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Research Overview

Dr. Joann Arce and her team focus on the following research areas:

  • Identification and characterization of molecular signatures using systems immunology approach ('omics and immunophenotyping assays)
  • Metabolic responses to vaccines and infections
  • Bacille Calmette Guerin and other neonatal vaccines in response to early life immunity
  • Multi-omic integration, network, and statistical modeling approaches
  • Cloud computing and data management of clinical and immunophenotyping data for large consortia and multi-institutional collaborations in the US and globally

Research Background

Dr. Joann Diray Arce has expertise in systems immunology in infectious diseases and vaccines. She is a faculty within the Precision Vaccines Program, an Assistant Professor at Harvard Medical School (HMS), and the Lead of the Data Management and Analysis Core (DMAC) of the Precision Vaccines Program (PVP) at Boston Children’s Hospital (BCH). She leads/co-investigates multiple NIH-funded programs in characterizing vaccine- and infection-induced immune responses using systems immunology approaches. She leads a team of data scientists under the Precision Vaccines Program who supports multiple international and multi-center consortia for clinical and data coordination, quality assurance protocols, and analyses of systems immunology profiling tools.

She led the "Immune Data Resource" under the Human Immunology Project Consortium, which is a compendium of curated systems vaccinology datasets with their corresponding immune responses from 53 cohorts and 24 different vaccines. Her academic productivity is exemplified by multiple first and co-authored publications in journals such as Science Immunology, Nature Immunology, Science Translational Medicine, Cell Reports, Frontiers in Immunology, mBio, and Vaccine, among many others, and have been highlighted in various media platforms.

Publications

  1. Longitudinal Meta-cohort study protocol using systems biology to identify vaccine safety biomarkers. Vaccine. 2025 Jul 26; 62:127504. View Abstract
  2. Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study. Front Med (Lausanne). 2025; 12:1604388. View Abstract
  3. MICBG406A polymorphism reduces risk of mechanical ventilation and death during viral acute lung injury. JCI Insight. 2025 Aug 08; 10(15). View Abstract
  4. Immune Development in Early Life (IDEaL) longitudinal cohort study protocol: Identifying biomarkers of vaccine responsiveness, respiratory infection, and asthma. J Allergy Clin Immunol Glob. 2025 Nov; 4(4):100517. View Abstract
  5. Empiric Azithromycin in COVID-19 Impacts the Respiratory Microbiome and Antimicrobial Resistome without Anti-inflammatory Benefit. Res Sq. 2025 Jun 20. View Abstract
  6. Type 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort. J Allergy Clin Immunol Glob. 2025 Nov; 4(4):100515. View Abstract
  7. Airway Immune Signatures in Severe and Fatal Infection with COVID-19. Am J Respir Cell Mol Biol. 2025 Jun; 72(6):708-712. View Abstract
  8. Patients Hospitalized with COVID-19 Demonstrate Distinct Plasma Cytokine and Chemokine Concentrations in vivo and TLR-Mediated Cytokine and Chemokine Production in Whole Blood in vitro. J Innate Immun. 2025; 17(1):288-301. View Abstract
  9. High affinity CD16 polymorphism associated with reduced risk of severe COVID-19. JCI Insight. 2025 May 22. View Abstract
  10. Minimalistic Transcriptomic Signatures Permit Accurate Early Prediction of COVID-19 Mortality. medRxiv. 2025 May 19. View Abstract
  11. Correction: Respiratory infection- and asthma-prone, low vaccine responder children demonstrate distinct mononuclear cell DNA methylation pathways. Clin Epigenetics. 2025 Mar 28; 17(1):53. View Abstract
  12. Network analysis reveals protein modules associated with childhood respiratory diseases. J Allergy Clin Immunol. 2025 Mar 06. View Abstract
  13. An Allele of the MTHFR one-carbon metabolism gene predicts severity of COVID-19. medRxiv. 2025 Mar 03. View Abstract
  14. Identification of a multi-omics factor predictive of long COVID in the IMPACC study. bioRxiv. 2025 Feb 14. View Abstract
  15. Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors. medRxiv. 2025 Feb 13. View Abstract
  16. Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients. Nat Commun. 2025 Jan 10; 16(1):586. View Abstract
  17. Biomarkers of vaccine safety and efficacy in vulnerable populations: Lessons from the fourth international precision vaccines conference. Vaccine. 2025 Jan 01; 43(Pt 2):126477. View Abstract
  18. Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping. bioRxiv. 2024 Nov 25. View Abstract
  19. Chronic Viral Reactivation and Associated Host Immune Response and Clinical Outcomes in Acute COVID-19 and Post-Acute Sequelae of COVID-19. bioRxiv. 2024 Nov 16. View Abstract
  20. Predictive gene expression signature diagnoses neonatal sepsis before clinical presentation. EBioMedicine. 2024 Dec; 110:105411. View Abstract
  21. The BNT162b2 mRNA vaccine demonstrates reduced age-associated TH1 support in vitro and in vivo. iScience. 2024 Nov 15; 27(11):111055. View Abstract
  22. Plasma adenosine deaminase-1 and -2 activities are lower at birth in Papua New Guinea than in The Gambia but converge over the first weeks of life. Front Immunol. 2024; 15:1425349. View Abstract
  23. DNA Methylation signatures underpinning blood neutrophil to lymphocyte ratio during first week of human life. Nat Commun. 2024 Sep 17; 15(1):8167. View Abstract
  24. Breastfeeding and Neonatal Age Influence Neutrophil-Driven Ontogeny of Blood Cell Populations in the First Week of Human Life. J Immunol Res. 2024; 2024:1117796. View Abstract
  25. Respiratory infection- and asthma-prone, low vaccine responder children demonstrate distinct mononuclear cell DNA methylation pathways. Clin Epigenetics. 2024 Jul 03; 16(1):85. View Abstract
  26. Network Analysis Reveals Protein Modules Associated with Childhood Respiratory Diseases. bioRxiv. 2024 Jun 17. View Abstract
  27. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. J Clin Invest. 2024 May 01; 134(9). View Abstract
  28. Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology. Sci Transl Med. 2024 04 17; 16(743):eadj5154. View Abstract
  29. Respiratory Infection- and Asthma-prone, Low Vaccine Responder Children Demonstrate Distinct Mononuclear Cell DNA Methylation Pathways. Res Sq. 2024 Apr 03. View Abstract
  30. Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology. medRxiv. 2024 Feb 13. View Abstract
  31. Author Correction: Co-adjuvanting DDA/TDB liposomes with a TLR7 agonist allows for IgG2a/c class-switching in the absence of Th1 cells. NPJ Vaccines. 2024 Jan 11; 9(1):13. View Abstract
  32. IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. Nat Commun. 2024 Jan 09; 15(1):404. View Abstract
  33. Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nat Commun. 2024 01 03; 15(1):216. View Abstract
  34. Nucleotide, Phospholipid, and Kynurenine Metabolites Are Robustly Associated with COVID-19 Severity and Time of Plasma Sample Collection in a Prospective Cohort Study. Int J Mol Sci. 2023 Dec 26; 25(1). View Abstract
  35. Co-adjuvanting DDA/TDB liposomes with a TLR7 agonist allows for IgG2a/c class-switching in the absence of Th1 cells. NPJ Vaccines. 2023 Dec 22; 8(1):189. View Abstract
  36. Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients. Res Sq. 2023 Dec 20. View Abstract
  37. The Implication of Sphingolipids in Viral Infections. Int J Mol Sci. 2023 Dec 09; 24(24). View Abstract
  38. Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants. bioRxiv. 2023 Nov 06. View Abstract
  39. Corrigendum to "Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: results from the IMPACC study" [eBioMedicine 83 (2022) 104208]. EBioMedicine. 2023 Dec; 98:104860. View Abstract
  40. Relationship of Heterologous Virus Responses and Outcomes in Hospitalized COVID-19 Patients. J Immunol. 2023 10 15; 211(8):1224-1231. View Abstract
  41. The value of prospective metabolomic susceptibility endotypes: broad applicability for infectious diseases. EBioMedicine. 2023 Oct; 96:104791. View Abstract
  42. Effective early antiretroviral therapy in perinatal-HIV infection reduces subsequent plasma inflammatory profile. Pediatr Res. 2023 11; 94(5):1667-1674. View Abstract
  43. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell Rep Med. 2023 06 20; 4(6):101079. View Abstract
  44. Publisher Correction: Carbohydrate fatty acid monosulphate: oil-in-water adjuvant enhances SARS-CoV-2 RBD nanoparticle-induced immunogenicity and protection in mice. NPJ Vaccines. 2023 Mar 03; 8(1):30. View Abstract
  45. Carbohydrate fatty acid monosulphate: oil-in-water adjuvant enhances SARS-CoV-2 RBD nanoparticle-induced immunogenicity and protection in mice. NPJ Vaccines. 2023 Feb 14; 8(1):18. View Abstract
  46. The mRNA vaccine BNT162b2 demonstrates impaired TH1 immunogenicity in human elders in vitro and aged mice in vivo. Res Sq. 2022 Dec 21. View Abstract
  47. Reduced Steroid Metabolites Identify Infection-Prone Children in Two Independent Pre-Birth Cohorts. Metabolites. 2022 Nov 13; 12(11). View Abstract
  48. A single birth dose of Hepatitis B vaccine induces polyfunctional CD4+ T helper cells. Front Immunol. 2022; 13:1043375. View Abstract
  49. Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses. Nat Immunol. 2022 12; 23(12):1788-1798. View Abstract
  50. Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination. Nat Immunol. 2022 12; 23(12):1777-1787. View Abstract
  51. The Immune Signatures data resource, a compendium of systems vaccinology datasets. Sci Data. 2022 10 20; 9(1):635. View Abstract
  52. Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine. 2022 Sep; 83:104208. View Abstract
  53. Bacille Calmette-Guérin vaccine reprograms human neonatal lipid metabolism in vivo and in vitro. Cell Rep. 2022 05 03; 39(5):110772. View Abstract
  54. An aluminum hydroxide:CpG adjuvant enhances protection elicited by a SARS-CoV-2 receptor binding domain vaccine in aged mice. Sci Transl Med. 2022 Jan 26; 14(629):eabj5305. View Abstract
  55. Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study. Sci Immunol. 2021 08 10; 6(62). View Abstract
  56. Human Newborn Monocytes Demonstrate Distinct BCG-Induced Primary and Trained Innate Cytokine Production and Metabolic Activation In Vitro. Front Immunol. 2021; 12:674334. View Abstract
  57. Alum:CpG adjuvant enables SARS-CoV-2 RBD-induced protection in aged mice and synergistic activation of human elder type 1 immunity. bioRxiv. 2021 May 21. View Abstract
  58. Integrative Metabolomics to Identify Molecular Signatures of Responses to Vaccines and Infections. Metabolites. 2020 Nov 30; 10(12). View Abstract
  59. Corrigendum: Clinical Protocol for a Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea. Front Pediatr. 2020; 8:610461. View Abstract
  60. Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life. Front Immunol. 2020; 11:578505. View Abstract
  61. Towards Precision Vaccines: Lessons From the Second International Precision Vaccines Conference. Front Immunol. 2020; 11:590373. View Abstract
  62. A cloud-based bioinformatic analytic infrastructure and Data Management Core for the Expanded Program on Immunization Consortium. J Clin Transl Sci. 2020 Sep 22; 5(1):e52. View Abstract
  63. BCG vaccination-induced emergency granulopoiesis provides rapid protection from neonatal sepsis. Sci Transl Med. 2020 05 06; 12(542). View Abstract
  64. Clinical Protocol for a Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea. Front Pediatr. 2020; 8:197. View Abstract
  65. Phosphoric Metabolites Link Phosphate Import and Polysaccharide Biosynthesis for Candida albicans Cell Wall Maintenance. mBio. 2020 03 17; 11(2). View Abstract
  66. BCG as a Case Study for Precision Vaccine Development: Lessons From Vaccine Heterogeneity, Trained Immunity, and Immune Ontogeny. Front Microbiol. 2020; 11:332. View Abstract
  67. Licensed Bacille Calmette-Guérin (BCG) formulations differ markedly in bacterial viability, RNA content and innate immune activation. Vaccine. 2020 02 24; 38(9):2229-2240. View Abstract
  68. Immunometabolic approaches to prevent, detect, and treat neonatal sepsis. Pediatr Res. 2020 01; 87(2):399-405. View Abstract
  69. Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa. PLoS One. 2019; 14(9):e0222940. View Abstract
  70. Dynamic molecular changes during the first week of human life follow a robust developmental trajectory. Nat Commun. 2019 03 12; 10(1):1092. View Abstract
  71. Adjuvant Effect of Bacille Calmette-Guérin on Hepatitis B Vaccine Immunogenicity in the Preterm and Term Newborn. Front Immunol. 2018; 9:29. View Abstract
  72. Efficient tRNA degradation and quantification in Escherichia coli cell extract using RNase-coated magnetic beads: A key step toward codon emancipation. Biotechnol Prog. 2017 Sep; 33(5):1401-1407. View Abstract
  73. Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. BMC Genomics. 2015 May 06; 16:353. View Abstract
  74. The Arabidopsis At1g30680 gene encodes a homologue to the phage T7 gp4 protein that has both DNA primase and DNA helicase activities. BMC Plant Biol. 2013 Mar 04; 13:36. View Abstract

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