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Immport Dataset Available (21)
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HIPC Centers
Benaroya Research Institute (13)
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HIPC 1 (2010) (701)
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HIPC 3 (2022) (203)
Icahn School of Medicine at Mount Sinai (31)
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Stanford (68)
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Publication Keywords
Immport Dataset Available (21)
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Pickering H, Schaenman J, Phan HV, Maguire C, Tsitsiklis A, Rouphael N, Higuita NIA, Atkinson MA, Brakenridge S, Fung M, Messer W, Salehi-Rad R, Altman MC, Becker PM, Bosinger SE, Eckalbar W, Hoch A, Doni Jayavelu N, Kim-Schulze S, Jenkins M, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, ...
Nature communications
2025-01-10
PMID: 39794319
Adult
Aged
Antibodies, Viral
Chemokines
COVID-19
Female
Gene Expression Profiling
HIPC 1 (2010)
HIPC 2 (2015)
HIPC 3 (2022)
Host Microbial Interactions
Humans
Immunity, Innate
Male
Middle Aged
Organ Transplantation
Prospective Studies
SARS-CoV-2
Transplant Recipients
Yale University
Abstract:
Coronavirus disease 2019 (COVID-19) poses significant risks for solid organ transplant recipients, who have atypical but poorly characterized immune responses to infection. We aim to understand the host immunologic and microbial features of COVID-19 in transplant recipients by leveraging a prospective multicenter cohort of 86 transplant recipients age- and sex-matched with 172 non-transplant controls. We find that transplant recipients have higher nasal SARS-CoV-2 viral abundance and impaired viral clearance, and lower anti-spike IgG levels. In addition, transplant recipients exhibit decreased plasmablasts and transitional B cells, and increased senescent T cells. Blood and nasal transcriptional profiling demonstrate unexpected upregulation of innate immune signaling pathways and increased levels of several proinflammatory serum chemokines. Severe disease in transplant recipients, however, is characterized by a less robust induction of pro-inflammatory genes and chemokines. Together, our study reveals distinct immune features and altered viral dynamics in solid organ transplant recipients.
Cortese M, Hagan T, Rouphael N, Wu SY, Xie X, Kazmin D, Wimmers F, Gupta S, van der Most R, Coccia M, Aranuchalam PS, Nakaya HI, Wang Y, Coyle E, Horiuchi S, Wu H, Bower M, Mehta A, Gunthel C, Bosinger SE, Kotliarov Y, Cheung F, Schwartzberg PL, Germain RN, Tsang J, ...
Nature immunology
2025-01-01
PMID: 39747435
Adjuvants, Immunologic
Adult
Antibodies, Viral
Antibody Formation
Blood Platelets
Female
HIPC 3 (2022)
Humans
Influenza, Human
Influenza Vaccines
Male
Megakaryocytes
Plasma Cells
Stanford
Vaccinology
Abstract:
We performed a systems vaccinology analysis to investigate immune responses in humans to an H5N1 influenza vaccine, with and without the AS03 adjuvant, to identify factors influencing antibody response magnitude and durability. Our findings revealed a platelet and adhesion-related blood transcriptional signature on day 7 that predicted the longevity of the antibody response, suggesting a potential role for platelets in modulating antibody response durability. As platelets originate from megakaryocytes, we explored the effect of thrombopoietin (TPO)-mediated megakaryocyte activation on antibody response longevity. We found that TPO administration enhanced the durability of vaccine-induced antibody responses. TPO-activated megakaryocytes also promoted survival of human bone-marrow plasma cells through integrin β1/β2-mediated cell-cell interactions, along with survival factors APRIL and the MIF-CD74 axis. Using machine learning, we developed a classifier based on this platelet-associated signature, which predicted antibody response longevity across six vaccines from seven independent trials, highlighting a conserved mechanism for vaccine durability.
Mikelov A, Nefediev G, Tashkeev A, Rodriguez OL, Aguilar Ortmans D, Skatova V, Izraelson M, Davydov AN, Poslavsky S, Rahmouni S, Watson CT, Chudakov D, Boyd SD, Bolotin D
Genome research
2024-12-23
PMID: 39433438
Algorithms
Alleles
Genetic Variation
High-Throughput Nucleotide Sequencing
HIPC 3 (2022)
Humans
Receptors, Antigen, B-Cell
Receptors, Antigen, T-Cell
Sequence Analysis, DNA
Software
Stanford
Abstract:
Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci. Here, we present a novel algorithm for extrasensitive and specific variable (V) and joining (J) gene allele inference, allowing the reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput novel allele discovery from a wide variety of existing data sets. The developed algorithm is a part of the MiXCR software. We demonstrate the accuracy of this approach using AIRR-seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) AIRR-seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA and TRB) AIRR-seq data set, representing 134 individuals. This allowed us to assess the genetic diversity within the IGH, TRA, and TRB loci in different populations and to establish a database of alleles of V and J genes inferred from AIRR-seq data and their population frequencies with free public access through VDJ.online database.
Wang S, Myers AJ, Irvine EB, Wang C, Maiello P, Rodgers MA, Tomko J, Kracinovsky K, Borish HJ, Chao MC, Mugahid D, Darrah PA, Seder RA, Roederer M, Scanga CA, Lin PL, Alter G, Fortune SM, Flynn JL, Lauffenburger DA
Cell systems
2024-12-18
PMID: 39504969
Administration, Intravenous
Animals
BCG Vaccine
B-Lymphocytes
HIPC 3 (2022)
Immune System
Macaca
Macaca mulatta
Markov Chains
Massachusetts Institute of technology
Tuberculosis
Vaccination
Abstract:
Analysis of multi-modal datasets can identify multi-scale interactions underlying biological systems but can be beset by spurious connections due to indirect impacts propagating through an unmapped biological network. For example, studies in macaques have shown that Bacillus Calmette-Guerin (BCG) vaccination by an intravenous route protects against tuberculosis, correlating with changes across various immune data modes. To eliminate spurious correlations and identify critical immune interactions in a public multi-modal dataset (systems serology, cytokines, and cytometry) of vaccinated macaques, we applied Markov fields (MFs), a data-driven approach that explains vaccine efficacy and immune correlations via multivariate network paths, without requiring large numbers of samples (i.e., macaques) relative to multivariate features. We find that integrating multiple data modes with MFs helps remove spurious connections. Finally, we used the MF to predict outcomes of perturbations at various immune nodes, including an experimentally validated B cell depletion that induced network-wide shifts without reducing vaccine protection.
Dib SM, Wimalasena S, Graciaa DS, Rouphael N
The Journal of infectious diseases
2024-12-16
PMID: 39424292
HIPC 3 (2022)
Humans
Precision Medicine
Stanford
Systems Biology
Vaccination
Vaccines
Vaccine Development
Vaccinology
Abstract:
Systems vaccinology integrates a range of "omics" technologies to identify key immune signatures and enhance vaccine development. This approach aids in understanding variations in immune responses, driven by genetics, health status, and the microbiome. Consequently, systems vaccinology helps pave the way for personalized vaccination strategies, essential for addressing diverse populations.
Davis-Porada J, George AB, Lam N, Caron DP, Gray JI, Huang J, Hwu J, Wells SB, Matsumoto R, Kubota M, Lee Y, Morrison-Colvin R, Jensen IJ, Ural BB, Shaabani N, Weiskopf D, Grifoni A, Sette A, Szabo PA, Teijaro JR, Sims PA, Farber DL
Immunity
2024-12-10
PMID: 39510068
Adult
Aged
Aged, 80 and over
B-Lymphocytes
Columbia University
COVID-19
COVID-19 Vaccines
Female
HIPC 2 (2015)
HIPC 3 (2022)
Humans
Immunologic Memory
Lung
Lymphoid Tissue
Male
Memory T Cells
Middle Aged
SARS-CoV-2
Spike Glycoprotein, Coronavirus
Vaccination
Young Adult
Abstract:
Memory T and B cells in tissues are essential for protective immunity. Here, we performed a comprehensive analysis of the tissue distribution, phenotype, durability, and transcriptional profile of COVID-19 mRNA vaccine-induced immune memory across blood, lymphoid organs, and lungs obtained from 63 vaccinated organ donors aged 23-86, some of whom experienced SARS-CoV-2 infection. Spike (S)-reactive memory T cells were detected in lymphoid organs and lungs and variably expressed tissue-resident markers based on infection history, and S-reactive B cells comprised class-switched memory cells resident in lymphoid organs. Compared with blood, S-reactive tissue memory T cells persisted for longer times post-vaccination and were more prevalent with age. S-reactive T cells displayed site-specific subset compositions and functions: regulatory cell profiles were enriched in tissues, while effector and cytolytic profiles were more abundant in circulation. Our findings reveal functional compartmentalization of vaccine-induced T cell memory where surveilling effectors and in situ regulatory responses confer protection with minimal tissue damage.
Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver CM, Aguayo-Mazzucato C, Baker DJ, Bernlohr DA, Jurk D, Mangarova DB, Quardokus EM, Enninga EAL, Schmidt EL, Chen F, Duncan FE, Cambuli F, Kaur G, Kuchel GA, ...
Nature reviews. Molecular cell biology
2024-12-01
PMID: 38831121
Animals
Biomarkers
Cellular Senescence
HIPC 1 (2010)
HIPC 2 (2015)
HIPC 3 (2022)
Humans
Mice
Organ Specificity
Yale University
Abstract:
Once considered a tissue culture-specific phenomenon, cellular senescence has now been linked to various biological processes with both beneficial and detrimental roles in humans, rodents and other species. Much of our understanding of senescent cell biology still originates from tissue culture studies, where each cell in the culture is driven to an irreversible cell cycle arrest. By contrast, in tissues, these cells are relatively rare and difficult to characterize, and it is now established that fully differentiated, postmitotic cells can also acquire a senescence phenotype. The SenNet Biomarkers Working Group was formed to provide recommendations for the use of cellular senescence markers to identify and characterize senescent cells in tissues. Here, we provide recommendations for detecting senescent cells in different tissues based on a comprehensive analysis of existing literature reporting senescence markers in 14 tissues in mice and humans. We discuss some of the recent advances in detecting and characterizing cellular senescence, including molecular senescence signatures and morphological features, and the use of circulating markers. We aim for this work to be a valuable resource for both seasoned investigators in senescence-related studies and newcomers to the field.
Maguire C, Chen J, Rouphael N, Pickering H, Phan HV, Glascock A, Chu V, Dandekar R, Corry D, Kheradmand F, Baden LR, Selaky R, McComsey GA, Haddad EK, Cairns CB, Pulendran B, Fernandez-Sesma A, Simon V, Metcalf JP, Higuita NIA, Messer WB, David MM, Nadeau KC, Kraft M, Bime C, ...
bioRxiv : the preprint server for biology
2024-11-16
PMID: 39605478
HIPC 1 (2010)
HIPC 2 (2015)
HIPC 3 (2022)
Yale University
Abstract:
Chronic viral infections are ubiquitous in humans, with individuals harboring multiple latent viruses that can reactivate during acute illnesses. Recent studies have suggested that SARS-CoV-2 infection can lead to reactivation of latent viruses such as Epstein-Barr Virus (EBV) and cytomegalovirus (CMV), yet, the extent and impact of viral reactivation in COVID-19 and its effect on the host immune system remain incompletely understood. Here we present a comprehensive multi-omic analysis of viral reactivation of all known chronically infecting viruses in 1,154 hospitalized COVID-19 patients, from the Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study, who were followed prospectively for twelve months. We reveal significant reactivation of Herpesviridae, Enteroviridae, and Anelloviridae families during acute stage of COVID-19 (0-40 days post-hospitalization), each exhibiting distinct temporal dynamics. We also show that viral reactivation correlated with COVID-19 severity, demographic characteristics, and clinical outcomes, including mortality. Integration of cytokine profiling, cellular immunophenotyping, metabolomics, transcriptomics, and proteomics demonstrated virus-specific host responses, including elevated pro-inflammatory cytokines (e.g. IL-6, CXCL10, and TNF), increased activated CD4+ and CD8+ T-cells, and upregulation of cellular replication genes, independent of COVID-19 severity and SARS-CoV-2 viral load. Notably, persistent Anelloviridae reactivation during convalescence (≥3 months post-hospitalization) was associated with Post-Acute Sequelae of COVID-19 (PASC) symptoms, particularly physical function and fatigue. Our findings highlight a remarkable prevalence and potential impact of chronic viral reactivation on host responses and clinical outcomes during acute COVID-19 and long term PASC sequelae. Our data provide novel immune, transcriptomic, and metabolomic biomarkers of viral reactivation that may inform novel approaches to prognosticate, prevent, or treat acute COVID-19 and PASC.
Moore AR, Zheng H, Ganesan A, Hasin-Brumshtein Y, Maddali MV, Levitt JE, van der Poll T, Scicluna BP, Giamarellos-Bourboulis EJ, Kotsaki A, Martin-Loeches I, Garduno A, Rothman RE, Sevransky J, Wright DW, Atreya MR, Moldawer LL, Efron PA, Marcela K, Karvunidis T, Giannini HM, Meyer NJ, Sweeney TE, Rogers AJ, Khatri P
bioRxiv : the preprint server for biology
2024-11-15
PMID: 39605502
HIPC 3 (2022)
Stanford
Abstract:
Progress in the management of critical care syndromes such as sepsis, Acute Respiratory Distress Syndrome (ARDS), and trauma has slowed over the last two decades, limited by the inherent heterogeneity within syndromic illnesses. Numerous immune endotypes have been proposed in sepsis and critical care, however the overlap of the endotypes is unclear, limiting clinical translation. The SUBSPACE consortium is an international consortium that aims to advance precision medicine through the sharing of transcriptomic data. By evaluating the overlap of existing immune endotypes in sepsis across over 6,000 samples, we developed cell-type specific signatures to quantify dysregulation in these immune compartments. Myeloid and lymphoid dysregulation were associated with disease severity and mortality across all cohorts. This dysregulation was not only observed in sepsis but also in ARDS, trauma, and burn patients, indicating a conserved mechanism across various critical illness syndromes. Moreover, analysis of randomized controlled trial data revealed that myeloid and lymphoid dysregulation is linked to differential mortality in patients treated with anakinra or corticosteroids, underscoring its prognostic and therapeutic significance. In conclusion, this novel immunology-based framework for quantifying cellular compartment dysregulation offers a valuable tool for prognosis and therapeutic decision-making in critical illness.
Brook B, Checkervarty AK, Barman S, Sweitzer C, Bosco AN, Sherman AC, Baden LR, Morrocchi E, Sanchez-Schmitz G, Palma P, Nanishi E, O'Meara TR, McGrath ME, Frieman MB, Soni D, van Haren SD, Ozonoff A, Diray-Arce J, Steen H, Dowling DJ, Levy O
iScience
2024-11-15
PMID: 39569372
HIPC 2 (2015)
Abstract:
mRNA vaccines demonstrate impaired immunogenicity and durability in vulnerable older populations. We hypothesized that human in vitro modeling and proteomics could elucidate age-specific mRNA vaccine actions. BNT162b2-stimulation changed the plasma proteome of blood samples from young (18-50Y) and older adult (≥60Y) participants, assessed by mass spectrometry, proximity extension assay, and multiplex. Young adult up-regulation (e.g., PSMC6, CPN1) contrasted reduced induction in older adults (e.g., TPM4, APOF, APOC2, CPN1, PI16). 30-85% lower TH1-polarizing cytokines and chemokines were induced in elderly blood (e.g., IFNγ, CXCL10). Analytes lower in older adult samples included human in vivo mRNA immunogenicity biomarkers (e.g., IFNγ, CXCL10, CCL4, IL-1RA). BNT162b2 also demonstrated reduced CD4+ TH1 responses in aged vs. young adult mice. Our study demonstrates the utility of human in vitro platforms modeling age-specific mRNA vaccine immunogenicity, highlights impaired support of TH1 polarization in older adults, and provides a rationale for precision mRNA vaccine adjuvantation to induce greater immunogenicity.
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