Evidence map›Paper›PMID 26311730›Full record

ArticleScience translational medicine2015

IgH sequences in common variable immune deficiency reveal altered B cell development and selection.

Krishna M Roskin, Noa Simchoni, Yi Liu, Ji-Yeun Lee, Katie Seo, Ramona A Hoh, Tho Pham, Joon H Park, David Furman, Cornelia L Dekker and 5 more

Registry-linked trialAbstract read
In one paragraph

Article in Science translational medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT01827462 (Immune Senescence in the Elderly), which is not on this map. Cited by 53 papers.

0numbers the graph read from it
0cells of the map it votes in
53citing papers in PubMed
3.3field-weighted citation impact, top 7% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

NCT01827462 phase4completednot on this map

Immune Senescence in the Elderly: Comparison of Immune Responses to Influenza Vaccine In Adults of Different Ages

TypeinterventionalSponsorStanford UniversityRan2007 to 2017Enrolled136ConditionsInfluenzaArmsTrivalent, inactivated influenza vaccine (TIV), Quadrivalent, inactivated influenza vaccine (IIV4), High-Dose Trivalent, inactivated influenza vaccine (TIV High-Dose)
3 · Its place in the literature

Who cites it

53 citing papers in PubMed, 94 citations in OpenAlex.

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  14. Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022
    Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors at 1 institution in 1 country.

Krishna M RoskinDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Noa SimchoniDepartments of Medicine and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Yi LiuDepartment of Pathology, Stanford University, Stanford, CA 94305, USA. Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA.
Ji-Yeun LeeDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Katie SeoDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Ramona A HohDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Tho PhamDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Joon H ParkDepartments of Medicine and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
David FurmanDepartment of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA.
Cornelia L DekkerDepartments of Medicine, Pediatrics, and Otolaryngology, Stanford University, Stanford, CA 94305, USA.
Mark M DavisDepartment of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA. Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Judith A JamesArthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation and Oklahoma Clinical and Translational Science Institute and Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
Kari C NadeauDepartments of Medicine, Pediatrics, and Otolaryngology, Stanford University, Stanford, CA 94305, USA.
Charlotte Cunningham-RundlesDepartments of Medicine and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. sboyd1@stanford.edu charlotte.cunningham-rundles@mssm.edu.
Scott D BoydDepartment of Pathology, Stanford University, Stanford, CA 94305, USA. sboyd1@stanford.edu charlotte.cunningham-rundles@mssm.edu.
Stanford University · US

Funding

Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5M
Tracking and Evaluation CoreU54GM104938 · NIGMS · UNIVERSITY OF OKLAHOMA HLTH SCIENCES CTR · PI PAUL G SPICER · 2013 to 2026
$68.2M
Spectrum Stanford Center for clinical and Translational Research and EducationUL1TR001085 · NCATS · STANFORD UNIVERSITY · PI CULLEN, MARK RICHARD, GREENBERG, HARRY BERNARD · 2013 to 2017
$37.1M
Regulation of IgA class switching in the intestinal mucosaP01AI061093 · NIAID · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI CUNNINGHAM-RUNDLES, CHARLOTTE · 2004 to 2021
$29.8M
MOUNT SINAI MEDICAL SCIENTIST TRAINING PROGRAMT32GM007280 · NIGMS · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI BARON, MARGARET H · 1985 to 2021
$22.8M
Stanford Center for Clinical and Translational Education and Research (SCCTER)UL1UL1RR025744 · NCRR · STANFORD UNIVERSITY · PI GREENBERG, HARRY BERNARD · 2008 to 2011
$22.4M
Vaccination and infection: indicators of immunological health and responsivenessU19AI090019 · NIAID · STANFORD UNIVERSITY · PI DAVIS, MARK MORRIS · 2010 to 2015
$17.3M
SNP Confirmation and High Throughput Genotyping CoreP30AR053483 · NIAMS · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI GUTHRIDGE, JOEL MARVIN · 2007 to 2017
$6.7M
TARGETING PRIMARY IMMUNODEFICIENCY AMONG MINORITIESR18AI048693 · NIAID · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI CUNNINGHAM-RUNDLES, CHARLOTTE · 2000 to 2016
$6.2M
Pre-Clinical Studies to Identify SLE Therapeutic TargetsU19AI082714 · NIAID · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI GAFFNEY, PATRICK M · 2009 to 2018
$6.2M
Understanding early events in lupus autoimmunity to aid preventionU01AI101934 · NIAID · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI JAMES, JUDITH A · 2012 to 2016
$2.3M
NCATS NIH HHS UL1 TR001085NCRR NIH HHS 1UL1 RR025744NCRR NIH HHS UL1 RR025744NIAID NIH HHS AI-0860037NIAID NIH HHS AI-1048693NIAID NIH HHS AI-1061093NIAID NIH HHS P01 AI061093NIAID NIH HHS R18 AI048693NIAID NIH HHS U01 AI101934NIAID NIH HHS U01AI101934NIAID NIH HHS U19 AI057229NIAID NIH HHS U19 AI082714NIAID NIH HHS U19AI082714NIAID NIH HHS U19 AI090019NIAMS NIH HHS P30 AR053483NIAMS NIH HHS P30AR053483NIGMS NIH HHS T32-GM007280NIGMS NIH HHS U54 GM104938NIGMS NIH HHS U54GM104938
6 · The paper itself

Abstract

Common variable immune deficiency (CVID) is the most common symptomatic primary immune deficiency, affecting ~1 in 25,000 persons. These patients suffer from impaired antibody responses, autoimmunity, and susceptibility to lymphoid cancers. To explore the cellular basis for these clinical phenotypes, we conducted high-throughput DNA sequencing of immunoglobulin heavy chain gene rearrangements from 93 CVID patients and 105 control subjects and sorted naïve and memory B cells from 13 of the CVID patients and 10 of the control subjects. The CVID patients showed abnormal VDJ rearrangement and abnormal formation of complementarity-determining region 3 (CDR3). We observed a decreased selection against antibodies with long CDR3s in memory repertoires and decreased variable gene replacement, offering possible mechanisms for increased patient autoreactivity. Our data indicate that patient immunodeficiency might derive from both decreased diversity of the naïve B cell pool and decreased somatic hypermutation in memory repertoires. The CVID patients also exhibited an abnormal clonal expansion of unmutated B cells relative to the controls. Although impaired B cell germinal center activation is commonly viewed as causative in CVID, these data indicate that CVID B cells diverge from controls as early as the pro-B stage, cell and suggest possible explanations for the increased incidence of autoimmunity, immunodeficiency, and lymphoma CVID patients.

Indexed as

B-LymphocytesCommon Variable ImmunodeficiencyDNAHigh-Throughput Nucleotide SequencingHumansImmunoglobulin Heavy ChainsLymphoma, B-CellMutationDNAImmunoglobulin Heavy Chains

Identifiers

PMID26311730
PMCPMC4584259
OpenAlexW2099351903

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Registered trials

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.