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      Strong Th1-biased CD4 T cell responses are associated with diminished SIV vaccine efficacy

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          Abstract

          Activated CD4 T cells are a major target of HIV infection. Results from the Step HIV vaccine trial highlighted a potential role for total activated CD4 T cells in promoting HIV acquisition. However, the influence of vaccine insert-specific CD4 T cell responses on HIV acquisition is not known. Here, using the data obtained from four macaque studies, we show that the DNA prime/modified vaccinia Ankara boost vaccine induced IFNγ+ CD4 T cells (Th1 cells) which rapidly migrate to multiple tissues including colon, cervix, and vaginal mucosa. These mucosal Th1 cells persisted at higher frequencies and expressed higher density of CCR5, a viral coreceptor, compared to cells in blood. Following intravaginal or intrarectal SIV/SHIV challenges, strong vaccine protection was evident only in animals that had lower frequencies of vaccine-specific Th1 cells but not in animals that had higher frequencies of Th1 cells, despite comparable vaccine-induced humoral and CD8 T cell immunity in both groups. An RNA transcriptome signature in blood at 7 days after priming immunization from one study was associated with induction of fewer Th1-type CD4 cells and enhanced protection. These results demonstrate that high and persisting frequencies of HIV vaccine-induced Th1-biased CD4 T cells in the intestinal and genital mucosa can mitigate beneficial effects of protective antibodies and CD8 T cells, highlighting a critical role of priming immunization and vaccine adjuvants in modulating HIV vaccine efficacy.

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          Vaccine-induced IFNγ+ CD4 T cells migrate to and persist in mucosal tissue and negatively associate with protection against SIV

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          Most cited references33

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          NLRP3 activation and mitosis are mutually exclusive events coordinated by NEK7, a new inflammasome component

          The NLRP3 inflammasome responds to microbes and danger signals by processing and activating proinflammatory cytokines including IL-1β and IL-18. We show that NLRP3 inflammasome activation is restricted to interphase of the cell cycle by NEK7, a serine/threonine kinase previously implicated in mitosis. NLRP3 inflammasome activation requires NEK7, which binds to the NLRP3 leucine-rich repeat domain in a kinase-independent manner downstream from the induction of mitochondrial ROS. This interaction is necessary for NLRP3-ASC complex formation, ASC oligomerization, and caspase-1 activation. NEK7 promotes the NLRP3-dependent cellular inflammatory response to intraperitoneal monosodium urate challenge, and the development of experimental autoimmune encephalitis in mice. Our findings suggest NEK7 serves as a cellular switch that enforces mutual exclusivity between the inflammasome response and cell division.
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            HIV-1 vaccine-induced immunity in the test-of-concept Step Study: a case-cohort analysis.

            In the Step Study, the MRKAd5 HIV-1 gag/pol/nef vaccine did not reduce plasma viraemia after infection, and HIV-1 incidence was higher in vaccine-treated than in placebo-treated men with pre-existing adenovirus serotype 5 (Ad5) immunity. We assessed vaccine-induced immunity and its potential contributions to infection risk. To assess immunogenicity, we characterised HIV-specific T cells ex vivo with validated interferon-gamma ELISPOT and intracellular cytokine staining assays, using a case-cohort design. To establish effects of vaccine and pre-existing Ad5 immunity on infection risk, we undertook flow cytometric studies to measure Ad5-specific T cells and circulating activated (Ki-67+/BcL-2(lo)) CD4+ T cells expressing CCR5. We detected interferon-gamma-secreting HIV-specific T cells (range 163/10(6) to 686/10(6) peripheral blood mononuclear cells) ex vivo by ELISPOT in 77% (258/354) of people receiving vaccine; 218 of 354 (62%) recognised two to three HIV proteins. We identified HIV-specific CD4+ T cells by intracellular cytokine staining in 58 of 142 (41%) people. In those with reactive CD4+ T cells, the median percentage of CD4+ T cells expressing interleukin 2 was 88%, and the median co-expression of interferon gamma or tumor necrosis factor alpha (TNFalpha), or both, was 72%. We noted HIV-specific CD8+ T cells (range 0.4-1.0%) in 117 of 160 (73%) participants, expressing predominantly either interferon gamma alone or with TNFalpha. Vaccine-induced HIV-specific immunity, including response rate, magnitude, and cytokine profile, did not differ between vaccinated male cases (before infection) and non-cases. Ad5-specific T cells were lower in cases than in non-cases in several subgroup analyses. The percentage of circulating Ki-67+BcL-2(lo)/CCR5+CD4+ T cells did not differ between cases and non-cases. Consistent with previous trials, the MRKAd5 HIV-1 gag/pol/nef vaccine was highly immunogenic for inducing HIV-specific CD8+ T cells. Our findings suggest that future candidate vaccines have to elicit responses that either exceed in magnitude or differ in breadth or function from those recorded in this trial.
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              Is Open Access

              integrOmics: an R package to unravel relationships between two omics datasets

              Motivation: With the availability of many ‘omics’ data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology platforms is becoming crucial to unravel the relationships between different biological functional levels. However, the development of such an analysis is a major computational and technical challenge as most approaches suffer from high data dimensionality. New methodologies need to be developed and validated. Results: integrOmics efficiently performs integrative analyses of two types of ‘omics’ variables that are measured on the same samples. It includes a regularized version of canonical correlation analysis to enlighten correlations between two datasets, and a sparse version of partial least squares (PLS) regression that includes simultaneous variable selection in both datasets. The usefulness of both approaches has been demonstrated previously and successfully applied in various integrative studies. Availability: integrOmics is freely available from http://CRAN.R-project.org/ or from the web site companion (http://math.univ-toulouse.fr/biostat) that provides full documentation and tutorials. Contact: k.lecao@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Journal
                101505086
                36963
                Sci Transl Med
                Sci Transl Med
                Science translational medicine
                1946-6234
                1946-6242
                4 April 2020
                20 November 2019
                20 July 2020
                : 11
                : 519
                : eaav1800
                Affiliations
                [1 ]Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
                [2 ]Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, Georgia 30322, USA
                [3 ]Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, School of Medicine, Seattle, Washington 981909, USA
                [4 ]Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
                [5 ]Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA
                [6 ]Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
                [7 ]Department of Pathology, Emory School of Medicine, Emory University, Atlanta, Georgia 30322, USA
                [8 ]Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia 30322, USA
                Author notes
                [‡]

                Current Address: New Iberia Research Center, University of Louisiana at Lafayette, New Iberia Louisiana 70560, USA

                [†]

                Contributed equally to this work

                Author Contributions: R.R.A. was responsible for overall experimental design and supervision of laboratory studies, manuscript writing and editing. V.C., P.B.J.R. and S.K were responsible for conducting experiments, data collection, data analysis, manuscript writing and editing. C.W., J.C. R.R.G., L.L. and M.G. were responsible for conducting microarray assays and microarray data analyses. S.G. and P.A.K. conducted antibody assays. V.V. contributed to Tfh analysis. P.B.J.R. was responsible for data from the M19 study. M.L. and S.S. performed the ICS assays in the P165 study. T.L. was responsible for isolating cells from various tissues in the M15 study. L.S.C contributed for in vitro infection assays. L.C. contributed to statistical analysis and preparation of figures. T.W. contributed to statistical analysis. G.S. and C.A.D. provided input on M15 and M19 studies and contributed in manuscript editing. F.V. coordinated the M15 and M19 studies. E.H. contributed to the design and performance of the M15 and M19 studies.

                [* ] Correspondence: Correspondence should be addressed to Dr. Rama Amara. Phone: (404) 727-8765; FAX: (404) 727-7768; ramara@ 123456emory.edu
                Article
                PMC7227795 PMC7227795 7227795 nihpa1580874
                10.1126/scitranslmed.aav1800
                7227795
                31748228
                6eee77cb-8967-4114-85a5-bb99368c9323
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