DR29 DataRelease

SDY570: UT_SSc
Status: New
Description: HLA Genotyping
Program/Contract:
ProgramContract
HLA Region Genetics in Immune-mediated Diseases II Studies of HLA Region Genomics in Systemic Sclerosis and Ankylosing Spondyilitis
DOI: 10.21430/M3IJD4LQR5
Subjects: 997
Study PI, contact:
NameOrganizationSite
Xiaodong Zhou UT Health University of Texas Health Science Center
Publications:
Association of the HLA-DRB1 with scleroderma in Chinese population.. PLoS One. Sep 2014. doi: 10.1371/journal.pone.0106939. eCollection 2014. [Pubmed: 25184637]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
HLA Typing 997
Clinical Assessments:None
SDY857: Prevention of Cardiac Allograft Vasculopathy Using Rituximab (Rituxan) Therapy in Cardiac Transplantation
Status: New
Description: All people who have a heart transplant are at risk for developing cardiac allograft vasculopathy (CAV). CAV means narrowing of the heart transplant vessels, which is associated with poor heart transplant function. People who develop antibodies after transplant have a higher risk of developing CAV. Infections, high cholesterol, and rejection also increase the risk of developing CAV. People who develop CAV usually have to receive another transplant. The purpose of this research study is to see if a study drug called Rituximab prevents CAV. Rituximab destroys certain types of white blood cells called B cells. B cells are important cells in the immune system that help the body fight infection by producing substances called antibodies. B cells and the antibodies they produce are also involved in some kinds of rejection after organ transplantation. Rituximab decreases the number of B cells in the blood and other tissues. The goal of this study is to determine if decreasing B cells with Rituximab can prevent injury to the transplanted heart.
Program/Contract:
ProgramContract
Clinical Trials in Organ Transplantation (CTOT) NOVEL THERAPIES OF CHRONIC ALLOGRAFT DYSFUNCTION (CTOT-02)
DOI: 10.21430/M33887D0YT
Subjects: 362
Study PI, contact:
NameOrganizationSite
Mohamed Sayegh Brigham and Women's Hospital Brigham and Women's Hospital
Publications:None
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT01278745]
Assays:None
Clinical Assessments:
Biopsy
Echocardiogram
SDY903: Human Immune Signature of Zika virus infection
Status: New
Description: The human Immune Signature of Zika virus infection was studied in a Zika endemic area, Brazil. T cell responses were compared in acute infected patients as well as convalescent patients.
Program/Contract:
ProgramContract
Human Immunology Project Consortium 2 (HIPC2) Human immune signatures of dengue virus and mycobacterium tuberculosis exposure in infection; disease and vaccination (HIPC2)
DOI: 10.21430/M340DHRY4Y
Subjects: 29
Study PI, contact:
NameOrganizationSite
Daniela Weiskopf La Jolla Institute for Allergy and Immunology La Jolla Institute for Allergy and Immunology
Publications:None
Resources:
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 72
HLA Typing 29
RNA sequencing 60
Clinical Assessments:None
SDY960: Viral Triggers in Pediatric Lung Transplantation
Status: New
Description: This is a non-randomized observational study to determine whether respiratory viral infections increase the risk of bronchiolitis obliterans syndrome, obliterative bronchiolitis, death or retransplantation in pediatric lung transplant recipients. Comprehensive molecular viral detection will be performed on nasopharyngeal swabs and BAL fluid. Recipient biopsy samples, BAL, serum and PBMC will be obtained at the timepoints outlined in Appendix 1 to assess viral infection, innate immune activity, and adaptive cellular and humoral immunity. Donor specimens (lymph nodes, spleen or blood) will be collected at transplant for use in cellular immune assays.
Program/Contract:
ProgramContract
Clinical Trials in Organ Transplantation in Children (CTOT-C) DEVELOPMENT OF TRANSPLANT STRATEGIES UNIQUELY RESPONSIVE TO THE NEEDS OF CHILDREN (CTOTC-02)
Clinical Trials in Organ Transplantation in Children (CTOT-C) VIRAL TRIGGERS OF ALLOIMMUNITY AND AUTOIMMUNITY IN PEDIATRIC LUNG TRANSPLANTATION (CTOTC-03)
DOI: 10.21430/M3Z0LCNUGG
Subjects: 78
Study PI, contact:
NameOrganizationSite
Stuart Sweet Washington University School of Medicine Washington University School of Medicine
Publications:
Role of Circulating MicroRNAs in the Immunopathogenesis of Rejection After Pediatric Lung Transplantation.. Transplantation. Oct 2017. doi: 10.1097/TP.0000000000001595. [Pubmed: 27941431]
None. None None None. doi: None [Pubmed: 28639398]
Anellovirus loads are associated with outcomes in pediatric lung transplantation.. Pediatr Transplant. Feb 2018. doi: /petr.13069. Epub 2017 Oct 29. [Pubmed: 29082660]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT00891865]
Assays:
Assay TypeNumber of Exp. Samples
Other 244
Clinical Assessments:
Adolescent Medication Barriers Scale
Biopsy
Parent Medication Barriers Scale
SDY1092: Transcriptional responses induced by controlled human malaria infection (CHMI)
Status: New
Description: Whole blood RNA-Seq was applied to investigate gene expression kinetics in Tanzanian males who underwent controlled malaria infection by intradermal injection with aseptic, purified, cryopreserved Plasmodium falciparum sporozoites. Building on PfSPZ challenge study: ClinicalTrials.gov Identifier: NCT01540903, PUBMED:PMC4155546
Program/Contract:
ProgramContract
Human Immunology Project Consortium 1 (HIPC1) Immune Profile and Network Analysis of Malaria Infection and Vaccination
DOI: 10.21430/M32AARFE8U
Subjects: 10
Study PI, contact:
NameOrganizationSite
Stephen Hoffman Sanaria Inc. Bagamoyo Clinical Trial Unit (BCTU) of the Ifakara Health Institute (IHI)
Publications:
Controlled human malaria infection of Tanzanians by intradermal injection of aseptic, purified, cryopreserved Plasmodium falciparum sporozoites.. Am J Trop Med Hyg. Sep 2014. doi: 10.4269/ajtmh.14-0119. Epub 2014 Jul 28. [Pubmed: 25070995]
Resources:
ClinicalTrials.gov https://www.clinicaltrials.gov/ct2/show/NCT01540903]
Assays:
Assay TypeNumber of Exp. Samples
RNA sequencing 40
Clinical Assessments:None
SDY1095: A Retrospective Multicenter Study to Determine 4-Year Clinical Outcomes in Subjects Previously Enrolled in the CTOT-05 Study
Status: New
Description: This study is a multicenter, non-randomized, retrospective study to collect long term (4 years post-transplant) clinical outcome data on subjects previously enrolled in the CTOT-05 study.
Program/Contract:
ProgramContract
Clinical Trials in Organ Transplantation (CTOT) NONINVASIVE MARKERS AND TRANSPLANT OUTCOME IN HUMANS (CTOT-01, CTOT-05)
DOI: 10.21430/M34I2CELSW
Subjects: 180
Study PI, contact:
NameOrganizationSite
Peter Heeger Mount Sinai School of Medicine, Ricanati Miller Transplant Institute Mount Sinai School of Medicine,
Publications:
Multicenter Analysis of Immune Biomarkers and Heart Transplant Outcomes: Results of the Clinical Trials in Organ Transplantation-05 Study.. Am J Transplant. Jan 2016. doi: 10.1111/ajt.13422. Epub 2015 Aug 10. [Pubmed: 26260101]
None. None None None. doi: None [Pubmed: 30549425]
Resources:
ClinicalTrials.gov https://www.clinicaltrials.gov/ct2/show/NCT02255123]
Assays:None
Clinical Assessments:
Death
Graft Function
SDY1119: Systems Biology of 2011 trivalent Influenza vaccine (TIV) in young and elderly individuals, healthy or with T2D (see companion study SDY61 2007, SDY270 2009, SDY56 2010)
Status: New
Description: Blood samples will be collected at days 0 (pre-vaccination) and 3,7,30,180 after vaccination. Peripheral blood mononuclear cells
Program/Contract:
ProgramContract
Human Immunology Project Consortium 1 (HIPC1) Systems Biological Analysis of Innate and Adaptive Responses to Vaccination
DOI: 10.21430/M3ZU72TO6V
Subjects: 78
Study PI, contact:
NameOrganizationSite
Bonnie Blomberg University of Miami UM Miller School of Medicine
Publications:
Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures. Immunity Dec 2015. doi: 10.1016/j.immuni.2015.11.012 [Pubmed: 26682988]
Resources:
Additional grant support http://grantome.com/grant/NIH/R01-AG032576-04]
Assays:
Assay TypeNumber of Exp. Samples
DNA microarray 177
Hemagglutination Inhibition 468
Clinical Assessments:None
SDY1294: A Systems Vaccinology Approach Reveals Temporal Transcriptomic Changes of Immune Responses to the Yellow Fever 17D Vaccine.
Status: New
Description: In this study, we used a systems vaccinology approach to identify temporal changes in immune response signatures to the yellow fever (YF)-17D vaccine, with the aim of comprehensively characterizing immune responses associated with protective immunity. We conducted a cohort study in which 21 healthy subjects in China were administered one dose of the YF-17D vaccine; PBMCs were collected at 0 h and then at 4 h and days 1, 2, 3, 5, 7, 14, 28, 84, and 168 postvaccination, and analyzed by transcriptional profiling and immunological assays. At 4 h postvaccination, genes associated with innate cell differentiation and cytokine pathways were dramatically downregulated, whereas receptor genes were upregulated, compared with their baseline levels at 0 h. Immune response pathways were primarily upregulated on days 5 and 7, accompanied by the upregulation of the transcriptional factors JUP, STAT1, and EIF2AK2. We also observed robust activation of innate immunity within 2 d postvaccination and a durable adaptive response, as assessed by transcriptional profiling. Coexpression network analysis indicated that lysosome activity and lymphocyte proliferation were associated with dendritic cell (DC) and CD4+ T cell responses; FGL2, NFAM1, CCR1, and TNFSF13B were involved in these associations. Moreover, individuals who were baseline-seropositive for Abs against another flavivirus exhibited significantly impaired DC, NK cell, and T cell function in response to YF-17D vaccination. Overall, our findings indicate that YF-17D vaccination induces a prompt innate immune response and DC activation, a robust Ag-specific T cell response, and a persistent B cell/memory B cell response.
Program/Contract:
ProgramContract
DOI: 10.21430/M3LT8WVHVH
Subjects: 21
Study PI, contact:
NameOrganizationSite
Yiming Shao Chinese Center for Disease Control and Prevention State Key Laboratory of Infectious Disease Prevention and Control
Publications:
A Systems Vaccinology Approach Reveals Temporal Transcriptomic Changes of Immune Responses to the Yellow Fever 17D Vaccine.. Journal of Immunology August 2017. doi: https://doi.org/10.4049/jimmunol.1700083 [Pubmed: 28687661]
Resources:
Publication http://www.jimmunol.org/content/199/4/1476.long]
NCBI GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82152]
Assays:
Assay TypeNumber of Exp. Samples
Transcription profiling by array 109
Clinical Assessments:None
SDY1295: Perceived Barriers to Patient Adherence after Pediatric Solid Organ Transplantation
Status: New
Description: This is a two part prospective, observational, multi-center cohort study of SOT recipients. The first part is a cross sectional comparison of perceived barriers to adherence to post-transplant immunosuppressant regimens in parents of children (0-11 years) versus adolescents (12-21 years). The second is a longitudinal study to evaluate whether perceived barriers to adherence increase with time during the first year following transplantation.
Program/Contract:
ProgramContract
Clinical Trials in Organ Transplantation in Children (CTOT-C) DEVELOPMENT OF TRANSPLANT STRATEGIES UNIQUELY RESPONSIVE TO THE NEEDS OF CHILDREN (CTOTC-02)
Clinical Trials in Organ Transplantation in Children (CTOT-C) VIRAL TRIGGERS OF ALLOIMMUNITY AND AUTOIMMUNITY IN PEDIATRIC LUNG TRANSPLANTATION (CTOTC-03)
DOI: 10.21430/M3VRZ0ZS5P
Subjects: 502
Study PI, contact:
NameOrganizationSite
Stuart Sweet Washington University School of Medicine Washington University School of Medicine
Publications:
Perceived barriers to medication adherence in pediatric and adolescent solid organ transplantation.. Pediatr Transplant. Mar 2016. doi: 10.1111/petr.12648. Epub 2015 Dec 16. [Pubmed: 26670870]
Resources:
ClinicalTrials.gov https://www.clinicaltrials.gov/ct2/show/NCT01370746]
Assays:None
Clinical Assessments:None
SDY1371: Profiling of NK cell ligands on moocytes infected with Influenza A virus
Status: New
Description: Goal for the study was to identify NK cell ligands regulated by influenza A virus infection. More specifically we asked whether A/California/07/2009 or A/Victoria/361/2011 virus influenza A viruses differentially modulate NK cell ligands. Using 9 healthy Stanford blood bank donors, we isolated monocytes and NK cells. Monocytes were infected for 1 hr, followed by co-culture with NK cells for 6 or 23 hr hours. Brefeldin adn Monenin were added for the last 4 hours. They were then stained with a CyTOF panel and run on a Helios Mass cytometer. Two major ligands we found that contributed to the variance between the two strains were CD54 and CD112.
Program/Contract:
ProgramContract
Cooperative Centers on Human Immunology Adaptive And Innate Immunity, Memory And Repertoire In Vaccination And Infection
2013 NIH Director's New Innovator Award Program (DP2) Harnessing Natural Killer Cell Memory To Fight Viruses
DOI: 10.21430/M3KPGT3BYF
Subjects: 9
Study PI, contact:
NameOrganizationSite
Lisa Kronstad Stanford University Stanford University
Publications:
None. None None None. doi: None [Pubmed: 30143589]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
CyTOF 107
Clinical Assessments:None
SDY1387: Mechanisms Underlying Asthma Exacerbations Prevented and Persistent With Immune-Based Therapy
Status: New
Description: ICAC-29/MUPPITS-1 is a prospective, longitudinal, nested case-control study designed to identify changes in gene transcription predictive of and associated with asthma exacerbations in children ages 6 to 17 years with difficult-to-control, exacerbation-prone asthma. Participants will be followed prospectively for the onset of a cold and a subsequent asthma exacerbation. An internet-based asthma and cold symptom diary will be accessed by participants using a hand-held device. When the participant reports development of a cold, a clinic visit will be scheduled as soon as possible (within 48 hours of cold symptom onset) to collect blood and nasal samples. A second clinic visit will occur 4-6 days from the onset of cold symptoms to obtain samples after the initial cold, but prior to the use of systemic corticosteroids. Participants will be followed for up to two colds or approximately 6 months after Visit 0, whichever comes first.
Program/Contract:
ProgramContract
DOI: 10.21430/M3Q1C6388O
Subjects: 227
Study PI, contact:
NameOrganizationSite
Daniel Jackson University of Wisconsin University of Wisconsin
Matthew Altman University of Wisconsin University of Wisconsin
Publications:None
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT02502890]
Assays:None
Clinical Assessments:None
SDY1389: Lymph node reservoirs for long-lived memory T cells
Status: New
Description: Translating studies on T cell function and modulation from mouse models to humans requires extrapolating in vivo results on mouse T cell responses in lymphoid organs (spleen and lymph nodes) to human peripheral blood T cells. However, our understanding of T cell responses in human lymphoid sites and their relation to peripheral blood remains sparse. Here, we used a unique human tissue resource to study human T cells in different anatomical compartments within individual donors, and identify a subset of memory CD8+T cells in LN which maintain a distinct differentiation and functional profile compared to memory CD8+T cells in blood, spleen, bone marrow (BM), and lungs. Whole transcriptome and high dimensional CyTOF profiling reveals that LN memory CD8+T cells express signatures of quiescence and self-renewal compared to corresponding populations in blood, spleen, BM and lung. LN memory T cells exhibit a distinct transcriptional signature including expression of stem cell-associated transcription factors TCF-1, LEF-1, T-follicular helper cell markers CXCR5, and CXCR4, and reduced expression of effector molecules. LN memory T cells display high homology to a subset of mouse CD8+T cells identified in chronic infection models which responds to checkpoint blockade immunotherapy. Functionally, human LN memory T cells exhibit increased proliferation to T cell receptor (TCR)-mediated stimulation and maintain higher TCR clonal diversity compared to memory T cells from blood and other sites. These findings establish human LN as reservoirs for memory T cells with high capacities for expansion and diverse recognition and important targets for immunotherapies.
Program/Contract:
ProgramContract
Tissue compartmentalization of human lymphocytes P01AI106697 Tissue compartmentalization of human lymphocytes
Human Immunology Project Consortium 2 (HIPC2) Human Anti-Viral Immune Responses In Tissues And Circulation
DOI: 10.21430/M3NBGEA98C
Subjects: 51
Study PI, contact:
NameOrganizationSite
Donna Farber Columbia University Columbia University Medical Center
Publications:
Human Lymph Nodes Maintain TCF-1hi Memory T Cells with High Functional Potential and Clonal Diversity throughout Life.. J Immunol Oct 2018. doi: 10.4049/jimmunol.1800716 [Pubmed: 30111633]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
CyTOF 15
Flow Cytometry 348
RNA sequencing 12
Clinical Assessments:None
SDY1390: CRISPR-Cas9 Engineering in Primary Cell Protocol
Status: New
Description: A detailed, peer-reviewed protocol published in Nature Protocols for optimizing CRISPR-Cas9 editing pipelines to primary cell types. A detailed example is provided for editing primary CD4+ T cells to identify HIV host factors.
Program/Contract:
ProgramContract
Human Immunology Project Consortium 2 (HIPC2) Dengue Human Immunology Project Consortium (DHIPC MSSM)
DOI: 10.21430/M3R9N6OS6C
Subjects: 0
Study PI, contact:
NameOrganizationSite
Judd Hultquist J. David Gladstone Institutes Gladstone Institutes
Publications:None
Resources:
Assays:None
Clinical Assessments:None
SDY1401: Lack of detection of a human placenta microbiome in samples from preterm and term deliveries
Status: New
Description: Historically the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences, which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples
Program/Contract:
ProgramContract
March of Dimes March of Dimes Human Microbiome
DOI: 10.21430/M3BCUKEU3X
Subjects: 40
Study PI, contact:
NameOrganizationSite
Frederic Bushman University of Pennsylvania School of Medicine University of Pennsylvania School of Medicine
Publications:None
Resources:
Assays:
Assay TypeNumber of Exp. Samples
16S rRNA gene sequencing 320
Sequencing 180
Clinical Assessments:
Pregancy Characteristics
SDY1409: MaHPIC: Host M. mulatta infected with homologous and heterologous strains of P. cynomolgi
Status: New
Description: Experiment 23 (Initial challenge with P. cynomolgi B strain) - Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for about 100 days, with pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. During the 100-day period subjects experienced periods of patent and sub-patent infection. The anti-malarial drug artemether was subcuratively administered to subjects after the initial peak of infection, if subjects were not able to self-resolve. Blood-stage curative artemether was administered to all subjects following peak infection, and following a period of relapse infection. All peaks were clinically determined for each subject. The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as 'Experiment 23'. This is an iteration of Experiment 04 with the same parasite-host combination and sampling and treatment adjustments made, and this is the first in a series of experiments that includes subsequent homologous (Experiment 24, P. cynomolgi B strain) and heterologous (Experiment 25, P. cynomolgi strain ceylonensis) challenges of individuals from the Experiment 23 cohort. One subject was not included in subsequent experiments due to persistent behavioral issues that prevented sample collection.

Experiment 24 (Homologous challenge with P. cynomolgi B strain) - Male rhesus macaques (Macaca mulatta), cleared of previous infection with P. cynomolgi B strain via treatment with the anti-malarial drugs artemether, chloroquine, and primaquine, approximately five years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, and metabolomic measurements. The experiment included, 1 pre-inoculation day, 35 experiment days, and 10 post-experiment days. The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood samples were collected at three time points for functional genomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as 'Experiment 24'. This is the second in a series of experiments that includes infection of malaria-naive subjects (Experiment 23, P. cynomolgi B strain) and heterologous challenge (Experiment 25, P. cynomolgi strain ceylonensis) for the individuals from the same cohort.

Experiment 25 (Heterologous challenge with P. cynomolgi strain ceylonensis) - Male rhesus macaques (Macaca mulatta), cleared of previous infection with P. cynomolgi B strain via treatment with the anti-malarial drugs artemether, chloroquine, and primaquine, approximately five years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment included, 8 pre-inoculation days, 49 experiment days, and 4 post-experiment days. The anti-malarial drug artemether was subcuratively administered to subjects at the initial peak of infection, if subjects were not able to self-resolve their parasitemias. Peak infection was determined clinically for each subject. The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood samples were collected at five time points for functional genomic, lipidomic, proteomic, and immunological analyses. Within the MaHPIC, this project is known as 'Experiment 25'. This is the third and final of a series of experiments that includes infection of malaria-naive subjects (Experiment 23, P. cynomolgi B strain) and homologous challenge (Experiment 24, P. cynomolgi B strain) of individuals from the same cohort.

These datasets were produced by Mary Galinski, Rabindra Tirouvanziam, and Tracey Lamb at Emory University. To access other publicly available results from 'E23', 'E24', 'E25', and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
Program/Contract:
ProgramContract
Systems Biology for Infectious Diseases Research Integrated Approach To Host-Pathogen Interactions
DOI: 10.21430/M3TSYO4T3L
Subjects: 6
Study PI, contact:
NameOrganizationSite
Mary Galinski Emory University N/A
Publications:None
Resources:
MaHPIC Project Website http://www.systemsbiology.emory.edu/]
MaHPIC Data Website http://plasmodb.org/plasmo/mahpic.jsp]
Assays:
Assay TypeNumber of Exp. Samples
Cytometric Bead Array Assay 82
ELISA 1117
Flow Cytometry 2253
Clinical Assessments:None
SDY1411: MaHPIC: Host M. mulatta infected with P. coatneyi
Status: New
Description: Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to all subjects at the initial peak of infection, one out of the five macaques received four additional subcurative treatments for subsequent recrudescence peaks. The experimental infection in one subject was ineffective but the macaque was followed-up for the same period of 100 days. The different clinical phases of the infection were clinically determined for each subject. Blood-stage curative doses of artemether were administered to all subjects at the end of the study. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as "Experiment 03". This dataset was produced by Mary Galinski, Rabindra Tirouvanziam, and Tracey Lamb at Emory University. To access other publicly available results from 'E03' and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
Program/Contract:
ProgramContract
Systems Biology for Infectious Diseases Research Integrated Approach To Host-Pathogen Interactions
DOI: 10.21430/M3J2FJIVPW
Subjects: 5
Study PI, contact:
NameOrganizationSite
Mary Galinski Emory University N/A
Publications:None
Resources:
MaHPIC Project Website http://www.systemsbiology.emory.edu/]
MaHPIC Data Website http://plasmodb.org/plasmo/mahpic.jsp]
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 530
Clinical Assessments:None
SDY1418: Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy
Status: New
Description: Biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy.
Program/Contract:
ProgramContract
March of Dimes March of Dimes Human Microbiome
DOI: 10.21430/M302L1ULGW
Subjects: 31
Study PI, contact:
NameOrganizationSite
Martin Angst Stanford University School of Medicine Stanford University School of Medicine
Brice Gaudilliere Stanford University School of Medicine Stanford University School of Medicine
Nima Aghaeepour Stanford University School of Medicine Stanford University School of Medicine
Publications:
Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinformatics July 2018. doi: https://doi.org/10.1093/bioinformatics/bty537 [Pubmed: 0]
Resources:
Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Pregnancy https://nalab.stanford.edu/multiomics-pregnancy/.]
Assays:None
Clinical Assessments:None
SDY1424: MaHPIC: Host Aotus nancymaae infected with P. vivax Brazil VII
Status: New
Description: Malaria-naive Aotus nancymaae were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. gambiae, An. stephensi, and An. freeborni) then profiled for clinical, hematological, parasitological, immunological, functional genomic, and metabolomic measurements. The experiment was performed for 121 days. The first inoculation attempt was virtually unsuccessful as only one of seven animals developed blood-stage infection. This animal was treated for the blood-stage infection. All animals were re-challenged approximately one month later. Upon re-challenge all animals developed blood-stage infections with similar parasitological kinetics. After infections became chronic, the anti-malarial drug artemether was administered to curatively treat blood-stage infections. No sub-curative treatments were administered during this study because none of the animals developed severe disease. At the end of the study, the anti-malarial drugs primaquine and chloroquine were administered to all animals for curative treatment of the liver and blood-stage infections, respectively. Venous blood samples were collected only on clinically determined 'timepoint' days for the measurement of CBCs, reticulocytes, parasitemias, and downstream omics and immunological analyses. Small sample volumes were collected daily or every other day for the measurement of parasitemia. Within the MaHPIC, this project is known as 'Experiment 15'. This dataset was produced by John Barnwell at the CDC. To access other publicly available results from E15 and other MaHPIC Experiments, including clinical results (specifics on drugs administered), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp. This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
Program/Contract:
ProgramContract
Systems Biology for Infectious Diseases Research Integrated Approach To Host-Pathogen Interactions
DOI: 10.21430/M32LN9GIBL
Subjects: 7
Study PI, contact:
NameOrganizationSite
Mary Galinski Emory University N/A
Publications:None
Resources:
MaHPIC Project Website http://www.systemsbiology.emory.edu/]
MaHPIC Data Website http://plasmodb.org/plasmo/mahpic.jsp]
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 135
Clinical Assessments:None
SDY1425: Optimization of Belatacept Usage As A Means of Avoiding CNI and steroids in Renal Transplantation
Status: New
Description: Dialysis or kidney transplant are the two ways to treat kidney failure. Transplant recipients have to take anti-rejection medications to prevent their immune system (the body's natural defense system against illness) from rejecting their new kidney. Most patients who undergo a kidney transplant must take these anti-rejection medications for the rest of their lives. Taking standard anti-rejection medications for a long time can cause serious side effects, including kidney damage. There would be a benefit to finding new anti-rejection medications that work just as well, but don't damage the kidney.
Program/Contract:
ProgramContract
DOI: 10.21430/M3W0NBNCXA
Subjects: 19
Study PI, contact:
NameOrganizationSite
Christian Larsen Emory University School of Medicine Emory University School of Medicine
Publications:
None. None None None. doi: None [Pubmed: 28556519]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT01436305]
Assays:None
Clinical Assessments:None
SDY1426: Prior dengue virus infection and risk of Zika: a pediatric cohort in Nicaragua
Status: New
Description: We describe the introduction of ZIKV into the Pediatric Dengue Cohort Study, a long-standing pediatric dengue cohort established in 2004 in Managua, Nicaragua, in which the DENV immune history of the participants is well-characterized. The incidence of symptomatic and inapparent ZIKV infections in 2016 was estimated, together with associated demographic risk factors. The effect of previous DENV infection on ZIKV infection and disease was also analyzed. Data are available upon request (eharris@berkeley.edu), as is required by the IRB-approved protocol for the Pediatric Dengue Cohort Study. The materials and data used in this study are covered by standard material transfer agreements.
Program/Contract:
ProgramContract
DOI: 10.21430/M3IBGBX9JO
Subjects: 0
Study PI, contact:
NameOrganizationSite
Eva Harris University of California, Berkeley University of California, Berkeley
Publications:None
Resources:
Assays:None
Clinical Assessments:None
SDY89: Systems Biology Analysis of the response to Licensed Hepatitis B Vaccine (Engerix-B) (see companion study SDY690)
Status: Updated
Description: This project will contribute to the overall vision and goals of this U19 by analyzing the role of adjuvants in the humoral response to hep B vaccination in healthy individuals.
Program/Contract:
ProgramContract
Human Immunology Project Consortium 1 (HIPC1) Systems Analysis Vaccine Responses in Healthy and Hyporesponsive Humans
DOI: 10.21430/M3AYWX8NOT
Subjects: 50
Study PI, contact:
NameOrganizationSite
Robert Coffman Dynavax Technologies Corporation Dynavax Technologies Corporation
Publications:
Demonstration of safety and enhanced seroprotection against hepatitis B with investigational HBsAg-1018 ISS vaccine compared to a licensed hepatitis B vaccine.. Vaccine. Mar 2012. doi: 10.1016/j.vaccine.2012.02.001. Epub 2012 Feb 14. [Pubmed: 22342916]
Immunogenicity and safety of an investigational hepatitis B vaccine with a Toll-like receptor 9 agonist adjuvant (HBsAg-1018) compared to a licensed hepatitis B vaccine in healthy adults 40-70 years of age.. Vaccine. Nov 2013. doi: 10.1016/j.vaccine.2013.05.068. Epub 2013 May 30. [Pubmed: 23727002]
Immunogenicity of an investigational hepatitis B vaccine with a toll-like receptor 9 agonist adjuvant (HBsAg-1018) compared with a licensed hepatitis B vaccine in subpopulations of healthy adults 18-70 years of age.. Vaccine. Jul 2015. doi: 10.1016/j.vaccine.2015.05.070. Epub 2015 Jun 9. [Pubmed: 26067185]
None. None None None. doi: None [Pubmed: 29289383]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
DNA microarray 441
Flow Cytometry 384
Virus Neutralization 147
Clinical Assessments:None
SDY224: Immune Responses to Seasonal TIV 2010-2011 Influenza Vaccination in Humans (see companion study SDY396,SDY564)
Status: Updated
Description: High-frequency sampling combined with systems biology analysis of human peripheral blood cells following influenza vaccination was used to investigate T cell and B cell responses. Functional principal component analysis was used to examine time varying B cell vaccine response highlighting a single subject-specific mathematical pattern explaining ninety percent of the transcriptome variation. In addtition, daily sampling and monitoring of the proliferation marker Ki-67, revealed influenza-specific CD4 T cells do respond to vaccination.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense II University of Rochester Center for Biodefense Immune Modeling II
DOI: 10.21430/M37KMO7JLW
Subjects: 14
Study PI, contact:
NameOrganizationSite
Hulin Wu University of Rochester Medical Center University of Rochester Medical Center
Martin Zand University of Rochester Medical Center University of Rochester Medical Center
Publications:
Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination.. Vaccine. Jun 2012. doi: 10.1016/j.vaccine.2012.04.059. Epub 2012 Apr 30. [Pubmed: 22554464]
High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature.. Sci Rep. - 2013. doi: 10.1038/srep02327. [Pubmed: 23900141]
Resources:
University of Rochester Center for Biodefense Immune Modeling https://cbim.urmc.rochester.edu/]
Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/sra?term=SRX259436]
Effect of influenza vaccination on PBMC and B cell gene expression profiles in healthy humans http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45764]
Assays:
Assay TypeNumber of Exp. Samples
ELISA 423
ELISPOT 120
Flow Cytometry 560
Hemagglutination Inhibition 543
Q-PCR 1548
Sequencing 110
Clinical Assessments:None
SDY299: Systems Biology Analysis of the response to Licensed Hepatitis B Vaccine (HEPLISAV) in Whole Blood (see companion studies SDY816 and SDY690)
Status: Updated
Description: This project will contribute to the overall vision and goals of this U19 by analyzing the role of adjuvants in the humoral response to hep B vaccination in healthy individuals.
Program/Contract:
ProgramContract
Human Immunology Project Consortium 1 (HIPC1) Systems Analysis Vaccine Responses in Healthy and Hyporesponsive Humans
DOI: 10.21430/M34QI37OT9
Subjects: 25
Study PI, contact:
NameOrganizationSite
Robert Coffman Dynavax Technologies Corporation Dynavax Technologies Corporation
Publications:
Demonstration of safety and enhanced seroprotection against hepatitis B with investigational HBsAg-1018 ISS vaccine compared to a licensed hepatitis B vaccine.. Vaccine. Mar 2012. doi: 10.1016/j.vaccine.2012.02.001. Epub 2012 Feb 14. [Pubmed: 22342916]
Immunogenicity and safety of an investigational hepatitis B vaccine with a Toll-like receptor 9 agonist adjuvant (HBsAg-1018) compared to a licensed hepatitis B vaccine in healthy adults 40-70 years of age.. Vaccine. Nov 2013. doi: 10.1016/j.vaccine.2013.05.068. Epub 2013 May 30. [Pubmed: 23727002]
Immunogenicity of an investigational hepatitis B vaccine with a toll-like receptor 9 agonist adjuvant (HBsAg-1018) compared with a licensed hepatitis B vaccine in subpopulations of healthy adults 18-70 years of age.. Vaccine. Jul 2015. doi: 10.1016/j.vaccine.2015.05.070. Epub 2015 Jun 9. [Pubmed: 26067185]
None. None None None. doi: None [Pubmed: 29289383]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
DNA microarray 225
Nanostring 75
Clinical Assessments:None
SDY520: Immunologic and genomic signatures of influenza vaccine response - 2013 (see companion studies SDY63, SDY404, SDY400)
Status: Updated
Description: Project 1: Immunologic and genomic signatures of influenza vaccine response - year4 2013
Program/Contract:
ProgramContract
Human Immunology Project Consortium 1 (HIPC1) Defining signatures for immune responsiveness by functional systems immunology HIPC1
DOI: 10.21430/M3KVVHM735
Subjects: 61
Study PI, contact:
NameOrganizationSite
David Hafler Yale Yale
Publications:None
Resources:
NA NA]
Assays:
Assay TypeNumber of Exp. Samples
Hemagglutination Inhibition 114
Transcription profiling by array 99
Clinical Assessments:None
SDY820: Human Immune Signature of Mycobacterium Tuberculosis infection. (See SDY1324 for sorted cell gene expression data)
Status: Updated
Description: The human immune signature of latent Mycobacterium tuberculosis infected patients as well as BCG vaccinated and BCG non-vaccinated individuals was studied by flow cytometry
Program/Contract:
ProgramContract
Human Immunology Project Consortium 2 (HIPC2) Human immune signatures of dengue virus and mycobacterium tuberculosis exposure in infection; disease and vaccination (HIPC2)
DOI: 10.21430/M3D02NOSVH
Subjects: 60
Study PI, contact:
NameOrganizationSite
Bjoern Peters La Jolla Institute for Allergy and Immunology La Jolla Institute for Allergy and Immunology
Publications:
An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry.. J Immunol. Feb 2017. doi: 10.4049/jimmunol.1601750. Epub 2017 Jan 9. [Pubmed: 28069807]
Transcriptomic Analysis of CD4+ T Cells Reveals Novel Immune Signatures of Latent Tuberculosis.. J Immunol. Mar 2018. doi: - [Pubmed: 29602771]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 60
HLA Typing 60
RNA sequencing 85
Clinical Assessments:None
SDY998: AMP Rheumatoid Arthritis Arthroplasty Phase 1
Status: Updated
Description: The primary goal for RA arthroplasty P1 studies are: To establish if molecular signatures and pathways identified using core AMP technologies differ between OA and RA in 20 RA surgical samples and 10 OA arthroplasty samples.
Program/Contract:
ProgramContract
Accelerating Medicines Partnership (AMP) Accelerating Medicines Partnership (AMP)
DOI: 10.21430/M3KXJHSP4T
Subjects: 40
Study PI, contact:
NameOrganizationSite
Jennifer Anolik Rochester Rochester
Vivian Bykerk HSS HSS
Larry Moreland Pittsburg Pittsburg
Michael Holers Colorado Colorado
Peter Gregersen Northwell Northwell
Gary Firestein UCSD UCSD
PJ Utz Stanford Stanford
Michael Weisman Cedars Sinai Cedars Sinai
Publications:None
Resources:
NIH AMP RA/SLE Program https://www.niams.nih.gov/Funding/Funded_Research/AMP_RA_Lupus/default.asp]
Assays:
Assay TypeNumber of Exp. Samples
CyTOF 105
Flow Cytometry 136
Microscopy 192
RNA sequencing 3856
Clinical Assessments:
Medical History
SDY999: AMP Rheumatoid Arthritis Synovial Phase 1
Status: Updated
Description: The primary goal for RA synovial P1 studies are: To establish feasibility of obtaining ultrasound-guided synovial biopsies in the United States (U.S.) by comparing to frozen synovial biopsies obtained in the United Kingdom (U.K.)
Program/Contract:
ProgramContract
Accelerating Medicines Partnership (AMP) Accelerating Medicines Partnership (AMP)
DOI: 10.21430/M3XRJHRPBC
Subjects: 22
Study PI, contact:
NameOrganizationSite
Jennifer Anolik Rochester Rochester
Vivian Bykerk HSS HSS
Gary Firestein UCSD UCSD
Peter Gregersen Northwell Northwell
Michael Holers Colorado Colorado
Larry Moreland Pittsburg Pittsburg
PJ Utz Stanford Stanford
Publications:None
Resources:
Assays:
Assay TypeNumber of Exp. Samples
CyTOF 70
Flow Cytometry 173
Microscopy 229
RNA sequencing 6333
Clinical Assessments:
Medical History
SDY1025: APIC
Status: Updated
Description: This study looks to define the phenotypic characteristics of Difficult-to-Treat asthma, among 650 children between the ages of 6 to 17 years, receiving one year of guidelines-based therapy for asthma and rhinitis/rhinosinusitis.
Program/Contract:
ProgramContract
Inner City Asthma Consortium (ICAC) Inner City Asthma Consortium (ICAC)
DOI: 10.21430/M39SEUM79K
Subjects: 717
Study PI, contact:
NameOrganizationSite
William Busse University of Wisconsin-Madison University of Wisconsin-Madison
Publications:
Asthma phenotypes in inner-city children.. J Allergy Clin Immunol. Oct 2016. doi: 10.1016/j.jaci.2016.06.061. [Pubmed: 27720016]
Distinguishing characteristics of difficult-to-control asthma in inner-city children and adolescents.. J Allergy Clin Immunol. Oct 2016. doi: 10.1016/j.jaci.2016.06.059. [Pubmed: 27720017]
Pathways through which asthma risk factors contribute to asthma severity in inner-city children.. J Allergy Clin Immunol. Oct 2016. doi: 10.1016/j.jaci.2016.06.060. [Pubmed: 27720018]
Obstruction phenotype as a predictor of asthma severity and instability in children.. J Allergy Clin Immunol. Nov 2017. doi: - [Pubmed: 29146272]
Expression of Corticosteroid Regulated Genes By Peripheral Blood Mononuclear Cells in Children with Asthma.. J Allergy Clin Immunol. Jul 2018. doi: - [Pubmed: 30059697]
Rhinitis in Children and Adolescents with Asthma: Ubiquitous, Difficult to Control, and Associated with Asthma Outcomes.. J Allergy Clin Immunol. Sep 2018. doi: - [Pubmed: 30213627]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/study/NCT01383941]
Assays:None
Clinical Assessments:
Allergen Skin Test
Body Mass Index
Composite Asthma Severity Index
Exhaled Nitric Oxide
Indoor Allergens
Ipratropium Reversibility
Methacholine Challenge
Perceived Stress Scale
Plesthymography
Rhinitis/Rhinosinusitis Diagnostic Questionnaire
Spirometry
SDY1026: BioCSI 2 (Biomarkers of Cockroach Sublingual Immunotherapy 2)
Status: Updated
Description: This study looks to compare two doses of glycerinated German cockroach allergenic extract versus placebo administered via the sublingual route in 99 children ages 5 to 17 years with perennial allergic rhinitis, asthma, or both. It is designed to study biomarkers of the immune response to allergen immunotherapy as well as the safety of this therapy.
Program/Contract:
ProgramContract
Inner City Asthma Consortium (ICAC) Inner City Asthma Consortium (ICAC)
DOI: 10.21430/M3LVUFRQOA
Subjects: 99
Study PI, contact:
NameOrganizationSite
Robert Wood Johns Hopkins University School of Medicine Johns Hopkins University School of Medicine
Publications:
Development of cockroach immunotherapy by the Inner-City Asthma Consortium.. J Allergy Clin Immunol. Mar 2014. doi: 10.1016/j.jaci.2013.08.047. Epub 2013 Nov 1. [Pubmed: 24184147]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/study/NCT01380327]
Assays:None
Clinical Assessments:None
SDY1027: Epigenetics
Status: Updated
Description: The study is designed to determine the relation between methylation of CpG motifs and asthma in children residing in the inner city.
Program/Contract:
ProgramContract
Inner City Asthma Consortium (ICAC) Inner City Asthma Consortium (ICAC)
DOI: 10.21430/M3SXDBHQTS
Subjects: 200
Study PI, contact:
NameOrganizationSite
David Schwartz National Jewish Health National Jewish Health
Andrew Liu National Jewish Health National Jewish Health
Herman Mitchell Rho, Inc. Rho, Inc.
Publications:
DNA methylation and childhood asthma in the inner city.. J Allergy Clin Immunol. Jul 2015. doi: 10.1016/j.jaci.2015.01.025. Epub 2015 Mar 11. [Pubmed: 25769910]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/study/NCT01382836]
Assays:
Assay TypeNumber of Exp. Samples
DNA methylation profiling assay 194
DNA microarray 194
Clinical Assessments:None
SDY1028: Preventative Omalizumab or Step-up Therapy for Severe Fall Exacerbations (PROSE)
Status: Updated
Description: A three-armed prospective randomized double-blind placebo-controlled trial investigating the efficacy of standard care plus 4-5 months of treatment with (a) a boost of inhaled corticosteroid therapy Flovent Diskus (fluticasone) versus (b) Xolair(omalizumab) or (c) placebo Xolair (omalizumab) and placebo Flovent Diskus (fluticasone) in reducing the exacerbations during the fall season.
Program/Contract:
ProgramContract
Inner City Asthma Consortium (ICAC) Inner City Asthma Consortium (ICAC)
DOI: 10.21430/M3HZZOS3Y5
Subjects: 513
Study PI, contact:
NameOrganizationSite
William Busse University of Wisconsin-Madison University of Wisconsin-Madison
Samuel Arbes Rho Rho
Publications:
Preseasonal treatment with either omalizumab or an inhaled corticosteroid boost to prevent fall asthma exacerbations.. J Allergy Clin Immunol. Dec 2015. doi: 10.1016/j.jaci.2015.09.008. Epub 2015 Oct 27. [Pubmed: 26518090]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/study/NCT01430403]
Assays:None
Clinical Assessments:
Asthma Control Test
Childhood Asthma Control Test
Dust Sample Lab Results
Exhaled Nitric Oxide
Spirometry
SDY1029: SCITCO (Subcutaneous Immunotherapy for Cockroach)
Status: Updated
Description: This is an open label single site trial of German cockroach allergenic extract administered by subcutaneous injection in 10 adults ages 18 to 55 years with perennial allergic rhinitis, asthma, or both. It is designed to study biomarkers of the immune response to allergen immunotherapy as well as the safety of this therapy.
Program/Contract:
ProgramContract
Inner City Asthma Consortium (ICAC) Inner City Asthma Consortium (ICAC)
DOI: 10.21430/M3XJ80W9FK
Subjects: 11
Study PI, contact:
NameOrganizationSite
Robert Wood Johns Hopkins University School of Medicine Johns Hopkins University School of Medicine
Publications:
Development of cockroach immunotherapy by the Inner-City Asthma Consortium.. J Allergy Clin Immunol. Mar 2014. doi: 10.1016/j.jaci.2013.08.047. Epub 2013 Nov 1. [Pubmed: 24184147]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/study/NCT01221285]
Assays:None
Clinical Assessments:None
SDY1176: Extensive homeostatic T cell phenotypic variation within the Collaborative Cross
Status: Updated
Description: The Collaborative Cross (CC) is a panel of reproducible recombinant inbred mouse strains with high levels of standing genetic variation, thereby affording unprecedented opportunity to perform experiments in a small animal model containing controlled genetic diversity while allowing for genetic replicates. Here, we advance the utility of this unique mouse resource for immunology research, as it allows for both examination and genetic dissection of mechanisms behind adaptive immune states in mice with distinct and defined genetic makeups. This approach is founded on quantitative trait locus mapping: identifying genetically variant genome regions associated with phenotypic variance in traits-of-interest. Furthermore, the CC can be utilized for mouse model development; distinct strains have unique immunophenotypes and immune properties, making them suitable for research on particular diseases and infections. Here, we describe variation in cellular immune phenotypes across F1 crosses of CC strains, and reveal novel quantitative trait loci responsible for several immune phenotypes.
Program/Contract:
ProgramContract
Systems Approach to Immunity and Inflammation Systems Immunogenetics of Biodefense Pathogens in the Collaborative Cross
DOI: 10.21430/M3RKBKOYKS
Subjects: 476
Study PI, contact:
NameOrganizationSite
Jennifer Lund Fred Hutchinson Cancer Research Center Vaccine and Infectious Disease Division
Publications:None
Resources:
https://research.fhcrc.org/lund/en.html Dr. Jennifer Lund's Lab]
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 822
Clinical Assessments:None
SDY1289: YFV integrated mulitlineage and polyfunctional responses
Status: Updated
Description: Correlates of immune-mediated protection to most viral and cancer vaccines are still unknown. This impedes the development of novel vaccines to incurable diseases such as HIV and cancer. In this study, we have used functional genomics and polychromatic flow cytometry to define the signature of the immune response to the yellow fever (YF) vaccine 17D (YF17D) in a cohort of 40 volunteers followed for up to 1 yr after vaccination. We show that immunization with YF17D leads to an integrated immune response that includes several effector arms of innate immunity, including complement, the inflammasome, and interferons, as well as adaptive immunity as shown by an early T cell response followed by a brisk and variable B cell response. Development of these responses is preceded, as demonstrated in three independent vaccination trials and in a novel in vitro system of primary immune responses (modular immune in vitro construct [MIMIC] system), by the coordinated up-regulation of transcripts for specific transcription factors, including STAT1, IRF7, and ETS2, which are upstream of the different effector arms of the immune response. These results clearly show that the immune response to a strong vaccine is preceded by coordinated induction of master transcription factors that lead to the development of a broad, polyfunctional, and persistent immune response that integrates all effector cells of the immune system. peripheral blood samples from human newborns
Program/Contract:
ProgramContract
Other Programs Canadian Network for Vaccines and Immunotherapeutics (CANVAC)
DOI: 10.21430/M37CO9E6FQ
Subjects: 30
Study PI, contact:
NameOrganizationSite
Rafick-Pierre Sekaly McGill University Department of Microbiology and Immunology, McGill University
Publications:
Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses.. J Exp Med December 2008. doi: 10.1084/jem.20082292 [Pubmed: 19047440]
Resources:
Publication http://jem.rupress.org/content/jem/205/13/3119.full.pdf?with-ds=yes]
NCBI GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13699]
Assays:
Assay TypeNumber of Exp. Samples
Neutralizing Antibody Titer Assay 160
Transcription profiling by array 142
Clinical Assessments:None
SDY1325: B-cell responses to meningococcal vaccine.
Status: Updated
Description: Background: Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A, C, W and Y) are available as plain-polysaccharide and protein-polysaccharide conjugate vaccines. Here we apply contemporary methods to describe B-cell responses to meningococcal polysaccharide and conjugate vaccines. Methods: Twenty adults were randomly assigned to receive either a meningococcal plain-polysaccharide or conjugate vaccine; one month later all received the conjugate vaccine. Blood samples were taken pre-vaccination and 7, 21 and 28 days after vaccination; B-cell responses were assessed by ELISpot, serum bactericidal assay, flow cytometry and gene expression microarray. Results: Seven days after an initial dose of either vaccine, a gene expression signature characteristic of plasmablasts was detectable. The frequency of newly generated plasma cells (CXCR3+HLA-DR+) and the expression of transcripts derived from IGKC and IGHG2 correlated with immunogenicity. Notably, using an independent dataset, the expression of glucosamine (N-acetyl)-6-sulfatase was found to reproducibly correlate with the magnitude of immune response. Transcriptomic and flow cytometric data revealed depletion of switched memory B cells following plain-polysaccharide vaccine.
Program/Contract:
ProgramContract
Other Programs NIHR Oxford Biomedical Research Centre
DOI: 10.21430/M3Q1ZBWOG2
Subjects: 20
Study PI, contact:
NameOrganizationSite
Daniel O'Connor NIHR Oxford Biomedical Research Centre. University of Oxford
Publications:
High-dimensional assessment of B-cell responses to quadrivalent meningococcal conjugate and plain polysaccharide vaccine.. Genome Medicine January 2017. doi: 10.1186/s13073-017-0400-x [Pubmed: 28137280]
Resources:
PubMed Central https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282650/]
GEO GSE92884 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92884]
Assays:
Assay TypeNumber of Exp. Samples
Transcription profiling by array 59
Clinical Assessments:None
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