598-021-86002-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/03/2021] [Indexed: 02/01/2023] Open
Abstract
SARS-CoV2 is a previously uncharacterized coronavirus and causative agent of the COVID-19 pandemic. The host response to SARS-CoV2 has not yet been fully delineated, hampering a precise approach to therapy. To address this, we carried out a comprehensive analysis of gene expression data from the blood, lung, and airway of COVID-19 patients. Our results indicate that COVID-19 pathogenesis is driven by populations of myeloid-lineage cells with highly inflammatory but distinct transcriptional signatures in each compartment. The relative absence of cytotoxic cells in the lung suggests a model in which delayed clearance of the virus may permit exaggerated myeloid cell activation that contributes to disease pathogenesis by the production of inflammatory mediators. The gene expression profiles also identify potential therapeutic targets that could be modified with available drugs. The data suggest that transcriptomic profiling can provide an understanding of the pathogenesis of COVID-19 in individual patients.
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Affiliation(s)
| | | | | | | | | | | | - Robert Robl
- AMPEL BioSolutions LLC, Charlottesville, VA, 22902, USA
| | - Sneha Shrotri
- AMPEL BioSolutions LLC, Charlottesville, VA, 22902, USA
| | | | - Peter E Lipsky
- AMPEL BioSolutions LLC, Charlottesville, VA, 22902, USA.
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Rendeiro AF, Casano J, Vorkas CK, Singh H, Morales A, DeSimone RA, Ellsworth GB, Soave R, Kapadia SN, Saito K, Brown CD, Hsu J, Kyriakides C, Chiu S, Cappelli LV, Cacciapuoti MT, Tam W, Galluzzi L, Simonson PD, Elemento O, Salvatore M, Inghirami G. Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression. Life Sci Alliance 2021; 4:e202000955. [PMID: 33361110 PMCID: PMC7768198 DOI: 10.26508/lsa.202000955] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/08/2023] Open
Abstract
With a rising incidence of COVID-19-associated morbidity and mortality worldwide, it is critical to elucidate the innate and adaptive immune responses that drive disease severity. We performed longitudinal immune profiling of peripheral blood mononuclear cells from 45 patients and healthy donors. We observed a dynamic immune landscape of innate and adaptive immune cells in disease progression and absolute changes of lymphocyte and myeloid cells in severe versus mild cases or healthy controls. Intubation and death were coupled with selected natural killer cell KIR receptor usage and IgM+ B cells and associated with profound CD4 and CD8 T-cell exhaustion. Pseudo-temporal reconstruction of the hierarchy of disease progression revealed dynamic time changes in the global population recapitulating individual patients and the development of an eight-marker classifier of disease severity. Estimating the effect of clinical progression on the immune response and early assessment of disease progression risks may allow implementation of tailored therapies.
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Affiliation(s)
- André F Rendeiro
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Joseph Casano
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles Kyriakos Vorkas
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Harjot Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ayana Morales
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert A DeSimone
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Grant B Ellsworth
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rosemary Soave
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shashi N Kapadia
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Kohta Saito
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher D Brown
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - JingMei Hsu
- Division of Hematology/Oncology, Department of Medicine Weill Cornell Medicine, New York, NY, USA
| | - Christopher Kyriakides
- Department of Rehabilitation Medicine at New York University Grossman School of Medicine New York, NY, USA
| | - Steven Chiu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luca Vincenzo Cappelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenzo Galluzzi
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Paul D Simonson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mirella Salvatore
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
- Division of Public Health Programs, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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6
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Rendeiro AF, Casano J, Kyriakos Vorkas C, Singh H, Morales A, DeSimone RA, Ellsworth GB, Soave R, Kapadia SN, Saito K, Brown CD, Hsu J, Kyriakides C, Chiu S, Cappelli L, Teresa Cacciapuoti M, Tam W, Galluzzi L, Simonson PD, Elemento O, Salvatore M, Inghirami G. Longitudinal immune profiling of mild and severe COVID-19 reveals innate and adaptive immune dysfunction and provides an early prediction tool for clinical progression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.08.20189092. [PMID: 32935114 PMCID: PMC7491529 DOI: 10.1101/2020.09.08.20189092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With a rising incidence of COVID-19-associated morbidity and mortality worldwide, it is critical to elucidate the innate and adaptive immune responses that drive disease severity. We performed longitudinal immune profiling of peripheral blood mononuclear cells from 45 patients and healthy donors. We observed a dynamic immune landscape of innate and adaptive immune cells in disease progression and absolute changes of lymphocyte and myeloid cells in severe versus mild cases or healthy controls. Intubation and death were coupled with selected natural killer cell KIR receptor usage and IgM+ B cells and associated with profound CD4 and CD8 T cell exhaustion. Pseudo-temporal reconstruction of the hierarchy of disease progression revealed dynamic time changes in the global population recapitulating individual patients and the development of an eight-marker classifier of disease severity. Estimating the effect of clinical progression on the immune response and early assessment of disease progression risks may allow implementation of tailored therapies.
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Affiliation(s)
- André F Rendeiro
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Joseph Casano
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles Kyriakos Vorkas
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Harjot Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ayana Morales
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert A DeSimone
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Grant B Ellsworth
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rosemary Soave
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shashi N Kapadia
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Kohta Saito
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher D Brown
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - JingMei Hsu
- Division of Hematology/Oncology, Department of Medicine Weill Cornell Medicine, New York, NY, 10065, USA
| | - Christopher Kyriakides
- Department of Rehabilitation Medicine at NYU Grossman School of Medicine New York, NY, USA
| | - Steven Chiu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luca Cappelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenzo Galluzzi
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Paul D Simonson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mirella Salvatore
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
- Division of Public Health Programs, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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