Baylor Institute for Immunology Research

Gandhi, M. J., D. Ferriola, C. Lind, J. L. Duke, A. Huynh, A. Papazoglou, K. Mackiewicz, M. Christiansen, W. Dong, S. Hsu, D. Thomas, B. Schneider, E. Pierce, J. Kearns, M. Kamoun, D. Monos and M. Askar (2017). “Assessing a single targeted next generation sequencing for human leukocyte antigen typing protocol for interoperability, as performed by users with variable experience.” Hum Immunol: 2017 Jul [Epub ahead of print].

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BACKGROUND: A simplified protocol for HLA-typing -by NGS, developed for use with the Illumina MiSeq, was performed by technologists with varying NGS experience to assess accuracy and reproducibility. METHODS: Technologists from six laboratories typed the same 16 samples at HLA-A, B, C, DRB1, and DQB1. The protocol includes long range PCR, library preparation, and paired-end 250bp sequencing. Two indexing strategies were employed: locus-specific indexing whereby each locus was tagged uniquely and sample-specific indexing whereby all 5 loci for a sample were pooled prior to library preparation. Sequence analysis was performed with two software packages, Target HLA (Omixon) and NGSengine (GenDx). RESULTS: The average number of sequence reads per library was 387,813; however, analysis was limited to 40,000 reads for locus-indexed libraries and 200,000 reads for sample-indexed libraries resulting in an average depth of coverage of 1444 reads per locus. Sufficient reads for genotype analysis were obtained for 98.4% of libraries. Genotype accuracy was >97% in pooled amplicons and >99% in individual amplicons by both software analysis. Inter-laboratory reproducibility was 99.7% and only cause of discordance was cross-contamination of a single amplicon. CONCLUSIONS: This NGS HLA-typing protocol is simple, reproducible, scalable, highly accurate and amenable to clinical testing.

Graham, J. P., P. Authie, A. Karolina Palucka and G. Zurawski (2017). “Targeting interferon-alpha to dendritic cells enhances a cd8+ t cell response to a human cd40-targeted cancer vaccine.” Vaccine: 2017 Jul [Epub ahead of print].

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Targeting antigens to antigen presenting cells (APC) enhances the potency of recombinant protein CD8+ T cell vaccines. Recent comparisons of recombinant protein-based dendritic cell (DC) targeting vaccines revealed differences in cross-presentation and identified CD40 as a potent human DC receptor target for antigen cross-presentation. Contrary to in vitro-derived monocyte (mo)DC, we found that interferon-alpha (IFNalpha) stimulation of human blood-derived DC was necessary for an antigen-specific IFNgamma CD8+ T cell response to a CD40 targeted cancer vaccine. Importantly, targeting an adjuvant in the form of IFNalpha to DC increased their potency to elicit antigen-specific production of IFNgamma by CD8+ T cells. Thus, we introduce the concept of DC adjuvant targeting to enhance the potency of vaccination.

Arostegui, J. I., J. Anton, I. Calvo, A. Robles, E. Iglesias, B. Lopez-Montesinos, R. Banchereau, S. Hong, Y. Joubert, G. Junge, V. Pascual and J. Yague (2017). “Open-label, phase ii study to assess efficacy and safety of canakinumab treatment in active hyperimmunoglobulinemia d with periodic fever syndrome.” Arthritis Rheumatol: 2017 May [Epub ahead of print].

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OBJECTIVE: To evaluate the efficacy and safety of canakinumab treatment in active hyperimmunoglobulinemia D with periodic fever syndrome (HIDS). METHODS: This was a 3-part, open-label study with a 6-month treatment period (P1; 300 mg or 4 mg/kg q6w), a 6-month withdrawal period (P2), and a 24-month treatment period (P3). The primary endpoint was reduction in frequency of attacks during treatment period compared with the historical period (HP; period in which patients did not receive drugs other than NSAIDs and/or steroids). RESULTS: All nine patients completed P1 and P2, whereas only eight completed P3. All patients achieved a complete response during P1, and only two required dose adjustments. The median number of attacks per patient decreased from 5 (3-12) during HP to 0 (0-2) during P1. During P2, seven out of nine patients flared with a median of 110 days (62-196) after the last canakinumab dose. Laboratory parameters were normalized at Day 15 and remained at normal levels throughout the study. The blood transcriptome assessed during P1 showed upregulated interferon and myeloid-related inflammatory responses in untreated patients compared to healthy controls, which rapidly decreased following canakinumab injection, reaching levels comparable to those of healthy controls. At least one adverse event (AE) was detected in all nine patients; most of them being mild in intensity, with infections being the most frequent AE. Serious AEs were reported in four patients. CONCLUSIONS: This study demonstrated the efficacy and safety of canakinumab treatment to control active HIDS and to suppress inflammatory transcriptional responses.

Miyazaki, M., K. Miyazaki, K. Chen, Y. Jin, J. Turner, A. J. Moore, R. Saito, K. Yoshida, S. Ogawa, H. R. Rodewald, Y. C. Lin, H. Kawamoto and C. Murre (2017). “The e-id protein axis specifies adaptive lymphoid cell identity and suppresses thymic innate lymphoid cell development.” Immunity 46(5): 818-834.

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Innate and adaptive lymphoid development is orchestrated by the activities of E proteins and their antagonist Id proteins, but how these factors regulate early T cell progenitor (ETP) and innate lymphoid cell (ILC) development remains unclear. Using multiple genetic strategies, we demonstrated that E proteins E2A and HEB acted in synergy in the thymus to establish T cell identity and to suppress the aberrant development of ILCs, including ILC2s and lymphoid-tissue-inducer-like cells. E2A and HEB orchestrated T cell fate and suppressed the ILC transcription signature by activating the expression of genes associated with Notch receptors, T cell receptor (TCR) assembly, and TCR-mediated signaling. E2A and HEB acted in ETPs to establish and maintain a T-cell-lineage-specific enhancer repertoire, including regulatory elements associated with the Notch1, Rag1, and Rag2 loci. On the basis of these and previous observations, we propose that the E-Id protein axis specifies innate and adaptive lymphoid cell fate.

Blazkova, J., S. Gupta, Y. Liu, B. Gaudilliere, E. A. Ganio, C. R. Bolen, R. Saar-Dover, G. K. Fragiadakis, M. S. Angst, S. Hasni, N. Aghaeepour, D. Stevenson, N. Baldwin, E. Anguiano, D. Chaussabel, M. C. Altman, M. J. Kaplan, M. M. Davis and D. Furman (2017). “Multicenter systems analysis of human blood reveals immature neutrophils in males and during pregnancy.” J Immunol 198(6): 2479-2488.

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Despite clear differences in immune system responses and in the prevalence of autoimmune diseases between males and females, there is little understanding of the processes involved. In this study, we identified a gene signature of immature-like neutrophils, characterized by the overexpression of genes encoding for several granule-containing proteins, which was found at higher levels (up to 3-fold) in young (20-30 y old) but not older (60 to >89 y old) males compared with females. Functional and phenotypic characterization of peripheral blood neutrophils revealed more mature and responsive neutrophils in young females, which also exhibited an elevated capacity in neutrophil extracellular trap formation at baseline and upon microbial or sterile autoimmune stimuli. The expression levels of the immature-like neutrophil signature increased linearly with pregnancy, an immune state of increased susceptibility to certain infections. Using mass cytometry, we also find increased frequencies of immature forms of neutrophils in the blood of women during late pregnancy. Thus, our findings show novel sex differences in innate immunity and identify a common neutrophil signature in males and in pregnant women.