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Rowley SD, Gunning TS, Pelliccia M, Della Pia A, Lee A, Behrmann J, Bangolo A, Jandir P, Zhang H, Kaur S, Suh HC, Donato M, Albitar M, Ip A. Using Targeted Transcriptome and Machine Learning of Pre- and Post-Transplant Bone Marrow Samples to Predict Acute Graft-versus-Host Disease and Overall Survival after Allogeneic Stem Cell Transplantation. Cancers (Basel) 2024; 16:1357. [PMID: 38611035 PMCID: PMC11011125 DOI: 10.3390/cancers16071357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Acute graft-versus-host disease (aGvHD) remains a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (HSCT). We performed RNA analysis of 1408 candidate genes in bone marrow samples obtained from 167 patients undergoing HSCT. RNA expression data were used in a machine learning algorithm to predict the presence or absence of aGvHD using either random forest or extreme gradient boosting algorithms. Patients were randomly divided into training (2/3 of patients) and validation (1/3 of patients) sets. Using post-HSCT RNA data, the machine learning algorithm selected 92 genes for predicting aGvHD that appear to play a role in PI3/AKT, MAPK, and FOXO signaling, as well as microRNA. The algorithm selected 20 genes for predicting survival included genes involved in MAPK and chemokine signaling. Using pre-HSCT RNA data, the machine learning algorithm selected 400 genes and 700 genes predicting aGvHD and overall survival, but candidate signaling pathways could not be specified in this analysis. These data show that NGS analyses of RNA expression using machine learning algorithms may be useful biomarkers of aGvHD and overall survival for patients undergoing HSCT, allowing for the identification of major signaling pathways associated with HSCT outcomes and helping to dissect the complex steps involved in the development of aGvHD. The analysis of pre-HSCT bone marrow samples may lead to pre-HSCT interventions including choice of remission induction regimens and modifications in patient health before HSCT.
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Affiliation(s)
- Scott D. Rowley
- Georgetown University School of Medicine, Washington, DC 20007, USA
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
| | - Thomas S. Gunning
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Michael Pelliccia
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Alexandra Della Pia
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
| | - Albert Lee
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - James Behrmann
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Ayrton Bangolo
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Parul Jandir
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Hong Zhang
- Genomic Testing Cooperative, Irvine, CA 92618, USA; (H.Z.); (M.A.)
| | - Sukhdeep Kaur
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Hyung C. Suh
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Michele Donato
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
| | - Maher Albitar
- Genomic Testing Cooperative, Irvine, CA 92618, USA; (H.Z.); (M.A.)
| | - Andrew Ip
- John Theurer Cancer Center, Hackensack, NJ 07601, USA; (A.D.P.); (S.K.); (M.D.)
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA; (T.S.G.); (M.P.); (A.L.); (J.B.); (A.B.); (P.J.)
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2
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Perez V, Zaobornyj T, Vico T, Vanasco V, Marchini T, Godoy E, Alvarez S, Evelson P, Donato M, Gelpi RJ, D'Annunzio V. Middle-age abolishes cardioprotection conferred by thioredoxin-1 in mice. Arch Biochem Biophys 2024; 753:109880. [PMID: 38171410 DOI: 10.1016/j.abb.2023.109880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
Thioredoxin-1 (Trx1) has cardioprotective effects on ischemia/reperfusion (I/R) injury, although its role in ischemic postconditioning (PostC) in middle-aged mice is not understood. This study aimed to evaluate if combining two cardioprotective strategies, such as Trx1 overexpression and PostC, could exert a synergistic effect in reducing infarct size in middle-aged mice. Young or middle-aged wild-type mice (Wt), transgenic mice overexpressing Trx1, and dominant negative (DN-Trx1) mutant of Trx1 mice were used. Mice hearts were subjected to I/R or PostC protocol. Infarct size, hydrogen peroxide (H2O2) production, protein nitration, Trx1 activity, mitochondrial function, and Trx1, pAkt and pGSK3β expression were measured. PostC could not reduce infarct size even in the presence of Trx1 overexpression in middle-aged mice. This finding was accompanied by a lack of Akt and GSK3β phosphorylation, and Trx1 expression (in Wt group). Trx1 activity was diminished and H2O2 production and protein nitration were increased in middle-age. The respiratory control rate dropped after I/R in Wt-Young and PostC restored this value, but not in middle-aged groups. Our results showed that Trx1 plays a key role in the PostC protection mechanism in young but not middle-aged mice, even in the presence of Trx1 overexpression.
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Affiliation(s)
- V Perez
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina
| | - T Zaobornyj
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - T Vico
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - V Vanasco
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - T Marchini
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - E Godoy
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina
| | - S Alvarez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - P Evelson
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Institute of Biochemistry and Molecular Medicine (IBIMOL UBA-CONICET), Argentina
| | - M Donato
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina
| | - R J Gelpi
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina
| | - V D'Annunzio
- Universidad de Buenos Aires, Facultad de Ciencias Médicas, Departamento de Patología - Institute of Cardiovascular Physiopathology, Argentina.
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3
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Ratnasiri K, Zheng H, Toh J, Yao Z, Duran V, Donato M, Roederer M, Kamath M, Todd JPM, Gagne M, Foulds KE, Francica JR, Corbett KS, Douek DC, Seder RA, Einav S, Blish CA, Khatri P. Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans. Cell Rep 2024; 43:113706. [PMID: 38294906 PMCID: PMC10915397 DOI: 10.1016/j.celrep.2024.113706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/02/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Viral pandemics and epidemics pose a significant global threat. While macaque models of viral disease are routinely used, it remains unclear how conserved antiviral responses are between macaques and humans. Therefore, we conducted a cross-species analysis of transcriptomic data from over 6,088 blood samples from macaques and humans infected with one of 31 viruses. Our findings demonstrate that irrespective of primate or viral species, there are conserved antiviral responses that are consistent across infection phase (acute, chronic, or latent) and viral genome type (DNA or RNA viruses). Leveraging longitudinal data from experimental challenges, we identify virus-specific response kinetics such as host responses to Coronaviridae and Orthomyxoviridae infections peaking 1-3 days earlier than responses to Filoviridae and Arenaviridae viral infections. Our results underscore macaque studies as a powerful tool for understanding viral pathogenesis and immune responses that translate to humans, with implications for viral therapeutic development and pandemic preparedness.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiaying Toh
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhiyuan Yao
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Veronica Duran
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Michele Donato
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph R Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirit Einav
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
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4
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Slight-Webb S, Thomas K, Smith M, Wagner CA, Macwana S, Bylinska A, Donato M, Dvorak M, Chang SE, Kuo A, Cheung P, Kalesinskas L, Ganesan A, Dermadi D, Guthridge CJ, DeJager W, Wright C, Foecke MH, Merrill JT, Chakravarty E, Arriens C, Maecker HT, Khatri P, Utz PJ, James JA, Guthridge JM. Ancestry-based differences in the immune phenotype are associated with lupus activity. JCI Insight 2023; 8:e169584. [PMID: 37606045 PMCID: PMC10543734 DOI: 10.1172/jci.insight.169584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/10/2023] [Indexed: 08/23/2023] Open
Abstract
Systemic lupus erythematosus (SLE) affects 1 in 537 Black women, which is >2-fold more than White women. Black patients develop the disease at a younger age, have more severe symptoms, and have a greater chance of early mortality. We used a multiomics approach to uncover ancestry-associated immune alterations in patients with SLE and healthy controls that may contribute biologically to disease disparities. Cell composition, signaling, epigenetics, and proteomics were evaluated by mass cytometry; droplet-based single-cell transcriptomics and proteomics; and bead-based multiplex soluble mediator levels in plasma. We observed altered whole blood frequencies and enhanced activity in CD8+ T cells, B cells, monocytes, and DCs in Black patients with more active disease. Epigenetic modifications in CD8+ T cells (H3K27ac) could distinguish disease activity level in Black patients and differentiate Black from White patient samples. TLR3/4/7/8/9-related gene expression was elevated in immune cells from Black patients with SLE, and TLR7/8/9 and IFN-α phospho-signaling and cytokine responses were heightened even in immune cells from healthy Black control patients compared with White individuals. TLR stimulation of healthy immune cells recapitulated the ancestry-associated SLE immunophenotypes. This multiomic resource defines ancestry-associated immune phenotypes that differ between Black and White patients with SLE, which may influence the course and severity of SLE and other diseases.
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Affiliation(s)
- Samantha Slight-Webb
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Kevin Thomas
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Miles Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Catriona A. Wagner
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Susan Macwana
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Aleksandra Bylinska
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection
- Center for Biomedical Informatics Research, Department of Medicine; and
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection
- Center for Biomedical Informatics Research, Department of Medicine; and
| | | | - Alex Kuo
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Peggie Cheung
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Laurynas Kalesinskas
- Institute for Immunity, Transplantation and Infection
- Center for Biomedical Informatics Research, Department of Medicine; and
| | - Ananthakrishnan Ganesan
- Institute for Immunity, Transplantation and Infection
- Center for Biomedical Informatics Research, Department of Medicine; and
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection
- Center for Biomedical Informatics Research, Department of Medicine; and
| | - Carla J. Guthridge
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Wade DeJager
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Christian Wright
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Mariko H. Foecke
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Joan T. Merrill
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Eliza Chakravarty
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Cristina Arriens
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection
- Center for Biomedical Informatics Research, Department of Medicine; and
| | - Paul J. Utz
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Judith A. James
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Joel M. Guthridge
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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5
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Albitar M, Zhang H, Charifa A, Ip A, Ma W, McCloskey J, Donato M, Siegel D, Waintraub S, Gutierrez M, Pecora A, Goy A. Combining cell-free RNA with cell-free DNA in liquid biopsy for hematologic and solid tumors. Heliyon 2023; 9:e16261. [PMID: 37251903 PMCID: PMC10208940 DOI: 10.1016/j.heliyon.2023.e16261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
Current use of liquid biopsy is based on cell-free DNA (cfDNA) and the evaluation of mutations or methylation pattern. However, expressed RNA can capture mutations, changes in expression levels due to methylation, and provide information on cell of origin, growth, and proliferation status. We developed an approach to isolate cell-free total nucleic acid (cfDNA) and used targeted next generation sequencing to sequence cell-free RNA (cfRNA) and cfDNA as new approach in liquid biopsy. We demonstrate that cfRNA is overall more sensitive than cfDNA in detecting mutations. We show that cfRNA is reliable in detecting fusion genes and cfDNA is reliable in detecting chromosomal gains and losses. cfRNA levels of various solid tumor biomarkers were significantly higher (P < 0.0001) in samples from solid tumors as compared with normal control. Similarly, cfRNA lymphoid markers and cfRNA myeloid markers were all higher in lymphoid and myeloid neoplasms, respectively as compared with control (P < 0.0001). Using machine learning we demonstrate cfRNA was highly predictive of diagnosis (AUC >0.98) of solid tumors, B-cell lymphoid neoplasms, T-cell lymphoid neoplasms, and myeloid neoplasms. In evaluating the host immune system, cfRNA CD4:CD8B and CD3D:CD19 ratios in normal controls were as expected (median: 5.92 and 6.87, respectively) and were significantly lower in solid tumors (P < 0.0002). This data suggests that liquid biopsy combining analysis of cfRNA with cfDNA is practical and may provide helpful information in predicting genomic abnormalities, diagnosis of neoplasms and evaluating both the tumor biology and the host response.
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Affiliation(s)
- Maher Albitar
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Hong Zhang
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Ahmad Charifa
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Andrew Ip
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Wanlong Ma
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - James McCloskey
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Michele Donato
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - David Siegel
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Stanley Waintraub
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Martin Gutierrez
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Andrew Pecora
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Andre Goy
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
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6
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Ty M, Sun S, Callaway PC, Rek J, Press KD, van der Ploeg K, Nideffer J, Hu Z, Klemm S, Greenleaf W, Donato M, Tukwasibwe S, Arinaitwe E, Nankya F, Musinguzi K, Andrew D, de la Parte L, Mori DM, Lewis SN, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Blish C, Utz PJ, Khatri P, Dorsey G, Kamya M, Boyle M, Feeney M, Ssewanyana I, Jagannathan P. Malaria-driven expansion of adaptive-like functional CD56-negative NK cells correlates with clinical immunity to malaria. Sci Transl Med 2023; 15:eadd9012. [PMID: 36696483 PMCID: PMC9976268 DOI: 10.1126/scitranslmed.add9012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Natural killer (NK) cells likely play an important role in immunity to malaria, but the effect of repeated malaria on NK cell responses remains unclear. Here, we comprehensively profiled the NK cell response in a cohort of 264 Ugandan children. Repeated malaria exposure was associated with expansion of an atypical, CD56neg population of NK cells that differed transcriptionally, epigenetically, and phenotypically from CD56dim NK cells, including decreased expression of PLZF and the Fc receptor γ-chain, increased histone methylation, and increased protein expression of LAG-3, KIR, and LILRB1. CD56neg NK cells were highly functional and displayed greater antibody-dependent cellular cytotoxicity than CD56dim NK cells. Higher frequencies of CD56neg NK cells were associated with protection against symptomatic malaria and high parasite densities. After marked reductions in malaria transmission, frequencies of these cells rapidly declined, suggesting that continuous exposure to Plasmodium falciparum is required to maintain this modified, adaptive-like NK cell subset.
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Affiliation(s)
- Maureen Ty
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Shenghuan Sun
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Perri C Callaway
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | - Jason Nideffer
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Zicheng Hu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sandy Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Michele Donato
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Dean Andrew
- Queensland Institute for Medical Research, Queensland, Australia
| | | | | | | | - Saki Takahashi
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Catherine Blish
- Department of Medicine, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - P J Utz
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Grant Dorsey
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda.,Department of Medicine, Makerere University, Kampala, Uganda
| | - Michelle Boyle
- Queensland Institute for Medical Research, Queensland, Australia
| | - Margaret Feeney
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Prasanna Jagannathan
- Department of Medicine, Stanford University, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
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7
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Ayoglu B, Donato M, Furst DE, Crofford LJ, Goldmuntz E, Keyes-Elstein L, James J, Macwana S, Mayes MD, McSweeney P, Nash RA, Sullivan KM, Welch B, Pinckney A, Mao R, Chung L, Khatri P, Utz PJ. Characterising the autoantibody repertoire in systemic sclerosis following myeloablative haematopoietic stem cell transplantation. Ann Rheum Dis 2023; 82:670-680. [PMID: 36653124 PMCID: PMC10176357 DOI: 10.1136/ard-2021-221926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/30/2022] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Results from the SCOT (Scleroderma: Cyclophosphamide Or Transplantation) clinical trial demonstrated significant benefits of haematopoietic stem cell transplant (HSCT) versus cyclophosphamide (CTX) in patients with systemic sclerosis. The objective of this study was to test the hypothesis that transplantation stabilises the autoantibody repertoire in patients with favourable clinical outcomes. METHODS We used a bead-based array containing 221 protein antigens to profile serum IgG autoantibodies in participants of the SCOT trial. RESULTS Comparison of autoantibody profiles at month 26 (n=23 HSCT; n=22 CTX) revealed antibodies against two viral antigens and six self-proteins (SSB/La, CX3CL1, glycyl-tRNA synthetase (EJ), parietal cell antigen, bactericidal permeability-increasing protein and epidermal growth factor receptor (EGFR)) that were significantly different between treatment groups. Linear mixed model analysis identified temporal increases in antibody levels for hepatitis B surface antigen, CCL3 and EGFR in HSCT-treated patients. Eight of 32 HSCT-treated participants and one of 31 CTX-treated participants had temporally varying serum antibody profiles for one or more of 14 antigens. Baseline autoantibody levels against 20 unique antigens, including 9 secreted proteins (interleukins, IL-18, IL-22, IL-23 and IL-27), interferon-α2A, stem cell factor, transforming growth factor-β, macrophage colony-stimulating factor and macrophage migration inhibitory factor were significantly higher in patients who survived event-free to month 54. CONCLUSIONS Our results suggest that HSCT favourably alters the autoantibody repertoire, which remains virtually unchanged in CTX-treated patients. Although antibodies recognising secreted proteins are generally thought to be pathogenic, our results suggest a subset could potentially modulate HSCT in scleroderma.
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Affiliation(s)
- Burcu Ayoglu
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Michele Donato
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Stanford Institute for Immunity Transplantation and Infection, Stanford, California, USA
| | - Daniel E Furst
- Department of Medicine, University of California, Los Angeles, California, USA
| | - Leslie J Crofford
- Division of Rheumatology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ellen Goldmuntz
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | | | - Judith James
- Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Susan Macwana
- Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Maureen D Mayes
- Department of Rheumatology, The University of Texas Health Science Center, Houston, Texas, USA
| | | | | | - Keith M Sullivan
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Beverly Welch
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | | | - Rong Mao
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Lorinda Chung
- Departments of Medicine & Dermatology, Stanford University, Stanford, California, USA.,Palo Alto VA Health Care System, Palo Alto, California, USA
| | - Purvesh Khatri
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA .,Stanford Institute for Immunity Transplantation and Infection, Stanford, California, USA
| | - Paul J Utz
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA .,Stanford Institute for Immunity Transplantation and Infection, Stanford, California, USA
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8
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Bai L, Dermadi D, Kalesinskas L, Dvorak M, Chang SE, Ganesan A, Rubin SJS, Kuo A, Cheung P, Donato M, Utz PJ, Habtezion A, Khatri P. Mass-cytometry-based quantitation of global histone post-translational modifications at single-cell resolution across peripheral immune cells in IBD. J Crohns Colitis 2022; 17:804-815. [PMID: 36571819 PMCID: PMC10155749 DOI: 10.1093/ecco-jcc/jjac194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND AIMS Current understanding of histone post-translational modifications (histone modifications) across immune cell types in patients with inflammatory bowel disease (IBD) during remission and flare is limited. The study aimed to quantify histone modifications at a single-cell resolution in IBD patients during remission and flare and how they differ compared to healthy controls. METHODS We performed a case-control study of 94 subjects (83 IBD patients and 11 healthy controls). IBD patients had either UC (n=38) or CD (n=45) in clinical remission or flare. We used epigenetic profiling by time-of-flight (EpiTOF) to investigate changes in histone modifications within peripheral blood mononuclear cells from IBD patients. RESULTS We discovered substantial heterogeneity in histone modifications across multiple immune cell types in IBD patients. They had a higher proportion of less differentiated CD34 + hematopoietic progenitors, and a subset of CD56 bright NK cells and γδ T cells characterized by distinct histone modifications associated with the gene transcription. The subset of CD56 bright NK cells had increased several histone acetylations. An epigenetically defined subset of NK was associated with higher levels of CRP in peripheral blood. CD14+ monocytes from IBD patients had significantly decreased cleaved H3T22, suggesting they were epigenetically primed for macrophage differentiation. CONCLUSION We describe the first systems-level quantification of histone modifications across immune cells from IBD patients at a single-cell resolution revealing the increased epigenetic heterogeneity that is not possible with traditional ChIP-seq profiling. Our data open new directions in investigating the association between histone modifications and IBD pathology using other epigenomic tools.
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Affiliation(s)
- Lawrence Bai
- Immunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305 USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Laurynas Kalesinskas
- Biomedical Informatics Training Program, Stanford University School of Medicine, 1265 Welch Road, MSOB X-343, Stanford, CA 94305 USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ananthakrishnan Ganesan
- Computational and Mathematical Engineering, Stanford University, 475 Via Ortega, Suite B060, Stanford, CA 94305 USA
| | - Samuel J S Rubin
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Alex Kuo
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peggie Cheung
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Paul J Utz
- Immunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305 USA.,Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aida Habtezion
- Immunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305 USA.,Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Purvesh Khatri
- Immunology Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305 USA.,Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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9
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Ganesan A, Dermadi D, Kalesinskas L, Donato M, Sowers R, Utz PJ, Khatri P. Inferring direction of associations between histone modifications using a neural processes-based framework. iScience 2022; 26:105756. [PMID: 36619977 PMCID: PMC9813700 DOI: 10.1016/j.isci.2022.105756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/19/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
Current technologies do not allow predicting interactions between histone post-translational modifications (HPTMs) at a system-level. We describe a computational framework, imputation-followed-by-inference, to predict directed association between two HPTMs using EpiTOF, a mass cytometry-based platform that allows profiling multiple HPTMs at a single-cell resolution. Using EpiTOF profiles of >55,000,000 peripheral mononuclear blood cells from 158 healthy human subjects, we show that neural processes (NP) have significantly higher accuracy than linear regression and k-nearest neighbors models to impute the abundance of an HPTM. Next, we infer the direction of association to show we recapitulate known HPTM associations and identify several previously unidentified ones in healthy individuals. Using this framework in an influenza vaccine cohort, we identify changes in associations between 6 pairs of HPTMs 30 days following vaccination, of which several have been shown to be involved in innate memory. These results demonstrate the utility of our framework in identifying directed interactions between HPTMs.
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Affiliation(s)
- Ananthakrishnan Ganesan
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Institute for Computational and Mathematical Engineering, School of Engineering, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Laurynas Kalesinskas
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rosalie Sowers
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Paul J. Utz
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Division of Immunology and Rheumatology, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA,Corresponding author
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10
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Albitar M, Zhang H, Charifa A, Ip A, De Dios I, Ma W, McCloskey JK, Donato M, Siegel DSD, Waintraub SE, Gutierrez M, Pecora AL, Goy A. Combining cell-free RNA (cfRNA) with cell-free total nucleic acid (cfTNA) as a new paradigm for liquid biopsy. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3048 Background: Expressed RNA can capture mutations, gene fusions, and biomarker profiles. In principle, each abnormal cell has one copy of mutated gene, but numerous copies of mutated RNA. Cell-free RNA (cfRNA) is not used due to the assumption that it is degraded. Next Generation Sequencing (NGS) by design is particularly adaptable for fragmented DNA and RNA. We developed an approach to isolate cell-free total nucleic acid (cfTNA) and cell-free RNA (cfRNA) from peripheral blood. Using targeted sequencing, we explored the potential of this approach to detect mutations, fusion mRNA, and copy number variation (CNV) in solid tumors and hematologic neoplasms. Methods: Peripheral blood cfTNA and cfRNA were extracted from B-cell lymphoid neoplasms (#105), T-cell neoplasms (#16), Myeloid neoplasms (#73), solid tumors (#44), and Normal individuals (#51), and sequenced using a targeted panel of 1459 genes. Results: Numbers of mutations detected in solid tumors and hematologic neoplasms were significantly (P > 0.0001) higher in cfRNA (No. = 1229) than in cfTNA (No. = 1004). Overall variant allele frequency (VAF) was significantly higher in cfRNA than in cfTNA (P < 0.0001). However, numerous mutations detected by RNA were not detected by cfTNA and vice versa. In general, nonsense mutations were more likely to be detected by cfTNA than by cfRNA and at higher VAF. Low-level mutations (VAF < 10%) were more likely to be detected by cfRNA than by cfTNA. For example, 136 mutations in TP53 gene were detected using cfRNA and only 70 mutations were detected in cfTNA. KRAS mutations were also higher in cfRNA (#33) as compared with cfTNA (#21). In contrast, when most of the mutations were nonsense, as in ASXL1 gene, more mutations were detected by cfTNA (24 vs 23). When mutations were detected in both cfRNA and cfTNA, mutation load (level of mutant copies) was overall slightly higher in cfTNA (P = 0.06), likely due to higher degradation of RNA, but varied significantly dependent on the type of mutated gene and type of mutation. cfRNA was reliable in detecting fusion transcripts in solid tumors and in hematologic neoplasms (SLC34A2-ROS1, DDX5-BCL6, ETV6-RUNX1, RUNX1T1-RUNX1, PML-RARA, RUNX1-ZFPM2, DEK-NUP214, EP300-ZNF384) irrespective of the breakpoint or partner gene. The cfTNA detected various CNVs expected by cytogenetic analysis when tumor fraction was adequate (VAF > 10%). Conclusions: This data demonstrates that using cfRNA and cfTNA provides complementary comprehensive information for evaluating mutations, fusion genes, and CNV. This approach increased sensitivity and reliability of liquid biopsy. Furthermore, the cfRNA provides critical information on relative expression of various genes that can be used as biomarkers in characterizing the neoplastic process (see ASCO abstract, Liquid Biopsy Based on Cell-Free RNA and Biomarkers profiling of hematologic and solid tumors).
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Affiliation(s)
| | | | | | - Andrew Ip
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | | | | | - James K. McCloskey
- The John Theurer Cancer Center at Hackensack Meridian Health, Hackensack, NJ
| | - Michele Donato
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | | | - Stanley E. Waintraub
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Martin Gutierrez
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Andrew L Pecora
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Andre Goy
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
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11
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Albitar M, Zhang H, Charifa A, Ip A, De Dios I, Ma W, McCloskey J, Donato M, Siegel DSD, Waintraub SE, Gutierrez M, Pecora AL, Goy A. Cell-free RNA in liquid biopsy and biomarkers profiling of hematologic and solid tumors. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3047 Background: Expressed RNA can capture mutations, changes in expression levels due to methylation, and provide information on cell of origin, growth, and proliferation status. We developed an approach to isolate fragmented RNA from peripheral blood plasma and explored its potential to be used in liquid biopsy. Methods: Peripheral blood cfRNA was extracted from patients with neoplasms in B-cell (#105), T-cell (#16), Myeloid (#73), and from solid tumors (#44), Normal individuals (#51), and reactive post-transplant (#137). RNA was sequenced using a 1459-gene panel. Expression profile was generated using Cufflinks. Results: cfRNA levels of various solid tumor biomarkers (CA-125, CA-15-3, CEA 8, Keratin19, Keratin6A...) were significantly higher (P < 0.0001) in samples from solid tumors as compared with normal control. Similarly, cfRNA lymphoid markers (CD19, CD22, CD79A, and CD79B...) and cfRNA myeloid markers (CD33, CD14, CD117, CD56...) were all higher in B-cell lymphoid neoplasms and myeloid neoplasms, respectively (P < 0.0001), as compared with control. In evaluating the host immune system, cfRNA CD4:CD8B and CD3D:CD19 ratios in normal controls were as expected (median: 5.92 and 6.87, respectively) and were significantly lower in solid tumors (median 3.40 and 2.23, respectively, P < 0.0002). Solid tumor cfRNA showed CTLA4:CD8B ratio significantly higher in tumors than in normal (median 0.74 vs 0.19, P = 0.0001), while there was no difference in cfRNA PD-L1:CD8B ratio (median 1.45 vs 1.77, P = 0.96). Similar distinct patterns are noted for various cytokine and chemokines. cfRNA was highly predictive of diagnosis (AUC > 0.98) of solid tumors, B-cell lymphoid neoplasms, T-cell lymphoid neoplasms, and myeloid neoplasms as compared with normal control. When a specific neoplastic disease was considered against all cases including control and other neoplasms, the AUC varied between 0.77 and 0.949. Conclusions: This data shows that liquid biopsy using targeted sequencing of cfRNA in patients with various types of cancer provides comprehensive and reliable information on the neoplastic disease as well as the host. [Table: see text]
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Affiliation(s)
| | | | | | - Andrew Ip
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | | | | | - James McCloskey
- John Theurer Cancer Center, Hackensack Unversity Medical Center, Hackensack, NJ
| | - Michele Donato
- John Theurer Cancer Center, Hackensack University Medical Center, Livingston, NJ
| | | | - Stanley E. Waintraub
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Martin Gutierrez
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Andrew L Pecora
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Andre Goy
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
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12
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Zhang H, Albitar M, Qureshi MA, Wahid M, Charifa A, Ehsan A, Ip A, De Dios I, Ma W, McCloskey J, Donato M, Siegel DSD, Gutierrez M, Pecora AL, Goy A. Differential diagnosis of hematologic and solid tumors using targeted transcriptome and artificial intelligence. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3018 Background: Diagnosis and classification of tumors is becoming increasingly dependent on biological and molecular biomarkers. RNA expression profiling using next generation sequencing (NGS) provides information on various biological and molecular changes in the cancer and in the microenvironment. We explored the potential of using targeted transcriptome and artificial intelligence (AI) in the differential diagnosis and classification of various hematologic and solid tumors. Methods: RNA from hematologic neoplasms (N = 2606) and solid tumors (N = 2038) as well as normal bone marrow and lymph node control (N = 806) were sequenced by NGS using a targeted 1408-gene panel. The hematologic neoplasms included 20 different subtypes. Solid tumors included 24 different subtypes. Machine learning is used for comparing two classes at a time. Geometric Mean Naïve Bayesian (GMNB) classifier is used to provide differential diagnosis across 45 diagnostic entities with assigned ranking. Results: Machine learning showed high accuracy in distinguishing between two diagnoses with AUC varied between 1 (Sarcoma vs GIST) and 0.841 (MDS vs normal control) (examples in Table). For differential diagnosis between all 45 different diagnoses, we used 3045 samples for training the GMNB algorithm and 1415 samples for testing. Correct first choice diagnosis was obtained in 100% of ALL, 88% of AML, 85% of DLBCL, 82% of colorectal cancer, 88% of lung cancer, 72% of CLL, and 72% of follicular lymphoma. The algorithm had difficulty in typically overlapping diagnoses and diagnosed as first choice 19% of MDS, 46% of normal, and 12% of MPN. Diagnosis improved significantly when second choice was considered. Conclusions: Targeted RNA profiling with proper AI can provide highly useful tools for the pathologic diagnosis and classification of various cancers. Additional information such as mutation profile and clinical information can improve these algorithms, reduce subjectivity, and minimize errors in pathologic diagnoses. [Table: see text]
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Affiliation(s)
| | | | | | - Mohsin Wahid
- Dow University of Health Sciences, Karachi, Pakistan
| | | | | | - Andrew Ip
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | | | | | - James McCloskey
- John Theurer Cancer Center, Hackensack Unversity Medical Center, Hackensack, NJ
| | - Michele Donato
- John Theurer Cancer Center, Hackensack University Medical Center, Livingston, NJ
| | | | - Martin Gutierrez
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Andrew L Pecora
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Andre Goy
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
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13
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McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF, Baranski A, Graf W, Kumar R, Bosse M, Fullaway CC, Ramdial PK, Forgó E, Jojic V, Van Valen D, Mehra S, Khader SA, Bendall SC, van de Rijn M, Kalman D, Kaushal D, Hunter RL, Banaei N, Steyn AJC, Khatri P, Angelo M. Author Correction: The immunoregulatory landscape of human tuberculosis granulomas. Nat Immunol 2022; 23:814. [PMID: 35277696 PMCID: PMC9098386 DOI: 10.1038/s41590-022-01178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Erin F McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michele Donato
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Alea Delmastro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sanjana Gupta
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Graf
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Rashmi Kumar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Pratista K Ramdial
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Smriti Mehra
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shabaana A Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Kalman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Robert L Hunter
- Department of Pathology and Laboratory Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Adrie J C Steyn
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Purvesh Khatri
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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14
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Liu YE, Saul S, Rao AM, Robinson ML, Agudelo Rojas OL, Sanz AM, Verghese M, Solis D, Sibai M, Huang CH, Sahoo MK, Gelvez RM, Bueno N, Estupiñan Cardenas MI, Villar Centeno LA, Rojas Garrido EM, Rosso F, Donato M, Pinsky BA, Einav S, Khatri P. An 8-gene machine learning model improves clinical prediction of severe dengue progression. Genome Med 2022; 14:33. [PMID: 35346346 PMCID: PMC8959795 DOI: 10.1186/s13073-022-01034-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Each year 3-6 million people develop life-threatening severe dengue (SD). Clinical warning signs for SD manifest late in the disease course and are nonspecific, leading to missed cases and excess hospital burden. Better SD prognostics are urgently needed. METHODS We integrated 11 public datasets profiling the blood transcriptome of 365 dengue patients of all ages and from seven countries, encompassing biological, clinical, and technical heterogeneity. We performed an iterative multi-cohort analysis to identify differentially expressed genes (DEGs) between non-severe patients and SD progressors. Using only these DEGs, we trained an XGBoost machine learning model on public data to predict progression to SD. All model parameters were "locked" prior to validation in an independent, prospectively enrolled cohort of 377 dengue patients in Colombia. We measured expression of the DEGs in whole blood samples collected upon presentation, prior to SD progression. We then compared the accuracy of the locked XGBoost model and clinical warning signs in predicting SD. RESULTS We identified eight SD-associated DEGs in the public datasets and built an 8-gene XGBoost model that accurately predicted SD progression in the independent validation cohort with 86.4% (95% CI 68.2-100) sensitivity and 79.7% (95% CI 75.5-83.9) specificity. Given the 5.8% proportion of SD cases in this cohort, the 8-gene model had a positive and negative predictive value (PPV and NPV) of 20.9% (95% CI 16.7-25.6) and 99.0% (95% CI 97.7-100.0), respectively. Compared to clinical warning signs at presentation, which had 77.3% (95% CI 58.3-94.1) sensitivity and 39.7% (95% CI 34.7-44.9) specificity, the 8-gene model led to an 80% reduction in the number needed to predict (NNP) from 25.4 to 5.0. Importantly, the 8-gene model accurately predicted subsequent SD in the first three days post-fever onset and up to three days prior to SD progression. CONCLUSIONS The 8-gene XGBoost model, trained on heterogeneous public datasets, accurately predicted progression to SD in a large, independent, prospective cohort, including during the early febrile stage when SD prediction remains clinically difficult. The model has potential to be translated to a point-of-care prognostic assay to reduce dengue morbidity and mortality without overwhelming limited healthcare resources.
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Affiliation(s)
- Yiran E. Liu
- grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Cancer Biology Graduate Program, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA
| | - Sirle Saul
- grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA
| | - Aditya Manohar Rao
- grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Immunology Graduate Program, School of Medicine, Stanford University, CA Stanford, USA
| | - Makeda Lucretia Robinson
- grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | | | - Ana Maria Sanz
- grid.477264.4Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
| | - Michelle Verghese
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Daniel Solis
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Mamdouh Sibai
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Chun Hong Huang
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Malaya Kumar Sahoo
- grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Rosa Margarita Gelvez
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Bucaramanga, Colombia
| | - Nathalia Bueno
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Bucaramanga, Colombia
| | | | | | | | - Fernando Rosso
- grid.477264.4Clinical Research Center, Fundación Valle del Lili, Cali, Colombia ,grid.477264.4Division of Infectious Diseases, Department of Internal Medicine, Fundación Valle del Lili, Cali, Colombia
| | - Michele Donato
- grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA
| | - Benjamin A. Pinsky
- grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Department of Pathology, School of Medicine, Stanford University, CA Stanford, USA
| | - Shirit Einav
- grid.168010.e0000000419368956Division of Infectious Diseases and Geographic Medicine, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Department of Microbiology and Immunology, School of Medicine, Stanford University, CA Stanford, USA
| | - Purvesh Khatri
- grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA Stanford, USA ,grid.168010.e0000000419368956Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA Stanford, USA
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Kolstad KD, Khatri A, Donato M, Chang SE, Li S, Steen VD, Utz PJ, Khatri P, Chung L. Cytokine signatures differentiate systemic sclerosis patients at high versus low risk for pulmonary arterial hypertension. Arthritis Res Ther 2022; 24:39. [PMID: 35139913 PMCID: PMC8827262 DOI: 10.1186/s13075-022-02734-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/01/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) affects approximately 10% of patients with systemic sclerosis (SSc) and is a leading cause of death. We sought to identify serum cytokine signatures that risk stratify SSc patients for this potentially fatal complication. METHODS Subjects at high risk for PAH and with incident PAH based on right heart catheterization (RHC) were enrolled in the multi-center prospective registry, Pulmonary Hypertension Assessment and Recognition of Outcomes in Scleroderma (PHAROS). Low-risk SSc patients were enrolled at Stanford and had normal pulmonary function test and echocardiogram parameters. Serum was available from 71 high-risk patients, 81 incident PAH patients, 10 low-risk patients, and 20 healthy controls (HC). Custom 14- and 65-plex arrays were used for cytokine analysis. Cytokine expression was compared between patient groups by principal component analysis and Tukey's test result. A multiple hypotheses corrected p value <0.05 was considered significant. RESULTS Exploratory analysis using principal components showed unique clustering for each patient group. There was a significant difference in cytokine expression in at least one group comparison for every cytokine. Overall, there was very little difference in cytokine expression comparing high-risk and PAH patient groups; however, these groups had substantially different cytokine profiles compared to low-risk patients and HC. CONCLUSION These data suggest that cytokine profiles can distinguish SSc patients who are at high-risk for or have PAH from SSc patients who may be at lower risk for PAH and HC. However, high-risk and PAH patients had very similar cytokine profiles, suggesting that these patients are on a disease continuum.
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Affiliation(s)
- Kathleen D. Kolstad
- grid.168010.e0000000419368956Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Palo Alto, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Rheumatology, University of California Los Angeles, Los Angeles, CA USA
| | - Avani Khatri
- grid.168010.e0000000419368956Institute for Immunity, Transplantation, and Infection, Stanford University, Palo Alto, CA USA
| | - Michele Donato
- grid.168010.e0000000419368956Institute for Immunity, Transplantation, and Infection, Stanford University, Palo Alto, CA USA
| | - Sarah E. Chang
- grid.168010.e0000000419368956Institute for Immunity, Transplantation, and Infection, Stanford University, Palo Alto, CA USA
| | - Shufeng Li
- grid.168010.e0000000419368956Department of Dermatology, Stanford University School of Medicine, Palo Alto, CA USA
| | - Virginia D. Steen
- grid.411667.30000 0001 2186 0438Division of Rheumatology, Georgetown University Medical Center, Washington, DC USA
| | - Paul J. Utz
- grid.168010.e0000000419368956Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Palo Alto, CA USA
| | - Purvesh Khatri
- grid.168010.e0000000419368956Institute for Immunity, Transplantation, and Infection, Stanford University, Palo Alto, CA USA ,grid.168010.e0000000419368956Department of Medicine, Center for Biomedical Informatics Research, Stanford University, Palo Alto, CA USA
| | - Lorinda Chung
- grid.168010.e0000000419368956Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Palo Alto, CA USA ,grid.280747.e0000 0004 0419 2556Department of Medicine, Division of Rheumatology, Palo Alto VA Health Care System, Palo Alto, CA USA
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Youn M, Smith SM, Lee AG, Chae HD, Spiteri E, Erdmann J, Galperin I, Jones LM, Donato M, Abidi P, Bittencourt H, Lacayo N, Dahl G, Aftandilian C, Davis KL, Matthews JA, Kornblau SM, Huang M, Sumarsono N, Redell MS, Fu CH, Chen IM, Alonzo TA, Eklund E, Gotlib J, Khatri P, Sweet-Cordero EA, Hijiya N, Sakamoto KM. Comparison of the Transcriptomic Signatures in Pediatric and Adult CML. Cancers (Basel) 2021; 13:cancers13246263. [PMID: 34944883 PMCID: PMC8699058 DOI: 10.3390/cancers13246263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary To investigate whether pediatric and adult chronic myeloid leukemia (CML) have unique molecular characteristics, we studied the transcriptomic signature of pediatric and adult CML cells using high-throughput RNA sequencing. We identified differentially expressed genes and pathways unique to pediatric CML cells compared to adult CML cells. The Rho pathway was significantly dysregulated in pediatric CML cells compared to adult CML cells, suggesting the potential importance in the pathogenesis of pediatric CML. Our study is the first to compare transcriptome profiles of CML across different age groups. A better understanding of the biology of CML across different ages may inform future treatment approaches. Abstract Children with chronic myeloid leukemia (CML) tend to present with higher white blood counts and larger spleens than adults with CML, suggesting that the biology of pediatric and adult CML may differ. To investigate whether pediatric and adult CML have unique molecular characteristics, we studied the transcriptomic signature of pediatric and adult CML CD34+ cells and healthy pediatric and adult CD34+ control cells. Using high-throughput RNA sequencing, we found 567 genes (207 up- and 360 downregulated) differentially expressed in pediatric CML CD34+ cells compared to pediatric healthy CD34+ cells. Directly comparing pediatric and adult CML CD34+ cells, 398 genes (258 up- and 140 downregulated), including many in the Rho pathway, were differentially expressed in pediatric CML CD34+ cells. Using RT-qPCR to verify differentially expressed genes, VAV2 and ARHGAP27 were significantly upregulated in adult CML CD34+ cells compared to pediatric CML CD34+ cells. NCF1, CYBB, and S100A8 were upregulated in adult CML CD34+ cells but not in pediatric CML CD34+ cells, compared to healthy controls. In contrast, DLC1 was significantly upregulated in pediatric CML CD34+ cells but not in adult CML CD34+ cells, compared to healthy controls. These results demonstrate unique molecular characteristics of pediatric CML, such as dysregulation of the Rho pathway, which may contribute to clinical differences between pediatric and adult patients.
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Affiliation(s)
- Minyoung Youn
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Stephanie M. Smith
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Alex Gia Lee
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA; (A.G.L.); (E.A.S.-C.)
| | - Hee-Don Chae
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Elizabeth Spiteri
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
- Cytogenetics Laboratory, Stanford Health Care, Stanford, CA 94304, USA; (J.E.); (I.G.)
| | - Jason Erdmann
- Cytogenetics Laboratory, Stanford Health Care, Stanford, CA 94304, USA; (J.E.); (I.G.)
| | - Ilana Galperin
- Cytogenetics Laboratory, Stanford Health Care, Stanford, CA 94304, USA; (J.E.); (I.G.)
| | - Lara Murphy Jones
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; (M.D.); (P.K.)
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; (M.D.); (P.K.)
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
| | - Parveen Abidi
- Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.A.); (J.G.)
| | - Henrique Bittencourt
- Hematology-Oncology Division, Charles Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC H3T 1C5, Canada;
| | - Norman Lacayo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Gary Dahl
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Catherine Aftandilian
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Kara L. Davis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Jairo A. Matthews
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; (J.A.M.); (S.M.K.)
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; (J.A.M.); (S.M.K.)
| | - Min Huang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Nathan Sumarsono
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
| | - Michele S. Redell
- Division of Pediatric Hematology/Oncology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Cecilia H. Fu
- Division of Hematology/Oncology, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
| | - I-Ming Chen
- Department of Pathology, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87102, USA;
| | - Todd A. Alonzo
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90032, USA;
| | - Elizabeth Eklund
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Jason Gotlib
- Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; (P.A.); (J.G.)
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; (M.D.); (P.K.)
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
| | | | - Nobuko Hijiya
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Kathleen M. Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.Y.); (S.M.S.); (H.-D.C.); (L.M.J.); (N.L.); (G.D.); (C.A.); (K.L.D.); (M.H.); (N.S.)
- Correspondence: ; Tel.: +1-650-725-7126; Fax: +1-650-723-6700
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Biran N, Gourna Paleoudis E, Feinman R, Vesole DH, Zenreich J, Wang S, Ahn J, Bansal M, Rowley S, Donato M, Pecora AL, Richter J, Anand P, McBride L, Ivanovski K, Korngold R, Siegel DS. Pembrolizumab, lenalidomide and dexamethasone post autologous transplant in patients with high-risk multiple myeloma. Am J Hematol 2021; 96:E430-E433. [PMID: 34435374 DOI: 10.1002/ajh.26333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Noa Biran
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | - Elli Gourna Paleoudis
- Office of Research Administration, Hackensack Meridian Health Hackensack New Jersey USA
| | - Rena Feinman
- Center for Discovery & Innovation, Hackensack Meridian Health Institute for Multiple Myeloma Hackensack New Jersey USA
| | - David H. Vesole
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | | | - Shuqi Wang
- Department of Biostatistics, Bioinformatics, and Biomathematics Georgetown University Washington District of Columbia USA
| | - Jaeil Ahn
- Department of Biostatistics, Bioinformatics, and Biomathematics Georgetown University Washington District of Columbia USA
| | - Meena Bansal
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | - Scott Rowley
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | - Michele Donato
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | - Andrew L. Pecora
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | | | - Palka Anand
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | - Laura McBride
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | - Kristin Ivanovski
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
| | - Robert Korngold
- Center for Discovery & Innovation, Hackensack Meridian Health Institute for Multiple Myeloma Hackensack New Jersey USA
| | - David S. Siegel
- John Theurer Cancer Center, Hackensack Meridian Health Hackensack New Jersey USA
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Cisneros Clavijo P, Donato M, Ajila J, Garzon K, Escobar F, Waibel A, Villalba V, Imbaquingo D. The efficacy of paclitaxel drug-eluting balloon angioplasty versus standard balloon angioplasty in stenosis of native hemodialysis arteriovenous fistulas. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.2047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
End stage renal disease is on increasing trend and haemodialysis is the main dialysis modality among these patients. Thus, a functioning dialysis vascular access is critical to the delivery of life-saving haemodialysis treatment to these patients. Conventional angioplasty is the first line of treatment; with a 50% of permeability rate (6 months). For this reason, new alternatives are necessary to maintain the access permeability.Hypothesis: Paclitaxel coated balloon is superior to conventional plain balloon angioplasty with decreased re-stenosis of target lesion, improved access circuit and target lesion patency, and decreased number of interventions needed to maintain patency.
Methods
A total of 39 patients were randomized to receive a paclitaxel-coated balloon (n=15) or plain angioplasty balloon (n=24) after satisfactory angioplasty with a high-pressure balloon. The inclusion criteria were clinical signs of vascular dysfunction confirmed by Doppler Ultrasound and/or angiography. The primary endpoint was target lesion patency defined as time elapsed between the completion of effective and the appearance of restenosis at 3, 6 and 12 months after angioplasty. Secondary endpoints included the relationship between the location of the stenosis, previous angioplasty, demographic variables and survival.
Results
We recruited 39 patients with dysfunctional vascular accesses; 24 were assigned to the conventional balloon angioplasty group and 15 drug-eluting balloon angioplasty (paclitaxel). With demographic characteristics in Table I. In group A, all were autologous acces. Group B 16% (4) of the accesses were prosthetic and 84% (20) autologous. In relation to the type and length of stenosis, group A was more frequent at the level and longer, whereas in group B it predominated in the central type and less than 20 mm.In our study, we also observed a high rate of total occlusions, frequently in central vessels in group B, while in group A, where peripheral vessels were predominant, total occlusion was less frequent. Table II. We had no complications in either group, and dialysis was immediate at the end of the procedure. Group A did not present restenosis. Table III. Table III shows DEB group (15p) with 100% of permeability according to follow-up and only one (1/15) of patients died due to myocardial infarction and cerebrovascular accident and this patient kept lasted 9 months without restenosis In Table IV. Group B had 2 (8%) patients with restenosis so it was necessary to reoperate using a drug eluting balloon and until now there is no restenosis. From this group we do not have mortality. One patient 1 (24%) had a recovered infarction.
Conclusions
Paclitaxel-coated balloon angioplasty resulted in superior survival of dysfunctional peripheral vascular access at 12 meses. Both arms show equivalent complications and similar mortality
Funding Acknowledgement
Type of funding sources: Public hospital(s). Main funding source(s): Enrique Garcés Hospital
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Affiliation(s)
| | - M Donato
- University of Buenos Aires, Fiosiology Department, Buenos Aires, Argentina
| | - J Ajila
- Pontifical Catholic University of Ecuador, Vascular and Endovacular Surgery, Quito, Ecuador
| | - K Garzon
- South Hospital Enrique Garces, Vascular and Endovacular Surgery, Quito, Ecuador
| | - F Escobar
- South Hospital Enrique Garces, Vascular and Endovacular Surgery, Quito, Ecuador
| | - A Waibel
- Hospital Dr. Gustavo Dominguez Zambrano, Vascular and Endovacular Surgery, Santo Domingo, Ecuador
| | - V Villalba
- Hospital Dr. Gustavo Dominguez Zambrano, Vascular and Endovacular Surgery, Santo Domingo, Ecuador
| | - D Imbaquingo
- Latacunga General Hospital, Vascular and Endovacular Surgery, Latacunga, Ecuador
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Hirani D, Alvira CM, Danopoulos S, Milla C, Donato M, Tian L, Mohr J, Dinger K, Vohlen C, Selle J, Koningsbruggen-Rietschel SV, Barbarino V, Pallasch C, Rose-John S, Odenthal M, Pryhuber GS, Mansouri S, Savai R, Seeger W, Khatri P, Al Alam D, Dötsch J, Alejandre Alcazar MA. Macrophage-derived IL-6 trans-signaling as a novel target in the pathogenesis of bronchopulmonary dysplasia. Eur Respir J 2021; 59:13993003.02248-2020. [PMID: 34446466 PMCID: PMC8850688 DOI: 10.1183/13993003.02248-2020] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/24/2021] [Indexed: 11/17/2022]
Abstract
Rationale Premature infants exposed to oxygen are at risk for bronchopulmonary dysplasia (BPD), which is characterised by lung growth arrest. Inflammation is important, but the mechanisms remain elusive. Here, we investigated inflammatory pathways and therapeutic targets in severe clinical and experimental BPD. Methods and results First, transcriptomic analysis with in silico cellular deconvolution identified a lung-intrinsic M1-like-driven cytokine pattern in newborn mice after hyperoxia. These findings were confirmed by gene expression of macrophage-regulating chemokines (Ccl2, Ccl7, Cxcl5) and markers (Il6, Il17A, Mmp12). Secondly, hyperoxia-activated interleukin 6 (IL-6)/signal transducer and activator of transcription 3 (STAT3) signalling was measured in vivo and related to loss of alveolar epithelial type II cells (ATII) as well as increased mesenchymal marker. Il6 null mice exhibited preserved ATII survival, reduced myofibroblasts and improved elastic fibre assembly, thus enabling lung growth and protecting lung function. Pharmacological inhibition of global IL-6 signalling and IL-6 trans-signalling promoted alveolarisation and ATII survival after hyperoxia. Third, hyperoxia triggered M1-like polarisation, possibly via Krüppel-like factor 4; hyperoxia-conditioned medium of macrophages and IL-6-impaired ATII proliferation. Finally, clinical data demonstrated elevated macrophage-related plasma cytokines as potential biomarkers that identify infants receiving oxygen at increased risk of developing BPD. Moreover, macrophage-derived IL6 and active STAT3 were related to loss of epithelial cells in BPD lungs. Conclusion We present a novel IL-6-mediated mechanism by which hyperoxia activates macrophages in immature lungs, impairs ATII homeostasis and disrupts elastic fibre formation, thereby inhibiting lung growth. The data provide evidence that IL-6 trans-signalling could offer an innovative pharmacological target to enable lung growth in severe neonatal chronic lung disease. M1-like macrophage activation is linked to IL-6/STAT3 axis in clinical and experimental BPD. Inhibition of macrophage-related IL-6 trans-signalling promotes ATII survival and lung growth in experimental BPD as a new therapy for preterm infants.https://bit.ly/3AhF7GP
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Affiliation(s)
- Dharmesh Hirani
- Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Experimental Pediatrics - Experimental Pulmonology, Koln, Germany.,University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC), Koln, Germany
| | - Cristina M Alvira
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Soula Danopoulos
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Carlos Milla
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michele Donato
- Biomedical Informatics Research-Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Jasmine Mohr
- Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Experimental Pediatrics - Experimental Pulmonology, Koln, Germany.,University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC), Koln, Germany
| | - Katharina Dinger
- Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Experimental Pediatrics - Experimental Pulmonology, Koln, Germany.,University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC), Koln, Germany
| | - Christina Vohlen
- Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Experimental Pediatrics - Experimental Pulmonology, Koln, Germany.,Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Koln, Germany
| | - Jaco Selle
- Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Experimental Pediatrics - Experimental Pulmonology, Koln, Germany
| | - Silke V Koningsbruggen-Rietschel
- Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Koln, Germany
| | - Verena Barbarino
- Department I of Internal Medicine, Center for Integrated Oncology (CIO) Köln-Bonn, University of Cologne, Koln, Germany
| | - Christian Pallasch
- Department I of Internal Medicine, Center for Integrated Oncology (CIO) Köln-Bonn, University of Cologne, Koln, Germany
| | - Stefan Rose-John
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Margarete Odenthal
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute for Pathology, Koln, Germany
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Siavash Mansouri
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Rajkumar Savai
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany.,Institute for Lung Health (ILH), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL)
| | - Werner Seeger
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany.,Institute for Lung Health (ILH), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL)
| | - Purvesh Khatri
- Biomedical Informatics Research-Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Jörg Dötsch
- Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Koln, Germany
| | - Miguel A Alejandre Alcazar
- Department of Pediatric and Adolescent Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Experimental Pediatrics - Experimental Pulmonology, Koln, Germany .,University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC), Koln, Germany.,Institute for Lung Health (ILH), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL).,University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne Excellence Cluster on Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
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20
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Donato M, Bolego C, Faggin E, Bertacco E, Agostini C, Rattazzi M. The selective activation of formyl peptide receptor 2 prevents the inflammatory and pro-calcific differentiation of interstitial aortic valve cells. Atherosclerosis 2021. [DOI: 10.1016/j.atherosclerosis.2021.06.270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Wimmers F, Donato M, Kuo A, Ashuach T, Gupta S, Li C, Dvorak M, Foecke MH, Chang SE, Hagan T, De Jong SE, Maecker HT, van der Most R, Cheung P, Cortese M, Bosinger SE, Davis M, Rouphael N, Subramaniam S, Yosef N, Utz PJ, Khatri P, Pulendran B. The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. Cell 2021; 184:3915-3935.e21. [PMID: 34174187 PMCID: PMC8316438 DOI: 10.1016/j.cell.2021.05.039] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell level. Vaccination against seasonal influenza induced persistently diminished H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to Toll-like receptor stimulation. Single-cell ATAC-seq analysis revealed an epigenomically distinct subcluster of monocytes with reduced chromatin accessibility at AP-1-targeted loci after vaccination. Similar effects were observed in response to vaccination with the AS03-adjuvanted H5N1 pandemic influenza vaccine. However, this vaccine also stimulated persistently increased chromatin accessibility at interferon response factor (IRF) loci in monocytes and mDCs. This was associated with elevated expression of antiviral genes and heightened resistance to the unrelated Zika and Dengue viruses. These results demonstrate that vaccination stimulates persistent epigenomic remodeling of the innate immune system and reveal AS03's potential as an epigenetic adjuvant.
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Affiliation(s)
- Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alex Kuo
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shakti Gupta
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mariko Hinton Foecke
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Hagan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sanne E De Jong
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mario Cortese
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mark Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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22
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Gu M, Donato M, Guo M, Wary N, Miao Y, Mao S, Saito T, Otsuki S, Wang L, Harper RL, Sa S, Khatri P, Rabinovitch M. iPSC-endothelial cell phenotypic drug screening and in silico analyses identify tyrphostin-AG1296 for pulmonary arterial hypertension. Sci Transl Med 2021; 13:13/592/eaba6480. [PMID: 33952674 DOI: 10.1126/scitranslmed.aba6480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/09/2021] [Indexed: 12/27/2022]
Abstract
Pulmonary arterial hypertension (PAH) is a progressive disorder leading to occlusive vascular remodeling. Current PAH therapies improve quality of life but do not reverse structural abnormalities in the pulmonary vasculature. Here, we used high-throughput drug screening combined with in silico analyses of existing transcriptomic datasets to identify a promising lead compound to reverse PAH. Induced pluripotent stem cell-derived endothelial cells generated from six patients with PAH were exposed to 4500 compounds and assayed for improved cell survival after serum withdrawal using a chemiluminescent caspase assay. Subsequent validation of caspase activity and improved angiogenesis combined with data analyses using the Gene Expression Omnibus and Library of Integrated Network-Based Cellular Signatures databases revealed that the lead compound AG1296 was positively associated with an anti-PAH gene signature. AG1296 increased abundance of bone morphogenetic protein receptors, downstream signaling, and gene expression and suppressed PAH smooth muscle cell proliferation. AG1296 induced regression of PA neointimal lesions in lung organ culture and PA occlusive changes in the Sugen/hypoxia rat model and reduced right ventricular systolic pressure. Moreover, AG1296 improved vascular function and BMPR2 signaling and showed better correlation with the anti-PAH gene signature than other tyrosine kinase inhibitors. Specifically, AG1296 up-regulated small mothers against decapentaplegic (SMAD) 1/5 coactivators, cAMP response element-binding protein 3 (CREB3), and CREB5: CREB3 induced inhibitor of DNA binding 1 and downstream genes that improved vascular function. Thus, drug discovery for PAH can be accelerated by combining phenotypic screening with in silico analyses of publicly available datasets.
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Affiliation(s)
- Mingxia Gu
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA.,Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Michele Donato
- Department of Medicine (Biomedical Informatics) and Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minzhe Guo
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Neil Wary
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yifei Miao
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA.,Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Shuai Mao
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Toshie Saito
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Shoichiro Otsuki
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Lingli Wang
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Rebecca L Harper
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Silin Sa
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Medicine (Biomedical Informatics) and Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marlene Rabinovitch
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA 94305, USA. .,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
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23
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van der Feen DE, Bossers GPL, Hagdorn QAJ, Moonen JR, Kurakula K, Szulcek R, Chappell J, Vallania F, Donato M, Kok K, Kohli JS, Petersen AH, van Leusden T, Demaria M, Goumans MJTH, De Boer RA, Khatri P, Rabinovitch M, Berger RMF, Bartelds B. Cellular senescence impairs the reversibility of pulmonary arterial hypertension. Sci Transl Med 2021; 12:12/554/eaaw4974. [PMID: 32727916 DOI: 10.1126/scitranslmed.aaw4974] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 10/26/2019] [Accepted: 06/04/2020] [Indexed: 12/24/2022]
Abstract
Pulmonary arterial hypertension (PAH) in congenital cardiac shunts can be reversed by hemodynamic unloading (HU) through shunt closure. However, this reversibility potential is lost beyond a certain point in time. The reason why PAH becomes irreversible is unknown. In this study, we used MCT+shunt-induced PAH in rats to identify a dichotomous reversibility response to HU, similar to the human situation. We compared vascular profiles of reversible and irreversible PAH using RNA sequencing. Cumulatively, we report that loss of reversibility is associated with a switch from a proliferative to a senescent vascular phenotype and confirmed markers of senescence in human PAH-CHD tissue. In vitro, we showed that human pulmonary endothelial cells of patients with PAH are more vulnerable to senescence than controls in response to shear stress and confirmed that the senolytic ABT263 induces apoptosis in senescent, but not in normal, endothelial cells. To support the concept that vascular cell senescence is causal to the irreversible nature of end-stage PAH, we targeted senescence using ABT263 and induced reversal of the hemodynamic and structural changes associated with severe PAH refractory to HU. The factors that drive the transition from a reversible to irreversible pulmonary vascular phenotype could also explain the irreversible nature of other PAH etiologies and provide new leads for pharmacological reversal of end-stage PAH.
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Affiliation(s)
- Diederik E van der Feen
- Center for Congenital Heart Diseases, University Medical Center Groningen, 9713 GZ Groningen, Netherlands.
| | - Guido P L Bossers
- Center for Congenital Heart Diseases, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Quint A J Hagdorn
- Center for Congenital Heart Diseases, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Jan-Renier Moonen
- Department of Pediatrics, Vera Moulton Wall Center for Pulmonary Vascular Disease and the Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Kondababu Kurakula
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Robert Szulcek
- Department of Pulmonology, VU University Medical Center, 1081 HV Amsterdam, Netherlands
| | - James Chappell
- Department of Pediatrics, Vera Moulton Wall Center for Pulmonary Vascular Disease and the Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Francesco Vallania
- Institute for Immunity, Transplantation and Infection, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Center of Biomedical Informatics Research, Department of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Center of Biomedical Informatics Research, Department of Medicine, Stanford, CA 94305, USA
| | - Klaas Kok
- Department of Genetics, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Jaskaren S Kohli
- European Research Institute for the Biology of Ageing, 9700 AD Groningen, Netherlands
| | - Arjen H Petersen
- Department of Medical Biology, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Tom van Leusden
- Department of Experimental Cardiology, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Marco Demaria
- European Research Institute for the Biology of Ageing, 9700 AD Groningen, Netherlands
| | - Marie-José T H Goumans
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Rudolf A De Boer
- Department of Experimental Cardiology, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford School of Medicine, Stanford, CA 94305, USA.,Stanford Center of Biomedical Informatics Research, Department of Medicine, Stanford, CA 94305, USA
| | - Marlene Rabinovitch
- Department of Pediatrics, Vera Moulton Wall Center for Pulmonary Vascular Disease and the Cardiovascular Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Rolf M F Berger
- Center for Congenital Heart Diseases, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Beatrijs Bartelds
- Center for Congenital Heart Diseases, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
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24
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Mitchell MI, Ben‐Dov IZ, Liu C, Ye K, Chow K, Kramer Y, Gangadharan A, Park S, Fitzgerald S, Ramnauth A, Perlin DS, Donato M, Bhoy E, Manouchehri Doulabi E, Poulos M, Kamali‐Moghaddam M, Loudig O. Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV-CATCHER): A customizable purification assay designed for small-RNA biomarker identification and evaluation of circulating small-EVs. J Extracell Vesicles 2021; 10:e12110. [PMID: 34122779 PMCID: PMC8173589 DOI: 10.1002/jev2.12110] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
Circulating nucleic acids, encapsulated within small extracellular vesicles (EVs), provide a remote cellular snapshot of biomarkers derived from diseased tissues, however selective isolation is critical. Current laboratory-based purification techniques rely on the physical properties of small-EVs rather than their inherited cellular fingerprints. We established a highly-selective purification assay, termed EV-CATCHER, initially designed for high-throughput analysis of low-abundance small-RNA cargos by next-generation sequencing. We demonstrated its selectivity by specifically isolating and sequencing small-RNAs from mouse small-EVs spiked into human plasma. Western blotting, nanoparticle tracking, and transmission electron microscopy were used to validate and quantify the capture and release of intact small-EVs. As proof-of-principle for sensitive detection of circulating miRNAs, we compared small-RNA sequencing data from a subset of small-EVs serum-purified with EV-CATCHER to data from whole serum, using samples from a small cohort of recently hospitalized Covid-19 patients. We identified and validated, only in small-EVs, hsa-miR-146a and hsa-miR-126-3p to be significantly downregulated with disease severity. Separately, using convalescent sera from recovered Covid-19 patients with high anti-spike IgG titers, we confirmed the neutralizing properties, against SARS-CoV-2 in vitro, of a subset of small-EVs serum-purified by EV-CATCHER, as initially observed with ultracentrifuged small-EVs. Altogether our data highlight the sensitivity and versatility of EV-CATCHER.
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Affiliation(s)
- Megan I. Mitchell
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Iddo Z. Ben‐Dov
- Laboratory of Medical TranscriptomicsHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Christina Liu
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Kenny Ye
- Department of Epidemiology and Population HealthAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Kar Chow
- BiorepositoryHackensack University Medical CenterHackensackNew JerseyUSA
| | - Yael Kramer
- BiorepositoryHackensack University Medical CenterHackensackNew JerseyUSA
| | - Anju Gangadharan
- BiorepositoryHackensack University Medical CenterHackensackNew JerseyUSA
| | - Steven Park
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Sean Fitzgerald
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Andrew Ramnauth
- Department of Pathology and Laboratory MedicineWeill Cornell MedicineNew YorkUSA
| | - David S. Perlin
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Michele Donato
- BiorepositoryHackensack University Medical CenterHackensackNew JerseyUSA
| | - Emily Bhoy
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Ehsan Manouchehri Doulabi
- Department of Immunology, Genetics and PathologyScience for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Michael Poulos
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
| | - Masood Kamali‐Moghaddam
- Department of Immunology, Genetics and PathologyScience for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Olivier Loudig
- Center for Discovery and InnovationHackensack Meridian HealthNutleyNew JerseyUSA
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25
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Felizardo T, Lum L, Ashmaig M, Mosquera Limas S, Zhu N, Bushera H, Glass D, Berry J, Korngold R, Donato M, Glass J, Munshi P, Rowley S, Fowler D. In vivo biologic activity of induced hybrid TREG/Th2 RAPA-501 cells for als therapy: correction of TSCM:TEMimbalance, normalization of IL-6 secretion, and reduction in serum NF-L levels. Cytotherapy 2021. [DOI: 10.1016/s146532492100431x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Zheng H, Rao AM, Dermadi D, Toh J, Murphy Jones L, Donato M, Liu Y, Su Y, Dai CL, Kornilov SA, Karagiannis M, Marantos T, Hasin-Brumshtein Y, He YD, Giamarellos-Bourboulis EJ, Heath JR, Khatri P. Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses. Immunity 2021; 54:753-768.e5. [PMID: 33765435 PMCID: PMC7988739 DOI: 10.1016/j.immuni.2021.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
Viral infections induce a conserved host response distinct from bacterial infections. We hypothesized that the conserved response is associated with disease severity and is distinct between patients with different outcomes. To test this, we integrated 4,780 blood transcriptome profiles from patients aged 0 to 90 years infected with one of 16 viruses, including SARS-CoV-2, Ebola, chikungunya, and influenza, across 34 cohorts from 18 countries, and single-cell RNA sequencing profiles of 702,970 immune cells from 289 samples across three cohorts. Severe viral infection was associated with increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells. We identified protective and detrimental gene modules that defined distinct trajectories associated with mild versus severe outcomes. The interferon response was decoupled from the protective host response in patients with severe outcomes. These findings were consistent, irrespective of age and virus, and provide insights to accelerate the development of diagnostics and host-directed therapies to improve global pandemic preparedness.
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Affiliation(s)
- Hong Zheng
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Aditya M Rao
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Jiaying Toh
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Lara Murphy Jones
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA; Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Stanford University, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Yiran Liu
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Cancer Biology program, Stanford University, CA 94305, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Cheng L Dai
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Minas Karagiannis
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | - Theodoros Marantos
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | | | | | | | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA.
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Saberian N, Peyvandipour A, Donato M, Ansari S, Draghici S. A new computational drug repurposing method using established disease-drug pair knowledge. Bioinformatics 2020; 35:3672-3678. [PMID: 30840053 DOI: 10.1093/bioinformatics/btz156] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 01/15/2019] [Accepted: 03/04/2019] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION Drug repurposing is a potential alternative to the classical drug discovery pipeline. Repurposing involves finding novel indications for already approved drugs. In this work, we present a novel machine learning-based method for drug repurposing. This method explores the anti-similarity between drugs and a disease to uncover new uses for the drugs. More specifically, our proposed method takes into account three sources of information: (i) large-scale gene expression profiles corresponding to human cell lines treated with small molecules, (ii) gene expression profile of a human disease and (iii) the known relationship between Food and Drug Administration (FDA)-approved drugs and diseases. Using these data, our proposed method learns a similarity metric through a supervised machine learning-based algorithm such that a disease and its associated FDA-approved drugs have smaller distance than the other disease-drug pairs. RESULTS We validated our framework by showing that the proposed method incorporating distance metric learning technique can retrieve FDA-approved drugs for their approved indications. Once validated, we used our approach to identify a few strong candidates for repurposing. AVAILABILITY AND IMPLEMENTATION The R scripts are available on demand from the authors. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nafiseh Saberian
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Azam Peyvandipour
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Michele Donato
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Sahar Ansari
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
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28
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McKenna M, Feinman R, Ahn J, Wang S, Vesole DH, Goldberg SL, Suero-Abreu GA, Gonzalez Velez M, Wang JC, Rehman A, McKiernan P, Donato M, Paleoudis EG, Siegel DSD, Biran N. The effect that β-lactam antibiotics have on progression free and overall survival in multiple myeloma patients undergoing autologous stem cell transplantation. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e20518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e20518 Background: Gut microbiome dysbiosis is correlated with graft-versus-host disease (GVHD) in allogeneic stem cell transplant (allo-SCT) patients. In the allo-SCT population, antibiotics have been associated with increased risk for GVHD mortality and relapse due to loss of gut obligate anaerobes . It has been shown that antibiotics may negatively impact the efficacy of checkpoint inhibitors for patients with solid tumors. Based on these studies, we performed a retrospective analysis to determine if antibiotic treatment affects outcomes of multiple myeloma (MM) patients after autologous SCT (ASCT). Methods: This is a single institution retrospective study at Hackensack University Medical Center. A list of consecutive MM patients treated from 1/2012 to 12/2015 was obtained and an electronic medical record review of the first 217 who received ASCT was performed. Baseline characteristics, treatment history, transplant course and antibiotic treatment (including β-lactams, fluoroquinolones, macrolides, metronidazole, and vancomycin) were reviewed. Prophylactic antibiotics were excluded. Response was defined using the IMWG criteria. Median progression free survival (PFS) and overall survival (OS) were estimated using the Kaplan-Meier method. Log rank tests were used to compare the difference in survival between stratified groups. The LASSO cox regression analysis method was used for multivariate analyses of PFS and OS. Results: Of the 217 patients, 205 patients were available for analysis. Median age at ASCT was 61. β-lactams were associated with decreased median PFS (1.95 vs 4.77 years (yrs), p < 0.01) and decreased median OS (7.51 vs 13.45 yrs, p = 0.01). Multivariate analysis adjusting for lasso-selected age, gender, complete remission (CR) after ASCT, and ISS demonstrated independent progression risk associated with β-lactam use (HR = 2.00, 95% CI, 1.28–3.12, p < 0.01). β-lactams were associated with worse OS in multivariate analysis adjusting for lasso-selected age, gender, CR after ASCT and high risk cytogenetics (HR = 1.89, 95% CI, 1.07–3.40, p = 0.03). Conclusions: In this preliminary study, β-lactams predicted for decreased PFS and OS compared to patients who did not receive β-lactams in MM patients undergoing ASCT. The study was limited by its retrospective nature but demonstrates one of the first evaluations of antibiotic effect on the ASCT population in MM. Prospective studies evaluating the impact of antimicrobials on patient outcomes and the gut microbiome are ongoing.
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Affiliation(s)
| | | | - Jaeil Ahn
- Georgetown University, Washington, DC
| | | | - David H. Vesole
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Stuart L. Goldberg
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | | | | | - Jun Chih Wang
- Rutgers University New Jersey Medical School, Newark, NJ
| | - Abdul Rehman
- New Jersey Medical School Department of Medicine, Newark, NJ
| | | | - Michele Donato
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | | | | | - Noa Biran
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
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Abstract
Currently, most diseases are diagnosed only after significant disease-associated transformations have taken place. Here, we propose an approach able to identify when systemic qualitative changes in biological systems happen, thus opening the possibility for therapeutic interventions before the occurrence of symptoms. The proposed method exploits knowledge from biological networks and longitudinal data using a system impact analysis. The method is validated on eight biological phenomena, three synthetic datasets and five real datasets, for seven organisms. Most importantly, the method accurately detected the transition from the control stage (benign) to the early stage of hepatocellular carcinoma on an eight-stage disease dataset.
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Affiliation(s)
- Cristina Mitrea
- Wayne State University, Department of Computer Science, Detroit, 48202, USA
- Wayne State University, Department of Oncology, Detroit, 48201, USA
| | - Aliccia Bollig-Fischer
- Wayne State University, Department of Oncology, Detroit, 48201, USA
- Karmanos Cancer Institute, Detroit, 48201, USA
| | - Călin Voichiţa
- Wayne State University, Department of Computer Science, Detroit, 48202, USA
| | - Michele Donato
- Stanford University, Institute for Immunity, Transplantation and Infection, Stanford, 94305, USA
| | - Roberto Romero
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NICHD/NIH/DHHS, Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Detroit, 48201, USA
- University of Michigan, Department of Obstetrics and Gynecology, Ann Arbor, 48109, USA
- Michigan State University, Department of Epidemiology and Biostatistics, East Lansing, 48824, USA
- Wayne State University, Center for Molecular Medicine and Genetics, Detroit, 48201, USA
| | - Sorin Drăghici
- Wayne State University, Department of Computer Science, Detroit, 48202, USA.
- Wayne State University, Department of Obstetrics and Gynecology, Detroit, 48201, USA.
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Gianni de Carvalho K, Gómez JE, Vallejo M, Marguet ER, Peroti NI, Donato M, Itri R, Colin VL. Production and properties of a bioemulsifier obtained from a lactic acid bacterium. Ecotoxicol Environ Saf 2019; 183:109553. [PMID: 31416012 DOI: 10.1016/j.ecoenv.2019.109553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/05/2019] [Accepted: 08/06/2019] [Indexed: 05/26/2023]
Abstract
In the present work, the production of bioemulsifier (BE) by a lactic acid bacterium (LAB) grown at 25 °C in lactic whey-based media for 24 h was evaluated. Maximum production was detected in a medium containing yeast extract, peptone and lactic whey (LAPLW medium), with a yield of 270 mg L-1. The BE proved to be more innocuous for Caco-2 cells, used as a toxicological indicator, than the non-ionic surfactant Triton X-100. In addition, the microbial product presented higher stability to changes in temperature (37 °C to 100 °C), pH (2-10), and salt concentration (5% and 20%, w/v) than the synthetic surfactant. Regarding emulsifying capacity tested against different hydrophobic substrates (kerosene, motor oil, diesel, sunflower oil, and grape oil), the BE displayed E24 values similar to or even better than those of Triton X-100. Finally, Triton X-100 caused irreversible modifications on the giant unilamellar vesicles (used as model membrane system), promoting the solubilization of the lipid bilayers. Nevertheless, BE induced temporary modifications of the membrane, which is associated with incorporation of the bioproduct in the outer layer. These results demonstrate the role of BE in biological processes, including reversible changes in microbial membranes to enhance the access to hydrophobic substrates.
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Affiliation(s)
- K Gianni de Carvalho
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pje. Caseros, 4000, Tucumán, Argentina
| | - J E Gómez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pje. Caseros, 4000, Tucumán, Argentina
| | - M Vallejo
- Laboratorio de Biotecnología Bacteriana, Universidad Nacional de la Patagonia San Juan Bosco, 9 de Julio 25, 9100, Trelew, Chubut, Argentina
| | - E R Marguet
- Laboratorio de Biotecnología Bacteriana, Universidad Nacional de la Patagonia San Juan Bosco, 9 de Julio 25, 9100, Trelew, Chubut, Argentina
| | - N I Peroti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pje. Caseros, 4000, Tucumán, Argentina
| | - M Donato
- Institute of Physics, University of Sao Paulo, SP, Brazil
| | - R Itri
- Institute of Physics, University of Sao Paulo, SP, Brazil
| | - V L Colin
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pje. Caseros, 4000, Tucumán, Argentina.
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Reis LR, Donato M, Almeida G, Castelhano L, Escada P. Nitinol versus non-Nitinol prostheses in otosclerosis surgery: a meta-analysis. ACTA ACUST UNITED AC 2019; 38:279-285. [PMID: 30197420 PMCID: PMC6146576 DOI: 10.14639/0392-100x-1950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/02/2018] [Indexed: 12/02/2022]
Abstract
The aim of this study is to perform a systematic review and meta-analysis of observational studies in which hearing outcomes after primary stapes surgery have been reported. After the surgical procedure, the effectiveness of stapes surgery using nickel titanium (Nitinol) or other prostheses were systematically compared and evaluated using a meta-analytic method. A systematic search for articles before January 2017 in Embase, Medline and Cochrane Library databases was conducted. Only articles in English were included. Inclusion criteria for qualitative synthesis consisted of a population of otosclerosis patients, intervention with primary stapes surgery using the Nitinol heat-crimping prosthesis compared with other type of stapes stapedotomy prostheses, and hearing outcome. Inclusion criteria for quantitative analysis consisted of application of audiometry guidelines of the American Academy of Otolaryngology Head and Neck Surgery Committee on Hearing and Equilibrium for evaluation of conductive hearing loss. A postoperative air-bone gap (ABG) ≤ 10 dB was considered effective. A bias assessment tool was developed according to Cochrane guidelines. To evaluate the mean age of the samples we used the chi-square test. Of the 4926 papers identified through the electronic database search (3695 in Pubmed/Cochrane and 1231 in Embase), 540 studies matched the selection criteria (436 in Pubmed/Cochrane and 104 in Embase) after application of filters and elimination of duplicate articles. After analysis of the title and abstract, 459 were excluded (396 in Pubmed/Cochrane and 63 in Embase). Of the remaining 81 papers, 74 were excluded according to the study selection criteria. A total of seven eligible studies with 1385 subjects, consisting of 637 in the Nitinol group and 748 in the non-Nitinol group, were included in our study. There were statistically significant differences in the effectiveness of stapes surgery between the Nitinol and non-Nitinol prostheses; the data showed a combined odds ratio (OR) of 2.56 (95% CI 1.38-4.76, p = 0.003). There were no statistically significant differences in the mean pre-operative age between Nitinol and non-Nitinol prostheses (p = 0.931). Our results suggest that the effectiveness of Nitinol was higher than non-Nitinol prostheses, with superiority of the number of patients with ABG ≤ 10 dB.
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Affiliation(s)
- L Roque Reis
- Department of Otolaryngology of Egas Moniz Hospital, West Lisbon Hospital Centre (CHLO), NOVA Medical School, Faculdade de Ciências Médicas, Lisbon, Portugall
| | - M Donato
- Department of Otolaryngology of Egas Moniz Hospital, West Lisbon Hospital Centre (CHLO), NOVA Medical School, Faculdade de Ciências Médicas, Lisbon, Portugall
| | - G Almeida
- Department of Otolaryngology of Egas Moniz Hospital, West Lisbon Hospital Centre (CHLO), NOVA Medical School, Faculdade de Ciências Médicas, Lisbon, Portugall
| | - L Castelhano
- Department of Otolaryngology of Egas Moniz Hospital, West Lisbon Hospital Centre (CHLO), NOVA Medical School, Faculdade de Ciências Médicas, Lisbon, Portugall
| | - P Escada
- Department of Otolaryngology of Egas Moniz Hospital, West Lisbon Hospital Centre (CHLO), NOVA Medical School, Faculdade de Ciências Médicas, Lisbon, Portugall
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32
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Dannewitz Prosseda S, Tian X, Kuramoto K, Boehm M, Sudheendra D, Miyagawa K, Zhang F, Solow-Cordero D, Saldivar JC, Austin ED, Loyd JE, Wheeler L, Andruska A, Donato M, Wang L, Huebner K, Metzger RJ, Khatri P, Spiekerkoetter E. FHIT, a Novel Modifier Gene in Pulmonary Arterial Hypertension. Am J Respir Crit Care Med 2019; 199:83-98. [PMID: 30107138 PMCID: PMC6353016 DOI: 10.1164/rccm.201712-2553oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/14/2018] [Indexed: 01/05/2023] Open
Abstract
RATIONALE Pulmonary arterial hypertension (PAH) is characterized by progressive narrowing of pulmonary arteries, resulting in right heart failure and death. BMPR2 (bone morphogenetic protein receptor type 2) mutations account for most familial PAH forms whereas reduced BMPR2 is present in many idiopathic PAH forms, suggesting dysfunctional BMPR2 signaling to be a key feature of PAH. Modulating BMPR2 signaling is therapeutically promising, yet how BMPR2 is downregulated in PAH is unclear. OBJECTIVES We intended to identify and pharmaceutically target BMPR2 modifier genes to improve PAH. METHODS We combined siRNA high-throughput screening of >20,000 genes with a multicohort analysis of publicly available PAH RNA expression data to identify clinically relevant BMPR2 modifiers. After confirming gene dysregulation in tissue from patients with PAH, we determined the functional roles of BMPR2 modifiers in vitro and tested the repurposed drug enzastaurin for its propensity to improve experimental pulmonary hypertension (PH). MEASUREMENTS AND MAIN RESULTS We discovered FHIT (fragile histidine triad) as a novel BMPR2 modifier. BMPR2 and FHIT expression were reduced in patients with PAH. FHIT reductions were associated with endothelial and smooth muscle cell dysfunction, rescued by enzastaurin through a dual mechanism: upregulation of FHIT as well as miR17-5 repression. Fhit-/- mice had exaggerated hypoxic PH and failed to recover in normoxia. Enzastaurin reversed PH in the Sugen5416/hypoxia/normoxia rat model, by improving right ventricular systolic pressure, right ventricular hypertrophy, cardiac fibrosis, and vascular remodeling. CONCLUSIONS This study highlights the importance of the novel BMPR2 modifier FHIT in PH and the clinical value of the repurposed drug enzastaurin as a potential novel therapeutic strategy to improve PAH.
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Affiliation(s)
- Svenja Dannewitz Prosseda
- Division of Pulmonary and Critical Care, Department of Medicine
- Wall Center for Pulmonary Vascular Disease
| | - Xuefei Tian
- Division of Pulmonary and Critical Care, Department of Medicine
- Wall Center for Pulmonary Vascular Disease
| | - Kazuya Kuramoto
- Division of Pulmonary and Critical Care, Department of Medicine
- Wall Center for Pulmonary Vascular Disease
| | - Mario Boehm
- Division of Pulmonary and Critical Care, Department of Medicine
- Wall Center for Pulmonary Vascular Disease
| | | | - Kazuya Miyagawa
- Wall Center for Pulmonary Vascular Disease
- Cardiovascular Institute
- Department of Pediatrics
| | - Fan Zhang
- Wall Center for Pulmonary Vascular Disease
| | | | | | - Eric D. Austin
- Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - James E. Loyd
- Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Lisa Wheeler
- Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Adam Andruska
- Division of Pulmonary and Critical Care, Department of Medicine
| | - Michele Donato
- Biomedical Informatics Research–Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California
| | - Lingli Wang
- Division of Pulmonary and Critical Care, Department of Medicine
- Wall Center for Pulmonary Vascular Disease
| | - Kay Huebner
- Molecular Genetics and Cancer Biology Program, Ohio State University, Columbus, Ohio
| | | | - Purvesh Khatri
- Biomedical Informatics Research–Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California
| | - Edda Spiekerkoetter
- Division of Pulmonary and Critical Care, Department of Medicine
- Wall Center for Pulmonary Vascular Disease
- Cardiovascular Institute
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33
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Peyvandipour A, Saberian N, Shafi A, Donato M, Draghici S. A novel computational approach for drug repurposing using systems biology. Bioinformatics 2018; 34:2817-2825. [PMID: 29534151 PMCID: PMC6084573 DOI: 10.1093/bioinformatics/bty133] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022] Open
Abstract
Motivation Identification of novel therapeutic effects for existing US Food and Drug Administration (FDA)-approved drugs, drug repurposing, is an approach aimed to dramatically shorten the drug discovery process, which is costly, slow and risky. Several computational approaches use transcriptional data to find potential repurposing candidates. The main hypothesis of such approaches is that if gene expression signature of a particular drug is opposite to the gene expression signature of a disease, that drug may have a potential therapeutic effect on the disease. However, this may not be optimal since it fails to consider the different roles of genes and their dependencies at the system level. Results We propose a systems biology approach to discover novel therapeutic roles for established drugs that addresses some of the issues in the current approaches. To do so, we use publicly available drug and disease data to build a drug-disease network by considering all interactions between drug targets and disease-related genes in the context of all known signaling pathways. This network is integrated with gene-expression measurements to identify drugs with new desired therapeutic effects based on a system-level analysis method. We compare the proposed approach with the drug repurposing approach proposed by Sirota et al. on four human diseases: idiopathic pulmonary fibrosis, non-small cell lung cancer, prostate cancer and breast cancer. We evaluate the proposed approach based on its ability to re-discover drugs that are already FDA-approved for a given disease. Availability and implementation The R package DrugDiseaseNet is under review for publication in Bioconductor and is available at https://github.com/azampvd/DrugDiseaseNet. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Adib Shafi
- Computer Science, Wayne State University, Detroit, MI, USA
| | - Michele Donato
- Computer Science, Wayne State University, Detroit, MI, USA
| | - Sorin Draghici
- Computer Science, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
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34
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Cheung P, Vallania F, Dvorak M, Chang SE, Schaffert S, Donato M, Rao AM, Mao R, Utz PJ, Khatri P, Kuo AJ. Single-cell epigenetics - Chromatin modification atlas unveiled by mass cytometry. Clin Immunol 2018; 196:40-48. [PMID: 29960011 DOI: 10.1016/j.clim.2018.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 12/13/2022]
Abstract
Modifications of histone proteins are fundamental to the regulation of epigenetic phenotypes. Dysregulations of histone modifications have been linked to the pathogenesis of diverse human diseases. However, identifying differential histone modifications in patients with immune-mediated diseases has been challenging, in part due to the lack of a powerful analytic platform to study histone modifications in the complex human immune system. We recently developed a highly multiplexed platform, Epigenetic landscape profiling using cytometry by Time-Of-Flight (EpiTOF), to analyze the global levels of a broad array of histone modifications in single cells using mass cytometry. In this review, we summarize the development of EpiTOF and discuss its potential applications in biomedical research. We anticipate that this platform will provide new insights into the roles of epigenetic regulation in hematopoiesis, immune cell functions, and immune system aging, and reveal aberrant epigenetic patterns associated with immune-mediated diseases.
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Affiliation(s)
- Peggie Cheung
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Francesco Vallania
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Steven Schaffert
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Aditya M Rao
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Rong Mao
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California 94305, USA.
| | - Alex J Kuo
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA.
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35
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Cheung P, Vallania F, Warsinske HC, Donato M, Schaffert S, Chang SE, Dvorak M, Dekker CL, Davis MM, Utz PJ, Khatri P, Kuo AJ. Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging. Cell 2018; 173:1385-1397.e14. [PMID: 29706550 PMCID: PMC5984186 DOI: 10.1016/j.cell.2018.03.079] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/27/2018] [Accepted: 03/28/2018] [Indexed: 12/17/2022]
Abstract
Post-translational modifications of histone proteins and exchanges of histone variants of chromatin are central to the regulation of nearly all DNA-templated biological processes. However, the degree and variability of chromatin modifications in specific human immune cells remain largely unknown. Here, we employ a highly multiplexed mass cytometry analysis to profile the global levels of a broad array of chromatin modifications in primary human immune cells at the single-cell level. Our data reveal markedly different cell-type- and hematopoietic-lineage-specific chromatin modification patterns. Differential analysis between younger and older adults shows that aging is associated with increased heterogeneity between individuals and elevated cell-to-cell variability in chromatin modifications. Analysis of a twin cohort unveils heritability of chromatin modifications and demonstrates that aging-related chromatin alterations are predominantly driven by non-heritable influences. Together, we present a powerful platform for chromatin and immunology research. Our discoveries highlight the profound impacts of aging on chromatin modifications.
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Affiliation(s)
- Peggie Cheung
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Francesco Vallania
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hayley C Warsinske
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Schaffert
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Alex J Kuo
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Dong N, McKiernan P, Siegel DSD, Vesole DH, Rowley SD, Andrews T, Ortega A, Skarbnik AP, Biran N, Richter JR, Pecora A, Goy A, Panchal R, Aleksidze N, Donato M. Autologous stem cell transplantation in multiple myeloma patients over age 75. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.8025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | - David H. Vesole
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Scott D. Rowley
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | | | | | | | - Noa Biran
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Joshua Ryan Richter
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Andrew Pecora
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Andre Goy
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | | | | | - Michele Donato
- John Theurer Cancer Center, Hackensack University Medical Center, Livingston, NJ
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Vijapura A, Levine HB, Donato M, Hartzband MA, Baker M, Klein GR. Total Hip Arthroplasty in Patients With Avascular Necrosis After Hematopoietic Stem Cell Transplantation. Orthopedics 2018; 41:e257-e261. [PMID: 29451944 DOI: 10.3928/01477447-20180213-02] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/15/2017] [Indexed: 02/03/2023]
Abstract
The immunosuppressive regimens required for hematopoietic stem cell transplantation predispose recipients to complications, including avascular necrosis. Cancer-related comorbidities, immunosuppression, and poor bone quality theoretically increase the risk for perioperative medical complications, infection, and implant-related complications in total joint arthroplasty. This study reviewed 20 primary total hip arthroplasties for avascular necrosis in 14 patients. Outcomes were assessed at routine clinical visits and Harris hip scores were calculated. Follow-up radiographs were evaluated for component malposition, loosening, polyethylene wear, and osteolysis. Average follow-up was 44.5 months for all patients. Postoperative clinical follow-up revealed good to excellent outcomes, with significant improvement in functional outcome scores. There were no periprosthetic infections or revisions for aseptic loosening. There was 1 dislocation on postoperative day 40, which was treated successfully with a closed reduction. Two patients with a prior history of venous thromboembolism developed a pulmonary embolus on postoperative day 13 and 77, respectively. Four patients died several months to years after arthroplasty of complications unrelated to the surgical procedure. Total hip arthroplasty can both be safely performed and greatly improve quality of life in recipients of hematopoietic stem cell transplantation who develop avascular necrosis. However, prolonged venous thromboembolism prophylaxis should be carefully considered in this high-risk patient population. [Orthopedics. 2018; 41(2):e257-e261.].
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Azad TD, Donato M, Heylen L, Liu AB, Shen-Orr SS, Sweeney TE, Maltzman JS, Naesens M, Khatri P. Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival. JCI Insight 2018; 3:95659. [PMID: 29367465 DOI: 10.1172/jci.insight.95659] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/12/2017] [Indexed: 12/22/2022] Open
Abstract
Late allograft failure is characterized by cumulative subclinical insults manifesting over many years. Although immunomodulatory therapies targeting host T cells have improved short-term survival rates, rates of chronic allograft loss remain high. We hypothesized that other immune cell types may drive subclinical injury, ultimately leading to graft failure. We collected whole-genome transcriptome profiles from 15 independent cohorts composed of 1,697 biopsy samples to assess the association of an inflammatory macrophage polarization-specific gene signature with subclinical injury. We applied penalized regression to a subset of the data sets and identified a 3-gene inflammatory macrophage-derived signature. We validated discriminatory power of the 3-gene signature in 3 independent renal transplant data sets with mean AUC of 0.91. In a longitudinal cohort, the 3-gene signature strongly correlated with extent of injury and accurately predicted progression of subclinical injury 18 months before clinical manifestation. The 3-gene signature also stratified patients at high risk of graft failure as soon as 15 days after biopsy. We found that the 3-gene signature also distinguished acute rejection (AR) accurately in 3 heart transplant data sets but not in lung transplant. Overall, we identified a parsimonious signature capable of diagnosing AR, recognizing subclinical injury, and risk-stratifying renal transplant patients. Our results strongly suggest that inflammatory macrophages may be a viable therapeutic target to improve long-term outcomes for organ transplantation patients.
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Affiliation(s)
- Tej D Azad
- Stanford Institute for Immunity, Transplantation and Infection and.,Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Michele Donato
- Stanford Institute for Immunity, Transplantation and Infection and.,Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Line Heylen
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Andrew B Liu
- Stanford Institute for Immunity, Transplantation and Infection and.,Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Shai S Shen-Orr
- Department of Immunology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection and.,Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Jonathan Scott Maltzman
- Division of Nephrology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Maarten Naesens
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection and.,Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
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Hernán Gómez Llambí H, Cao G, Donato M, Suárez D, Ottaviano G, Müller A, Buchholz B, Gelpi R, Otero-Losada M, Milei J. Left ventricular hypertrophy does not prevent heart failure in experimental hypertension. Int J Cardiol 2017; 238:57-65. [PMID: 28410843 DOI: 10.1016/j.ijcard.2017.03.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 03/04/2017] [Accepted: 03/24/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Left ventricular hypertrophy (LVH) secondary to hypertension has been accepted to prevent heart failure (HF) while paradoxically increasing cardiovascular morbi-mortality. OBJECTIVES To evaluate whether antihypertensive treatment inhibits LVH, restores beta-adrenergic response and affects myocardial oxidative metabolism. METHODS Ninety spontaneously hypertensive rats (SHR) were distributed into groups and treated (mg/kg, p.o.) with: losartan 30 (L), hydralazine 11 (H), rosuvastatin 10 (R), carvedilol 20 (C). Hypertension control group comprised 18 normotensive rats (Wistar-Kyoto, WKY). Following euthanasia at 16months, contractility was measured in 50% of rats (Langendorff system) before and after isoproterenol (Iso) 10-9M, 10-7M and 10-5M stimulation. Left ventricular weight (LVW) was measured in the remaining hearts, and normalized by BW. Expression of thioredoxin 1 (Trx-1), peroxyredoxin 2 (Prx-2), glutaredoxin 3 (Grx-3), caspase-3 and brain natriuretic peptide (BNP) was determined. RESULTS Systolic blood pressure (mmHg): 154±3 (L), 137±1 (H), 190±3 (R)*, 206±3 (SHR)*, 183±1 (C)**, and 141±1 (WKY) (*p<0.05 vs. L, H, WKY, **p<0.05 vs. L, H, WKY, SHR). LVW/BW was higher in SHR and R (p<0.05). Groups SHR, R and C evidenced baseline contractile depression. Response to Iso 10-5M was similar in WKY and L. Expression of Trx-1, Prx-2 and Grx-3 increased in C, H, R and L (p<0.01). CONCLUSIONS Present findings argue against the traditional idea and support that LVH might not be required to prevent HF. Increased expression of thioredoxins by antihypertensive treatment might be involved in protection from HF.
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Affiliation(s)
- H Hernán Gómez Llambí
- Institute of Cardiological Research, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
| | - G Cao
- Institute of Cardiological Research, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
| | - M Donato
- Institute of Cardiovascular Pathophysiology, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
| | - D Suárez
- Institute of Cardiological Research, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
| | - G Ottaviano
- Institute of Cardiological Research, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
| | - A Müller
- Institute of Cardiological Research, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
| | - B Buchholz
- Institute of Cardiovascular Pathophysiology, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
| | - R Gelpi
- Institute of Cardiovascular Pathophysiology, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
| | - M Otero-Losada
- Institute of Cardiological Research, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina.
| | - J Milei
- Institute of Cardiological Research, School of Medicine, University of Buenos Aires, UBA-CONICET, Buenos Aires, Argentina
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Ansari S, Donato M, Saberian N, Draghici S. An approach to infer putative disease-specific mechanisms using neighboring gene networks. Bioinformatics 2017; 33:1987-1994. [PMID: 28200075 PMCID: PMC5870849 DOI: 10.1093/bioinformatics/btx097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/18/2017] [Accepted: 02/10/2017] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The ultimate goal of any experiment is to understand the biological phenomena underlying the condition investigated. This process often results in genes network through which a certain biological mechanism is explained. Such networks have been proven to be extremely useful, for the prediction of mechanisms of action of drugs or the responses of an organism to a specific impact (e.g. a disease, a treatment, etc.). Here, we introduce an approach able to build a network that captures the putative mechanisms at play in the given condition, by using datasets from multiple experiments studying the same phenotype. This method takes advantage of known interactions extracted from multiple sources such as protein-protein interactions and curated biological pathways. Based on such prior knowledge, we overcome the drawbacks of snap-shot data by considering the possible effects of each gene on its neighbors. RESULTS We show the effectiveness of this approach in three different case studies and validate the results in two ways considering the identified genes and interactions between them. We compare our findings with the results of two widely-used methods in the same category as well as the classical approach of selecting differentially expressed (DE) genes in an investigated condition. The results show that 'neighbor-net' analysis is able to report biological mechanisms that are significantly relevant to the given diseases in all the three case studies, and performs better compared to all reference methods using both validation approaches. AVAILABILITY AND IMPLEMENTATION The proposed method is implemented as in R and will be available an a Bioconductor package. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sahar Ansari
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Michele Donato
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Nafiseh Saberian
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
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Richter JR, Wang Z, Vesole DH, Biran N, Donato M, Rowley SD, Skarbnik AP, Pecora A, Siegel DSD. Autologous stem cell transplantation as a treatment modality for type 1 cryoglobulinemia in monoclonal gammopathy of renal significance. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e19500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e19500 Background: Type I cryoglobulinemia (CRYO) can be driven by disorders such as plasma cell dyscrasias. Monoclonal gammopathy of renal significance (MGRS) represents a group of kidney disorders characterized by the presence of a paraprotein; though not fitting the criteria for a hematologic malignancy. There exists no standard approach to manage these patients. Our patient is a 56-year-old man who was initially evaluated for edema. Workup revealed worsening renal function and proteinuria (Figure 1). Renal biopsy revealed abundant cryofibrinogen deposits and cryoglobulinemic glomerulonephritis with membranoproliferative pattern. Bloodwork showed type I (IgG Kappa) CRYO. Bone marrow evaluation revealed 7% clonal plasma cells. Further evaluation did not confirm a diagnosis of myeloma. Methods: Treatment was initiated with bortezomib, cyclophosphamide and dexamethasone. After 3 cycles of therapy the patient had normalization of his creatinine and marked improvement in edema. Peripheral blood stem cells were mobilized following the administration of high-dose cyclophosphamide (2gm/m2) plus filgrastim. He was subsequently conditioned for transplantation with high-dose melphalan (200mg/m2; HDM) followed by autologous stem cell rescue. He tolerated the procedure well without any unexpected toxicities; achieving prompt hematologic recovery Results: Evaluations post transplant revealed resolution of any circulating cryoglobulins and reduction in proteinuria. At 1 year post transplant, the patient has returned to his premorbid condition. Conclusions: Type 1 CRYO associated MGRS represents a complicated disorder for which there is no consensus treatment approach. As this process may be driven by clonal plasma cells, classical anti-myeloma therapy may provide a strategy for management. Given the typical low plasma cell burden in these patients, HDM has the potential to offer deep and durable remissions. Prospective studies are needed to validate this approach. [Table: see text]
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Affiliation(s)
- Joshua Ryan Richter
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Zhen Wang
- Rutgers New Jersey Medical School, Newark, NJ
| | - David H. Vesole
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Noa Biran
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | - Michele Donato
- John Theurer Cancer Center, Hackensack University Medical Center, Livingston, NJ
| | - Scott D. Rowley
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | | | - Andrew Pecora
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
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Abstract
A major challenge in life science research is understanding the mechanism involved in a given phenotype. The ability to identify the correct mechanisms is needed in order to understand fundamental and very important phenomena such as mechanisms of disease, immune systems responses to various challenges, and mechanisms of drug action. The current data analysis methods focus on the identification of the differentially expressed (DE) genes using their fold change and/or p-values. Major shortcomings of this approach are that: i) it does not consider the interactions between genes; ii) its results are sensitive to the selection of the threshold(s) used, and iii) the set of genes produced by this approach is not always conducive to formulating mechanistic hypotheses. Here we present a method that can construct networks of genes that can be considered putative mechanisms. The putative mechanisms constructed by this approach are not limited to the set of DE genes, but also considers all known and relevant gene-gene interactions. We analyzed three real datasets for which both the causes of the phenotype, as well as the true mechanisms were known. We show that the method identified the correct mechanisms when applied on microarray datasets from mouse. We compared the results of our method with the results of the classical approach, showing that our method produces more meaningful biological insights.
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Affiliation(s)
- Samer Hanoudi
- Department of Computer Science, Wayne State University, Detroit, MI, United States of America
| | - Michele Donato
- Department of Computer Science, Wayne State University, Detroit, MI, United States of America
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, United States of America
- Department of Obstetrics and Gynecology, Detroit, MI, United States of America
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Ansari S, Voichita C, Donato M, Tagett R, Draghici S. A novel pathway analysis approach based on the unexplained disregulation of genes. Proc IEEE Inst Electr Electron Eng 2017; 105:482-495. [PMID: 30337764 PMCID: PMC6190577 DOI: 10.1109/jproc.2016.2531000] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A crucial step in the understanding of any phenotype is the correct identification of the signaling pathways that are significantly impacted in that phenotype. However, most current pathway analysis methods produce both false positives as well as false negatives in certain circumstances. We hypothesized that such incorrect results are due to the fact that the existing methods fail to distinguish between the primary dis-regulation of a given gene itself and the effects of signaling coming from upstream. Furthermore, a modern whole-genome experiment performed with a next-generation technology spends a great deal of effort to measure the entire set of 30,000-100,000 transcripts in the genome. This is followed by the selection of a few hundreds differentially expressed genes, step that literally discards more than 99% of the collected data. We also hypothesized that such a drastic filtering could discard many genes that play crucial roles in the phenotype. We propose a novel topology-based pathway analysis method that identifies significantly impacted pathways using the entire set of measurements, thus allowing the full use of the data provided by NGS techniques. The results obtained on 24 real data sets involving 12 different human diseases, as well as on 8 yeast knock-out data sets show that the proposed method yields significant improvements with respect to the state-of-the-art methods: SPIA, GSEA and GSA. AVAILABILITY Primary dis-regulation analysis is implemented in R and included in ROntoTools Bioconductor package (versions ≥ 2.0.0). https://www.bioconductor.org/packages/release/bioc/html/ROntoTools.html.
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Affiliation(s)
- Sahar Ansari
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Calin Voichita
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Michele Donato
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Rebecca Tagett
- Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA
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Ciceri F, Bonini C, Labopin M, Oliveira G, Nagler A, Yannaki E, Stanghellini MTL, Bondanza A, Greco R, Olavarria E, Weissinger E, Stadler M, Bunjes D, Niederwieser D, Uharek L, Bethge W, DiPersio J, Pecora AL, Donato M, Colombi S, Lambiase A, Bordignon C, Mohty M. Safety and Efficacy of Donor T Cells Engineered with Herpes Simplex Virus Thymidine-Kinase Suicide Gene (TK Cells) Given after T-Cell Depleted (TCD) Haploidentical Hematopoietic Transplantation (Haplo-HSCT): Results of a 14-Year Follow-Up in 45 Patients. Biol Blood Marrow Transplant 2017. [DOI: 10.1016/j.bbmt.2017.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Mauad M, Siri A, Donato M. Does Type of Substratum Affects Chironomid Larvae Assemblage Composition? A Study in a River Catchment in Northern Patagonia, Argentina. Neotrop Entomol 2017; 46:18-28. [PMID: 27541752 DOI: 10.1007/s13744-016-0429-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
Chironomid larvae assemblages were investigated at seven sampling stations in relation to stream habitat type in the Challhuaco-Ñireco river system located in the Nahuel Huapi National Park, in the North-Western part of Rio Negro Province, Argentina. A total of 2229 individuals were sampled and 43 Chironomidae taxa were recorded with Orthocladiinae (29) being the best represented subfamily, followed by Diamesinae (5), Tanypodinae (3), Podonominae (3) and Chironominae (3). Stictocladius spF, Cricotopus (Paratrichocladius) sp6, Cricotopus sp2, Cricotopus sp3 and Parapsectrocladius sp2 were the most abundant taxa. Sites near the source of the river system were dominated by Podonomus sp., Limnophyes sp., Parapsectrocladius sp. and Stictocladius spF, whereas sites close to the river mouth were dominated by Diamesinae sp5 and Cricotopus sp. Rank/abundance plots show that all the analysed sites displayed dominance of some species. Stictocladius spF, Cricotopus sp2, Cricotopus sp3, Cricotopus (Paratrichocladius) sp6, Parapsectrocladius sp. and Limnophyes sp. resulted as dominant species, or being part of a group of dominant species, at least in one sample. Eleven taxa were associated with habitats related with riffle areas and stable substrates with filamentous algae. Species-environment relationships were examined using ordination analysis. Elevation was the most significant environmental variable that explained 22% of the total variability of the chironomid assemblages, showing stronger relationships among sites within an altitudinal gradient than among habitat type. Abundance of chironomids increased from headwaters to the outflow in Nahuel Huapi Lake responding to an altitude gradient as well as some environmental factors such as coarse matter and nutrient concentrations.
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Affiliation(s)
- M Mauad
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA) (CONICET, UNLP) La Plata, ILPLA, Boulevard 122 and 60 S/N, La Plata, 1900, Argentina.
| | - A Siri
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA) (CONICET, UNLP) La Plata, ILPLA, Boulevard 122 and 60 S/N, La Plata, 1900, Argentina
| | - M Donato
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA) (CONICET, UNLP) La Plata, ILPLA, Boulevard 122 and 60 S/N, La Plata, 1900, Argentina
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Noerenberg A, Tolosa L, Gómez Lechón M, Runge N, Johannssen T, López S, Guzmán C, Castell J, Donato M, Jover R. Characterization of proliferating human hepatocytes as a model system for drug interaction studies and toxicity screenings. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Tomoiaga A, Westfall P, Donato M, Draghici S, Hassan S, Romero R, Tellaroli P. Pathway crosstalk effects: Shrinkage and disentanglement using a Bayesian hierarchical model. Stat Biosci 2016; 8:374-394. [PMID: 33456621 DOI: 10.1007/s12561-016-9160-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Identifying the biological pathways that are related to various clinical phenotypes is an important concern in biomedical research. Based on estimated expression levels and/or p-values, over-representation analysis (ORA) methods provide rankings of pathways, but they are tainted because pathways overlap. This crosstalk phenomenon has not been rigorously studied and classical ORA does not take into consideration: (i) that crosstalk effects in cases of overlapping pathways can cause incorrect rankings of pathways, (ii) that crosstalk effects can cause both excess type I errors and type II errors, (iii) that rankings of small pathways are unreliable and (iv) that type I error rates can be inflated due to multiple comparisons of pathways. We develop a Bayesian hierarchical model that addresses these problems, providing sensible estimates and rankings, and reducing error rates. We show, on both real and simulated data, that the results of our method are more accurate than the results produced by the classical over-representation analysis, providing a better understanding of the underlying biological phenomena involved in the phenotypes under study. The R code and the binary datasets for implementing the analyses described in this article are available online at: http://www.eng.wayne.edu/page.php?id=6402.
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Affiliation(s)
- Alin Tomoiaga
- Center for Advanced Analytics and Business Intelligence, Texas Tech University, Lubbock, TX 79409, U.S.A
| | - Peter Westfall
- Center for Advanced Analytics and Business Intelligence, Texas Tech University, Lubbock, TX 79409, U.S.A
| | - Michele Donato
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, 48201, MI, U.S.A
| | - Sorin Draghici
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, 48201, MI, U.S.A
| | - Sonia Hassan
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Detroit, MI, U.S.A
| | - Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Detroit, MI, U.S.A
| | - Paola Tellaroli
- Department of Statistical Sciences, University of Padua, Italy
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48
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Zhang S, Biran N, Siegel DSD, Donato M, Vesole DH, Pecora A, Richter JR, Skarbnik AP, Goy A, Goldberg SL, Feldman TA, Brown E, Buttner K, DelFavero M, Hong SH, Kim D, Rowley SD. Melphalan + bortezomib (MelVel) and Mel + Vel + thalidomide (MelVelThal) as a conditioning regimen for autologous peripheral blood stem cell transplantation (ASCT) in patients (pts) with advanced multiple myeloma (MM): An updated analysis of 2 phase I/II studies. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.8027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Shijia Zhang
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ
| | - Noa Biran
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | | | - Michele Donato
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - David H. Vesole
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Andrew Pecora
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Joshua Ryan Richter
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Alan P. Skarbnik
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Andre Goy
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Stuart L. Goldberg
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Tatyana A. Feldman
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Emily Brown
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Kathryn Buttner
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Marie DelFavero
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Sung H. Hong
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Daniel Kim
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
| | - Scott D. Rowley
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ
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49
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Tellaroli P, Bazzi M, Donato M, Brazzale AR, Drăghici S. Cross-Clustering: A Partial Clustering Algorithm with Automatic Estimation of the Number of Clusters. PLoS One 2016; 11:e0152333. [PMID: 27015427 PMCID: PMC4807765 DOI: 10.1371/journal.pone.0152333] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/11/2016] [Indexed: 11/19/2022] Open
Abstract
Four of the most common limitations of the many available clustering methods are: i) the lack of a proper strategy to deal with outliers; ii) the need for a good a priori estimate of the number of clusters to obtain reasonable results; iii) the lack of a method able to detect when partitioning of a specific data set is not appropriate; and iv) the dependence of the result on the initialization. Here we propose Cross-clustering (CC), a partial clustering algorithm that overcomes these four limitations by combining the principles of two well established hierarchical clustering algorithms: Ward’s minimum variance and Complete-linkage. We validated CC by comparing it with a number of existing clustering methods, including Ward’s and Complete-linkage. We show on both simulated and real datasets, that CC performs better than the other methods in terms of: the identification of the correct number of clusters, the identification of outliers, and the determination of real cluster memberships. We used CC to cluster samples in order to identify disease subtypes, and on gene profiles, in order to determine groups of genes with the same behavior. Results obtained on a non-biological dataset show that the method is general enough to be successfully used in such diverse applications. The algorithm has been implemented in the statistical language R and is freely available from the CRAN contributed packages repository.
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Affiliation(s)
- Paola Tellaroli
- Department of Statistical Sciences, University of Padova, Padova, Italy
- * E-mail:
| | - Marco Bazzi
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Michele Donato
- Department of Computer Science, Wayne State University, Detroit, MI, United States of America
| | | | - Sorin Drăghici
- Department of Computer Science, Wayne State University, Detroit, MI, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States of America
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50
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Rodríguez M, Buchholz B, D’Annuzio V, Donato M, González G, A. Goyeneche M, Mazo T, Pérez V, Wilensky L, Gelpi R. Cardiac ischemic preconditioning prevents dystrophin proteolysis by MMP-2 inhibition. BIOCELL 2016. [DOI: 10.32604/biocell.2016.40.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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