DR38 DataRelease

SDY1591: Th17 reprograming of T cells in systemic juvenile idiopathic arthritis
Status: New
Description: Systemic juvenile idiopathic arthritis (sJIA) begins with fever, rash, and high-grade systemic inflammation but commonly progresses to a persistent afebrile arthritis. The basis for this transition is unknown. To evaluate a role for lymphocyte polarization, we characterized T cells from patients with acute and chronic sJIA.
Program/Contract:
ProgramContract
NIAMS Rheumatic Diseases Research Resource-based Centers (P30) RFA-AR-16-002 Joint Biology Consortium Research-Based Center
NIH Program Reprogramming Of Regulatory T Cells To A Th17 Phenotype In Systemic Juvenile Idiopathic Arthritis
DOI: 10.21430/M3129QBMS5
Subjects: 69
Study PI, contact:
NameOrganizationSite
Lauren Henderson Division of Immunology, Boston Children's Hospital Boston Children's Hospital
Publications:
Th17 reprogramming of T cells in systemic juvenile idiopathic arthritis.. JCI insight Mar 2020. doi: 10.1172/jci.insight.132508 [Pubmed: 32213704]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
RNA sequencing 56
Clinical Assessments:None
SDY1596: Licensed BCG formulations differ markedly in innate immune activation
Status: New
Description: Bacille Calmette-Gurin (BCG), the live attenuated tuberculosis vaccine, is manufactured under different conditions across the globe generating formulations that may differ in clinical efficacy. Innate immune recognition of live BCG contributes to immunogenicity suggesting that differences in BCG viability may contribute to divergent activity of licensed formulations.
Program/Contract:
ProgramContract
Human Immunology Project Consortium (HIPC) RFA-AI-15-041 Systems Biology To Identify Biomarkers Of Neonatal Vaccine Immunogenicity (Boston Children's)
DOI: 10.21430/M3QX318KNW
Subjects: 28
Study PI, contact:
NameOrganizationSite
Simon van Haren Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Boston Children's Hospital, Harvard Medical School
Ofer Levy Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Boston Children's Hospital, Harvard Medical School
Publications:None
Resources:
Assays:
Assay TypeNumber of Exp. Samples
Luminex xMAP 495
Clinical Assessments:None
SDY1620: Treated HIV infection induces alterations in phenotype but not HIV-specific function of peripheral blood natural killer cells
Status: New
Description: Natural killer (NK) cells are the predominant antiviral cells of the innate immune system, and may play an important role in acquisition and disease progression of HIV. While untreated HIV infection is associated with distinct alterations in the peripheral blood NK cell repertoire, less is known about how NK phenotype is altered in the setting of long-term viral suppression with antiretroviral therapy (ART), as well as how NK memory can impact functional responses. As such, we sought to identify changes in NK cell phenotype and function using high-dimensional mass cytometry to simultaneously analyze both surface and functional marker expression of peripheral blood NK cells in a cohort of ART-suppressed, HIV+ patients and HIV- healthy controls.
Program/Contract:
ProgramContract
NIH Director's New Innovator Award Program (DP2) 2013 Harnessing Natural Killer Cell Memory To Fight Viruses
Bill and Melinda Gates Foundation (BMGF) ITI/Bill & Melinda Gates Foundation Pilot Grant
NIH Program Targeting Natural Killer Cells To Hiv In Intravenous Drug Users
DOI: 10.21430/M30J52ENN6
Subjects: 20
Study PI, contact:
NameOrganizationSite
Catherine Blish Stanford University Stanford University
Publications:
Treated HIV Infection Alters Phenotype but Not HIV-Specific Function of Peripheral Blood Natural Killer Cells.. Frontiers in immunology May 2020. doi: 10.3389/fimmu.2020.00829 [Pubmed: 32477342]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
CyTOF 40
Clinical Assessments:None
SDY1625: Double Expressor Assessment
Status: New
Description: Determine the frequency of double expressor lymphocytes of frozen PBMCs from T1D patients and health controls through flow cytometry.
Program/Contract:
ProgramContract
NIH Program Immune Function And The Progression To Type 1 Diabetes
DOI: 10.21430/M3Z5UFK8GC
Subjects: 28
Study PI, contact:
NameOrganizationSite
Todd Brusko University of Florida University of Florida
Michael Betts University of Pennsylvania University of Pennsylvania
Publications:None
Resources:
Assays:
Assay TypeNumber of Exp. Samples
ELISA 28
Flow Cytometry 112
Clinical Assessments:None
SDY1647: CD16 is upregulated in HIV-exposed seronegative women and may mediate enhanced antibody-dependent cytotoxicity
Status: New
Description: Performed a mass cytometry-based screen of NK cell receptor expression patterns in healthy controls and HIV-exposed seronegative women individuals and then focused mechanistic studies on the expression CD16
Program/Contract:
ProgramContract
NIH Director's New Innovator Award Program (DP2) 2013 Harnessing Natural Killer Cell Memory To Fight Viruses
NIH Program Targeting Natural Killer Cells To Hiv In Intravenous Drug Users
Other Programs Burroughs Wellcome Fund Investigators in the Pathogenesis of Infectious Diseases
DOI: 10.21430/M3HV2PQM3C
Subjects: 30
Study PI, contact:
NameOrganizationSite
Catherine Blish Stanford University Stanford University
Publications:
Natural killer cell phenotype is altered in HIV-exposed seronegative women.. PloS one Sep 2020. doi: 10.1371/journal.pone.0238347 [Pubmed: 32870938]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
CyTOF 30
Clinical Assessments:None
SDY1660: Rituximab for Treatment of Systemic Sclerosis-Associated Pulmonary Arterial Hypertension (SSc-PAH) (ASC01)
Status: New
Description: This prospective, double-blind, placebo-controlled, multi-center, randomized trial will evaluate the effect of rituximab on disease progression in subjects with SSc-PAH receiving concurrent stable-dose standard medical therapy with a prostanoid, endothelin receptor antagonist, and/or phosphodiesterase 5 (PDE-5) inhibitor. The study will focus on assessment of clinical response and safety measures longitudinally. In addition, the effects of treatment with rituximab on the underlying immune mechanisms associated with B-cell dysregulation and pathogenic autoantibody response in this disease will be investigated. 1000 mg of rituximab or placebo will be administered as two IV infusions given two weeks apart. Clinical assessments and sample collection will occur at monthly visits through Week 48. If a participant has not recovered B cells by Week 48, B cell studies will be conducted quarterly until reconstitution is documented or for 2 years after initial treatment. This trial will include a sub-study, entitled ""Right Ventricular Response to Rituximab in Systemic Sclerosis-Associated Pulmonary Arterial Hypertension - A Magnetic Resonance Imaging Sub-study"" (RESTORE Sub-study). The objective of the RESTORE sub-study is to evaluate the therapeutic effect of rituximab on the right ventricle of patients with SSc-PAH. Changes in right ventricular end diastolic volume index (RVEDVI) and stroke volume (SV) determined by cardiac MRI will be used as surrogates of right ventricle function and prognosis. Enrollment for the RESTORE sub-study will parallel that of main trial. Twenty patients from each treatment arm, distributed among all participating sites, will be recruited for this sub-study. Each patient will be studied at baseline (i.e. prior to initiation of study drug) and after 24 weeks or at time of discontinuation. In addition to the data collection and testing specified in the main trial, participants in RESTORE will undergo comprehensive cardiac MRI evaluation. All main trial study inclusion and exclusion criteria apply, as well as additional exclusion criteria that pertain only to the RESTORE sub-study: 1) known hypersensitivity to Gadolinium; 2) inability to tolerate or cooperate with MRI; 3) morbid obesity; and 4) presence of metallic objects or pacemakers.
Program/Contract:
ProgramContract
Autoimmunity Centers of Excellence (ACE) AI-12-060, AI-12-059 ACE: Autoimmunity Center Of Excellence (ACE) At Stanford
DOI: 10.21430/M3AWCQNWDW
Subjects: 57
Study PI, contact:
NameOrganizationSite
Mark Nicolls Stanford University School of Medicine Stanford University School of Medicine
David Badesch University of Colorado Health Sciences Center University of Colorado Health Sciences Center
Publications:
Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis.. Science immunology Sep 2017. doi: 10.1126/sciimmunol.aan8289 [Pubmed: 28963118]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT01086540]
Assays:None
Clinical Assessments:None
SDY1666: KSHV tropism in B lymphocytes
Status: New
Description: Study of Tonsil Biospecimens via ex vivo infection with KSHV to determine KSHV tropism for B lymphocytes in human tonsil
Program/Contract:
ProgramContract
NIH Program Identifying Susceptibility Factors For KSHV Infection In Human Tonsil
DOI: 10.21430/M3QC31XEYE
Subjects: 40
Study PI, contact:
NameOrganizationSite
Jennifer Totonchy Chapman University Chapman University
Publications:None
Resources:
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 180
Clinical Assessments:None
SDY1667: Cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans
Status: New
Description: Many unknowns exist about human immune responses to the SARS-CoV-2 virus. SARS-CoV-2 reactive CD4+ T cells have been reported in unexposed individuals, suggesting pre-existing cross-reactive T cell memory in 20-50% of people. However, the source of those T cells has been speculative. Using human blood samples derived before the SARS-CoV-2 virus was discovered in 2019, we demonstrate a range of pre-existing memory CD4+ T cells that are cross-reactive with comparable affinity to SARS-CoV-2 and the common cold coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63, or HCoV-HKU1. Thus, variegated T cell memory to coronaviruses that cause the common cold may underlie at least some of the extensive heterogeneity observed in COVID-19 disease.
Program/Contract:
ProgramContract
Cooperative Centers on Human Immunology RFA-AI-17-040 Functional and Dysfunctional Human CD4 T cell and B cell Responses to Bacteria and Viruses (RFA-AI-17-040)
DOI: 10.21430/M3R9UGV228
Subjects: 45
Study PI, contact:
NameOrganizationSite
Publications:
Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans.. Science (New York, N.Y.) Oct 2020. doi: 10.1126/science.abd3871 [Pubmed: 32753554]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 360
Clinical Assessments:None
SDY1672: Immune Response to IAV
Status: New
Description: Using the Collaborative Cross, a population of recombinant inbred mouse strains with high levels of genetic variation, we measured antibody response and weight change after infection with influenza-A virus.
Program/Contract:
ProgramContract
Systems Approach to Immunity and Inflammation RFA-AI-16-050 Systems Immunogenetics Of Biodefense And Emerging Pathogens In The Collaborative Cross RFA-AI-16-050
DOI: 10.21430/M33IIY5ARD
Subjects: 3640
Study PI, contact:
NameOrganizationSite
Mark Heise University of North Carolina University of North Carolina
Publications:
Complex Genetic Architecture Underlies Regulation of Influenza-A-Virus-Specific Antibody Responses in the Collaborative Cross.. Cell reports Apr 2020. doi: 10.1016/j.celrep.2020.107587 [Pubmed: 32348764]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
ELISA 76382
Clinical Assessments:
Physical Exam
SDY1696: The interaction between the vaginal microbiome, cervical length and vaginal progesterone treatment for preterm birth risk
Status: New
Description: Preterm birth is the primary cause of infant death worldwide. A short cervix in the second trimester of pregnancy is a risk factor for preterm birth. In specific patient cohorts, vaginal progesterone reduces this risk. By using 16S rRNA gene sequencing in women at risk of preterm birth (n?=?161), the study assessed 1) the relationship between vaginal microbiota and cervical length in the second trimester and preterm birth risk and 2) the impact of vaginal progesterone on vaginal bacterial communities in women with a short cervix.
Program/Contract:
ProgramContract
March of Dimes March of Dimes
DOI: 10.21430/M3I5KIC0BC
Subjects: 228
Study PI, contact:
NameOrganizationSite
David MacIntyre Imperial College London Division of the Institute of Reproduction and Developmental Biology
Publications:
The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk.. Microbiome Jan 2017. doi: 10.1186/s40168-016-0223-9 [Pubmed: 28103952]
Resources:
PRJEB12577 https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB12577]
PRJEB11895 https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB11895]
ENA seq reads https://www.ebi.ac.uk/ena/browser/view/PRJEB12577]
paper_link https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0223-9]
Assays:None
Clinical Assessments:None
SDY1702: Mid-gestation serum lipidomic profile of PTB are influenced by BMI
Status: New
Description: BMIs is one of risk factors for spontaneous preterm birth (sPTB). To identify BMI-associated metabolic perturbations and potential mid-gestation serum biomarkers of sPTB, the study compared metabolomics/lipidomics in sPTB and FTB (Full term birth) women stratified by BMIs categories: underweight, normal weight, and obese. Technique: combining untargeted metabolomics and lipidomics with targeted metabolic profiling of major regulators of inflammation and metabolism, including oxylipins, endocannabinoids, bile acids and ceramides. Results: 1) underweight/sPTB showed dyslipidemia characterized by elevated phospholipids, unsaturated triglycerides, sphingomyelins, cholesteryl esters and long-chain acylcarnitines. 2) normalweight/sPTB showed altered relative abundance of 14(15)-epoxyeicosatrienoic acid and 14,15-dihydroxyeicosatrienoic acids to other regioisomers at mid-pregnancy. 3) obese/sPTB: showed elevated oxidative stress and dyslipidemia characterized by elevated serum free fatty acids. In conclusion, using metabolomics can distinct BMI-dependent metabolic manifestations among women who had sPTB
Program/Contract:
ProgramContract
March of Dimes March of Dimes
DOI: 10.21430/M3QKUPQS46
Subjects: 0
Study PI, contact:
NameOrganizationSite
Kamil Borkowski University of California-Davis West Coast Metabolomic Center, Genome Center
Publications:
Mid-gestation serum lipidomic profile associations with spontaneous preterm birth are influenced by body mass index.. PloS one Nov 2020. doi: 10.1371/journal.pone.0239115 [Pubmed: 33201881]
Resources:
targeted Lipid mediators https://metabolomics.ucdavis.edu/research-labs/newman-laboratory-for-lipid-mediators]
untargeted metabolomes https://metabolomics.ucdavis.edu/core-services/assays-and-services]
HILIC-MS/MS library http://massbank.us]
paper_link https://doi.org/10.1371/journal.pone.0239115]
California Biobank Program https://www.cdph.ca.gov/Programs/CFH/DGDS/Pages/cbp/default.aspx]
Assays:None
Clinical Assessments:None
SDY1707: Maternal plasma miRNAs as potential biomarkers for detecting risk of SGA
Status: New
Description: Small-for-gestational-age fetuses (SGA) (birthweight <10th centile) are at high risk for stillbirth or long-term adverse outcomes. To identify maternal plasma miRNAs as potential biomarkers for detecting risk of SGA, the study sampled 29 women (16 delivered normally grown babies and 13 delivered SGA (birthweight <5th centile)) and determined their plasma miRNA profiles (~800 miRNAs) by using the Nanostring nCounter miRNA assay. The comparative analysis between SGA and normal groups identified seven miRNAs at 12?14+6 weeks gestation. Four of these were technically validated by RT-qPCR. Differential expression of two miRNA markers; hsa-miR-374a-5p (p = 0?0176) and hsa-let-7d-5p (p = 0?0036), were validated in an independent population of 95 women (SGA n = 12, Control n = 83). In the validation cohort, which was enriched for SGA cases, the ROC AUCs were 0?71 for hsa-miR-374a-5p, and 0?74 for hsa-let-7d-5p, and 0?77 for the two combined
Program/Contract:
ProgramContract
March of Dimes March of Dimes
DOI: 10.21430/M3QPGX9UYA
Subjects: 0
Study PI, contact:
NameOrganizationSite
Sung Kim Imperial College London Department of Metabolism, Digestion and Reproduction
Publications:
Maternal plasma miRNAs as potential biomarkers for detecting risk of small-for-gestational-age births.. EBioMedicine Dec 2020. doi: 10.1016/j.ebiom.2020.103145 [Pubmed: 33260001]
Resources:
paper_link https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(20)30521-1/fulltext]
miRNAassay(nanoString) https://www.nanostring.com/products/mirna-assays/mirna-assays-overview]
Assays:None
Clinical Assessments:None
SDY1710: Early Prediction of Preeclampsia via Machine Learning
Status: New
Description: An early prediction model for preeclampsia was developed with the use of machine learning methods that analyzed all available clinical and laboratory data during routine prenatal visits. Using the elastic net algorithm, a subset of the most informative features from all variables can be automatically identified. The obtained prediction model for preeclampsia yielded an area under the curve of 0.79 (95% confidence interval, 0.75?0.83), sensitivity of 45.2%, and false-positive rate of 8.1%. The prediction model for early-onset preeclampsia achieved an area under the curve of 0.89 (95% confidence interval, 0.84?0.95), true-positive rate of 72.3%, and false-positive rate of 8.8%.
Program/Contract:
ProgramContract
March of Dimes March of Dimes
DOI: 10.21430/M3G6ZCU1UC
Subjects: 0
Study PI, contact:
NameOrganizationSite
Ivana Maric Stanford University School of Medicine Department of Pediatrics
Publications:
Early prediction of preeclampsia via machine learning.. American journal of obstetrics & gynecology MFM May 2020. doi: 10.1016/j.ajogmf.2020.100100 [Pubmed: 33345966]
Resources:
Paper_link https://www.ajogmfm.org/article/S2589-9333(20)30030-6/fulltext]
All Tables https://www.ajogmfm.org/article/S2589-9333(20)30030-6/fulltext#tables]
Assays:None
Clinical Assessments:None
SDY1712: Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria gastrointestinal tract (GI)
Status: New
Description: We have a mutually beneficial relationship with the trillions of microorganisms inhabiting our gastrointestinal tract. However, maintaining this relationship requires recognizing these organisms as affable and restraining inflam- matory responses to these organisms when encountered in hostile settings. How and when the immune system develops tolerance to our gut microbial members is not well understood. We identify a specific preweaning inter- val in which gut microbial antigens are encountered by the immune system to induce antigen-specific tolerance to gut bacteria. For some bacterial taxa, physiologic encounters with the immune system are restricted to this inter- val, despite abundance of these taxa in the gut lumen at later times outside this interval. Antigen-specific tolerance to gut bacteria induced during this preweaning interval is stable and maintained even if these taxa are encountered later in life in an inflammatory setting. However, inhibiting microbial antigen encounter during this interval or ex- tending these encounters beyond the normal interval results in a failure to induce tolerance and robust antigen- specific effector responses to gut bacteria upon reencounter in an inflammatory setting. Thus, we have identified a defined preweaning interval critical for developing tolerance to gut bacteria and maintaining the mutually bene- ficial relationship with our gut microbiota.
Program/Contract:
ProgramContract
Immunity in Neonates and Infants (U01) RFA-AI-16-001 Gut Specific And Time-Limited Events In Early Life Promoting Tolerance
DOI: 10.21430/M3AJSRNM6B
Subjects: 18
Study PI, contact:
NameOrganizationSite
Rodney Newberry Washington University School of Medicine Washington University School of Medicine
Publications:None
Resources:
Assays:None
Clinical Assessments:None
SDY1722: Perturbation of ILF3 in Human MDDCs
Status: New
Description: MDDCs were transduced with lentiviral constructs expressing mRNA coding for various isoforms of ILF3 or isoforms lacking specific domains.
Program/Contract:
ProgramContract
Systems Approach to Immunity and Inflammation RFA-AI-16-050 Systems Approach To Immunity And Inflammation
DOI: 10.21430/M3GS4EP88P
Subjects: 7
Study PI, contact:
NameOrganizationSite
Alan Aderem Seattle Children's Hospital Seattle Chldren's Hospital
Publications:None
Resources:
Assays:
Assay TypeNumber of Exp. Samples
DNA microarray 9
RNA sequencing 12
Clinical Assessments:None
SDY1723: gso32 infected with Mtb
Status: New
Description: Gene expression analysis of gso32 bone marrow derived macrophages treated with IFNbeta and/or infected with live or heat killed Mycobacterium tuberculosis
Program/Contract:
ProgramContract
Systems Approach to Immunity and Inflammation RFA-AI-16-050 Systems Approach To Immunity And Inflammation
DOI: 10.21430/M3QUUM0902
Subjects: 8
Study PI, contact:
NameOrganizationSite
Alan Diercks Seattle Children's Research Institute Seattle Children's Research Institute
Publications:None
Resources:
Assays:
Assay TypeNumber of Exp. Samples
RNA sequencing 72
Clinical Assessments:None
SDY1725: Response of human MDDCs to HIV
Status: New
Description: Chromatin accessibility was measured by ATAC-seq in human MDDCs following infection with HIV-GFP at several time points over the first 48 hours.
Program/Contract:
ProgramContract
Systems Approach to Immunity and Inflammation RFA-AI-16-050 Systems Approach To Immunity And Inflammation
DOI: 10.21430/M3KWDR5VTS
Subjects: 3
Study PI, contact:
NameOrganizationSite
Mickael Menager Imagine Institute Imagine Institute
Publications:
A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV.. Cell reports Jan 2020. doi: 10.1016/j.celrep.2019.12.054 [Pubmed: 31968263]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
Other 30
Clinical Assessments:None
SDY1732: Maternal gut microbiota reflecting poor diet quality is associated with sPTB
Status: New
Description: The study conducted comparative analysis in case-control datasets on the data of fecal gut microbiota, fecal and plasma metabolites, and diet in the late second trimester. Results: 1) A decrease in ?-diversity was strongly associated with the development of SPTB, especially in the taxonomic class of Betaproteobacteria. 2) Of 824 fecal metabolites, 22 metabolites (mostly lipids) differed between cases and controls (P < 0.01). The most significant fecal metabolite module (FDR-adjusted P = 0.008) was dominated by DHA and EPA. 3) A low-fiber, high-fat diet in the late second trimester is strongly associated with the development of SPTB. Conclusions: Reduced ?-diversity of the gut microbiota and higher excretion of omega-3 (n?3) fatty acids in stool may provide a novel biomarker signature predicting SPTB in women with a low-fiber, high-fat diet. Further investigation of these markers in a larger sample is needed for validation
Program/Contract:
ProgramContract
March of Dimes March of Dimes
DOI: 10.21430/M3AM77XTU7
Subjects: 47
Study PI, contact:
NameOrganizationSite
Charlene Compher University of Pennsylvania School of Nursing
Publications:
Maternal gut microbiota reflecting poor diet quality is associated with spontaneous preterm birth in a prospective cohort study.. The American journal of clinical nutrition Jan 2021. doi: 10.1093/ajcn/nqaa361 [Pubmed: 33515003]
Resources:
Github_data_tools https://github.com/yli0131/MGM]
NDSR_software ( nutrients calculation) http://www.ncc.umn.edu/products/]
Paper_link https://academic.oup.com/ajcn/advance-article-abstract/doi/10.1093/ajcn/nqaa361/6123954?redirectedFrom=fulltext]
Assays:
Assay TypeNumber of Exp. Samples
16S rRNA gene sequencing 47
Mass Spectrometry 94
Clinical Assessments:None
SDY1737: A Research Trial of Aralast in New Onset Diabetes (RETAIN) (ITN041AI)
Status: New
Description: The drug Alpha-1 Antitrypsin (AAT, Aralast NP) is being tested in this study as an anti-inflammatory drug (a medication that decreases inflammation, which is part of the body's normal ability to fight infection and respond to injuries) that affects the cells thought to be involved in the development of type 1 diabetes mellitus (T1DM, T1D). All subjects enrolled in this study have new-onset T1DM (diagnosis of T1DM within 100 days of Visit 0; T1DM diagnosis fulfilling American Diabetes Association standard T1DM criteria). The focus of Part I of this trial (NCT01183468) is pharmacokinetics (PK), pharmacodynamics (PD) and safety. Upon completion of Part I, including a satisfactory safety review, enrollment in Part II (NCT01183455, Phase II Clinical Trial) will begin.
Program/Contract:
ProgramContract
ITN: Collaborative Network for Clinical Research on Immune Tolerance Network Immune Tolerance Network
DOI: 10.21430/M3ALD4RXIE
Subjects: 16
Study PI, contact:
NameOrganizationSite
Gordon Weir Joslin Diabetes Center Joslin Diabetes Center
Publications:
Alpha-1 antitrypsin treatment of new-onset type 1 diabetes: An open-label, phase I clinical trial (RETAIN) to assess safety and pharmacokinetics.. Pediatric diabetes Aug 2018. doi: 10.1111/pedi.12660 [Pubmed: 29473705]
Resources:
ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT01183468]
Assays:None
Clinical Assessments:None
SDY1738: Multiomics Characterization of PTB in Low- and Middle-Income Countries
Status: New
Description: This study analyzed multiomics data of plasma and urine samples collected from May 2014 to June 2017 from pregnant women in 5 biorepository cohorts in low- and middle-income countries. The comparative analysis of Cell-free transcriptomics, urine metabolomics, and plasma proteomics between term and preterm birth concluded that major biological adaptations during term pregnancy follow a generalizable model and the predictive accuracy for PTB was augmented by combining various omics data sets
Program/Contract:
ProgramContract
March of Dimes March of Dimes
DOI: 10.21430/M32WAWRYE2
Subjects: 81
Study PI, contact:
NameOrganizationSite
Nima Aghaeepour Stanford University Division of Neonatal and Developmental Medicin
Publications:
Multiomics Characterization of Preterm Birth in Low- and Middle-Income Countries.. JAMA network open Dec 2020. doi: 10.1001/jamanetworkopen.2020.29655 [Pubmed: 33337494]
Resources:
paper_link https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2774321]
data and software https://nalab.stanford.edu/multiomicsmulticohortpreterm/]
Analysis tool (feature evaluation scores and pathway enrichment) https://anes-naapp01.stanford.edu]
Assays:
Assay TypeNumber of Exp. Samples
Mass Spectrometry 81
Protein microarray 81
RNA sequencing 81
Clinical Assessments:None
SDY472: Plasmablast response to inactivated and live attenuated influenza vaccines (TIV3/TIV3 ID) in SLVP021 2013
Status: Updated
Description: The aim of this study is to compare the response to different formulations of licensed influenza vaccines. The type of seasonal influenza vaccination(s) received independently by volunteers in the year(s) since their last study visit will not impact eligibility. Volunteers will be assigned into one of three vaccine groups (intramuscular trivalent inactivated influenza vaccine (TIV); live attenuated influenza vaccine (LAIV- given year 1 only) or intradermal TIV, based on the type of study vaccine they received in 2010, 2011, 2012, or 2013. All participants will receive a single dose of their assigned seasonal influenza vaccine. Volunteers will complete 3 study visits at Day 0, Day 6-8 and Day 24-32.
Program/Contract:
ProgramContract
Human Immunology Project Consortium (HIPC) RFA-AI-14-007, RFA-AI-09-040 Vaccination and infection: indicators of immunological health and responsiveness
DOI: 10.21430/M3KHTSSSN7
Subjects: 24
Study PI, contact:
NameOrganizationSite
Harry Greenberg Stanford University Stanford University
Publications:
The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system.. Scientific data Oct 2019. doi: 10.1038/s41597-019-0213-4 [Pubmed: 31636302]
Resources:
clinicaltrials.gov https://clinicaltrials.gov/ct2/show/NCT02141581]
Assays:
Assay TypeNumber of Exp. Samples
CyTOF 24
Hemagglutination Inhibition 136
Luminex xMAP 46
Clinical Assessments:None
SDY1381: Host Determinants Of Protection Against Tuberculosis In Adolescents
Status: Updated
Description: The bacterium that causes tuberculosis (TB), Mycobacterium tuberculosis (M.tb), has infected one quarter of the world's population. Infection occurs when the pathogen is inhaled, following exposure to a patient with lung TB. 10% of infected persons progress to disease, while 90% never do. We don't understand why some people develop disease, while others do not: this is the focus of this application. To address protection against TB, we have established a cohort of 6,363 South African adolescents. 53% were infected with M.tb at baseline. During 2 years of follow-up, 76 of these participants developed TB disease. As blood was collected and stored every 6 months, we have a unique opportunity to compare host responses between adolescents who developed disease and those who have remained healthy. We will have two approaches to defining protection. Our first focus will be on T cells, which are immune cells shown to be critical for protection against TB. Current assays focus on limited aspects of the T cell response, but have not been successful in defining protection. We have devised a new paradigm - we hypothesize that a model including multiple T cell functional attributes plus their regulation by multiple immune cells will define protection. We propose that relative "immune quiescence", i.e., an optimal but relatively silent immune response, is associated with protection. We and others have preliminary data to suggest that too much inflammation, or too much activation of the immune system, may be detrimental. The rationale for our second focus is that our knowledge of host control of M.tb infection remains incomplete - we therefore propose an unbiased approach that will facilitate discovery of novel pathways involved in protection. We will assess genome-wide gene expression in blood cells, including purified immune cell populations, to delineate new pathways involved in protection. Our preliminary studies of protection against TB in infants have shown the incredible power of this approach. The longitudinal nature of the adolescent cohort, and state-of-the-art bioinformatic approaches, afford unique muscle for uncovering host determinants of protection. We will immediately validate findings by studying further groups of adolescents, from the same cohort. This will be followed by mechanistic studies aimed at understanding how newly described markers may act to protect us against TB. Knowledge of host determinants of protection against TB disease could impact TB control in many ways. For example, targeted prophylactic therapy for infected persons could be implemented, as well as rapid clinical testing of novel TB vaccines. Knowledge gained will also stimulate development of new vaccines and drugs against TB.
Program/Contract:
ProgramContract
Bill and Melinda Gates Foundation (BMGF) Identify prospective immune correlates of risk of tuberculosis (TB) disease following natural infection with Mycobacterium tuberculosis
NIH Program Host Determinants Of Protection Against Tuberculosis In Adolescents
DOI: 10.21430/M3E5CED0HU
Subjects: 150
Study PI, contact:
NameOrganizationSite
Thomas Scriba University of Cape Town University of Cape Town
Publications:
A blood RNA signature for tuberculosis disease risk: a prospective cohort study.. Lancet (London, England) Jun 2016. doi: 10.1016/S0140-6736(15)01316-1 [Pubmed: 27017310]
Resources:
Gates Foundation https://www.impatientoptimists.org/Topics/Tuberculosis]
SATVI http://www.satvi.uct.ac.za/]
SRA https://www.ncbi.nlm.nih.gov/sra?term=SRP071965]
GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79362]
ZivaHub https://zivahub.uct.ac.za/articles/Clinical_Variables_for_the_Adolescent_Cohort_Study_in_the_Worcester_region_of_South_Africa/7618532/1]
Assays:
Assay TypeNumber of Exp. Samples
HLA Typing 106
Other 373
Q-PCR 2394
RNA sequencing 1671
Clinical Assessments:None
SDY1618: Superior mouse eosinophil depletion in vivo targeting transgenic Siglec-8 instead of endogenous Siglec-F: mechanisms and pitfalls
Status: Updated
Description: We uncovered shortcomings when using certain antibodies that target Siglec-F to deplete mouse eosinophils, while administration of anti-Siglec-8 antibody to Siglec-8 transgenic mice works well.
Program/Contract:
ProgramContract
Asthma and Allergic Diseases Cooperative Research Centers (AADCRC) RFA-AI-16-065 Using Siglecs and their ligands to treat allergic diseases SALTAD
DOI: 10.21430/M348T28T35
Subjects: 12
Study PI, contact:
NameOrganizationSite
Bruce Bochner Northwestern University Northwestern University
Publications:
Frontline Science: Superior mouse eosinophil depletion in vivo targeting transgenic Siglec-8 instead of endogenous Siglec-F: Mechanisms and pitfalls.. Journal of leukocyte biology Jul 2020. doi: 10.1002/JLB.3HI0120-381R [Pubmed: 32134149]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 244
Clinical Assessments:None
SDY1640: T and B cell responses to SARS-CoV-2 coronavirus
Status: Updated
Description: Understanding adaptive immunity to SARS-CoV-2 is important for vaccine development, interpreting coronavirus disease 2019 (COVID-19) pathogenesis, and calibration of pandemic control measures. Using HLA class I and II predicted peptide megapools, circulating SARS-CoV-2-specific CD8+ and CD4+ T cells were identified. Anti-SARS-CoV-2 IgG, IgM and IgA titers against the spike protein were determined.
Program/Contract:
ProgramContract
Human Immunology Project Consortium (HIPC) RFA-AI-15-041 Human immune signatures of dengue virus and mycobacterium tuberculosis exposure in infection; disease and vaccination (La Jolla)
Cooperative Centers on Human Immunology RFA-AI-17-040 Functional and Dysfunctional Human CD4 T cell and B cell Responses to Bacteria and Viruses (RFA-AI-17-040)
DOI: 10.21430/M3CZDHCXKV
Subjects: 40
Study PI, contact:
NameOrganizationSite
Alessandro Sette La Jolla Institute for Immunology La Jolla Institute for Immunology
Publications:
Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals.. Cell May 2020. doi: 10.1016/j.cell.2020.05.015 [Pubmed: 32473127]
Resources:
Assays:
Assay TypeNumber of Exp. Samples
ELISA 120
Flow Cytometry 180
Clinical Assessments:None
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