Qunying Yang

High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets

Developing T cells face a series of cell fate choices in the thymus and in the periphery. The role of the individual T cell receptor (TCR) in determining decisions of cell fate remains unresolved. The stochastic/selection model postulates that the initial fate of the cell is independent of TCR specificity, with survival dependent on additional TCR/coreceptor “rescue” signals. The “instructive” model holds that cell fate is initiated by the interaction of the TCR with a cognate peptide-MHC complex. T cells are then segregated on the basis of TCR specificity with the aid of critical coreceptors and signal modulators [Chan S, Correia-Neves M, Benoist C, Mathis (1998) Immunol Rev 165: 195–207]. The former would predict a random representation of individual TCR across divergent T cell lineages whereas the latter would predict minimal overlap between divergent T cell subsets. To address this issue, we have used high-throughput sequencing to evaluate the TCR distribution among key T cell developmental and effector subsets from a single donor. We found numerous examples of individual subsets sharing identical TCR sequence, supporting a model of a stochastic process of cell fate determination coupled with dynamic patterns of clonal expansion of T cells bearing the same TCR sequence among both CD4+ and CD8+ populations.

Interaction of normal and expanded CAG repeat sizes influences age at onset of Huntington disease

Huntington disease (HD) is a neurodegenerative disorder caused by the abnormal expansion of CAG repeats in the HD gene on chromosome 4p16.3. Past studies have shown that the size of expanded CAG repeat is inversely associated with age at onset (AO) of HD. It is not known whether the normal Huntington allele size influences the relation between the expanded repeat and AO of HD. Data collected from two independent cohorts were used to test the hypothesis that the unexpanded CAG repeat interacts with the expanded CAG repeat to influence AO of HD. In the New England Huntington Disease Center Without Walls (NEHD) cohort of 221 HD affected persons and in the HD‐MAPS cohort of 533 HD affected persons, we found evidence supporting an interaction between the expanded and unexpanded CAG repeat sizes which influences AO of HD (P = 0.08 and 0.07, respectively). The association was statistically significant when both cohorts were combined (P = 0.012). The estimated heritability of the AO residual was 0.56 after adjustment for normal and expanded repeats and their interaction. An analysis of tertiles of repeats sizes revealed that the effect of the normal allele is seen among persons with large HD repeat sizes (47–83). These findings suggest that an increase in the size of the normal repeat may mitigate the expression of the disease among HD affected persons with large expanded CAG repeats.

Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires

Processes that define immunoglobulin repertoires are commonly presumed to be the same for all murine B cells. However, studies here that couple high-dimensional FACS sorting with large-scale quantitative IgH deep-sequencing demonstrate that B-1a IgH repertoire differs dramatically from the follicular and marginal zone B cells repertoires and is defined by distinct mechanisms. We track B-1a cells from their early appearance in neonatal spleen to their long-term residence in adult peritoneum and spleen. We show that de novo B-1a IgH rearrangement mainly occurs during the first few weeks of life, after which their repertoire continues to evolve profoundly, including convergent selection of certain V(D)J rearrangements encoding specific CDR3 peptides in all adults and progressive introduction of hypermutation and class-switching as animals age. This V(D)J selection and AID-mediated diversification operate comparably in germ-free and conventional mice, indicating these unique B-1a repertoire-defining mechanisms are driven by antigens that are not derived from microbiota. DOI: http://dx.doi.org/10.7554/eLife.09083.001

Belimumab promotes negative selection of activated autoreactive B cells in systemic lupus erythematosus patients

Belimumab has therapeutic benefit in active systemic lupus erythematosus (SLE), especially in patients with high-titer anti-dsDNA antibodies. We asked whether the profound B cell loss in belimumab-treated SLE patients is accompanied by shifts in the immunoglobulin repertoire. We enrolled 15 patients who had been continuously treated with belimumab for more than 7 years, 17 matched controls, and 5 patients who were studied before and after drug initiation. VH genes of sort-purified mature B cells and plasmablasts were subjected to next-generation sequencing. We found that B cell-activating factor (BAFF) regulates the transitional B cell checkpoint, with conservation of transitional 1 (T1) cells and approximately 90% loss of T3 and naive B cells after chronic belimumab treatment. Class-switched memory B cells, B1 B cells, and plasmablasts were also substantially depleted. Next-generation sequencing revealed no redistribution of VH, DH, or JH family usage and no effect of belimumab on representation of the autoreactive VH4-34 gene or CDR3 composition in unmutated IgM sequences, suggesting a minimal effect on selection of the naive B cell repertoire. Interestingly, a significantly greater loss of VH4-34 was observed among mutated IgM and plasmablast sequences in chronic belimumab-treated subjects than in controls, suggesting that belimumab promotes negative selection of activated autoreactive B cells.

22 T-cell Receptor β (TCR β) Complementarity-Determining Region 3 (CDR3) Sequencing Provides a Distinct Profile Defining IBD Patients and Identifies Unique TCR β CDR3 Regions Significantly Associated With Crohn's Disease or Ulcerative Colitis

Background: Rotavirus (RV), the worlds leading cause of severe viral gastroenteritis amongst children, primarily infects small intestinal epithelial cells (IECs) and is responsible for over 500,000 deaths and millions of physician visits/hospitalizations per year. While successful resolution of infection and protection against future infection is mediated by adaptive immunity, particularly mucosal IgA, relatively little is known how innate immunity contains acute infection and drives the adaptive immune response to this virus. In light of the broad role of MyD88 in signaling by TLRs and inflammasome cytokine receptors signaling, our goal was examine the consequence of absence of MyD88 in a mouse model of RV infection as means to mechanistically explore innate immunity to this virus. Methods: Suckling and adult mice (WT, MyD88KO, Caspase-1KO, and various bone-marrow irradiation chimeras) mice were inoculated with mouse-passaged RVEC strain. Infection was assessed by ELISA and qRT-PCR. RV replication was assessed by quantitating + to strand ratios. Diarrhea was scored visually. RV-specific immune responses were measured by fecal/serum ELISA. Results: Loss of MyD88 markedly impaired innate immunity to RV resulting in higher levels of virus in feces, intestinal lysates, and peripheral blood cells as well as increased RV replicative ability. Such increased RV levels correlated with a marked increase in the incidence and duration of diarrhea in neonatal mice. These results were fully phenocopied by loss of Caspase-1 and partially mimicked by loss of IL-1 and IL-18 suggesting a role for inflammasome signaling in innate control of RV infection. Such inability to control RV was not observed in irradiated WTmice reconstituted with MyD88KO or Caspase-1KO bone marrow nor could WT bone marrow restore innate immunity to RV in MyD88KO or Caspase-1KO mice suggesting a prominent role for inflammasome signaling in IEC in limiting RV infection/ pathogenesis. Loss of MyD88 also profoundly impaired adaptive immunity to RV. Specifically, MyD88KOmice produced less serum RV-specific IgG and IgA and have Th2 skewed antibody responses indicative of improper Th responses and isotype class switching. In contrast to the role of MyD88 in innate immunity, MyD88-mediated adaptive immunity was independent of Caspase-1, IL-1, and IL-18 and was mediated by MyD88 in bone marrow derived cells. Conclusion: Inflammasome signaling, in IECs, plays a major role in limiting RV infection and, consequently, the diarrheal disease that the great mortality/morbidity caused by this pathogen. TLR signaling in bone-marrow derived cells is important for driving the humoral immune responses that provide lasting protection against this pathogen.