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Functional genomic analysis of the 68-1 RhCMV-Mycobacteria tuberculosis vaccine reveals an IL-15 response signature that is conserved with vector attenuation

ABSTRACT: Functional genomic analysis of the 68-1 RhCMV-Mycobacteria tuberculosis vaccine reveals an IL-15 response signature that is conserved with vector attenuation

PROVIDER: PRJNA1143901 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30123300_1.fastq.gz	Fastqsanger.gz
	SRR30123300_2.fastq.gz	Fastqsanger.gz
	SRR30123400_1.fastq.gz	Fastqsanger.gz
	SRR30123400_2.fastq.gz	Fastqsanger.gz
	SRR30123500_1.fastq.gz	Fastqsanger.gz

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Functional genomic analysis of the 68-1 RhCMV-Mycobacteria tuberculosis vaccine reveals an IL-15 response signature that is conserved with vector attenuation

Project description:Here we conducted a bulk RNA-seq analysis of whole blood samples collected from RMs administered with RhCMV vector vaccines using a prime-boost strategy. Two vaccines were used in this study, including 68-1 RhCMV/TB-6Ag (encoding 6 Mtb protein immunogens) and its attenuated variant, 68-1 RhCMV/Δpp71-TB-6Ag (a cell to cell spread-deficient vaccine vector lacking the Rh110 gene encoding the pp71 tegument protein).

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Comparative genome sequencing of wild type rhesus cytomegalovirus (RhCMV) with a recombinant RhCMV lacking ORF 178

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Project description:Recombinant RhCMV was created to study super-infection of Rhesus macaques. These viruses (RhCMV Δ178;RhCMV Δ182-189;RhCMV Δ178Δ182-189) were co-hybridized with a wild-type BAC-derived RhCMV to a RhCMV tiling array to ensure that there were no additional mutations beyond the intended deleted regions.

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Functional genomic analysis of the 68-1 RhCMV-<i>Mycobacteria tuberculosis</i> vaccine reveals an IL-15 response signature that is conserved with vector attenuation.

Project description:Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is a deadly infectious disease having a major impact on global health. Using the CMV vector for development of novel vaccines is a promising new strategy that elicits strong and durable, high frequency memory T cell responses against heterologous immunogens. We conducted functional transcriptomic analysis of whole blood samples collected from cohorts of rhesus (Rh) macaques that were administered RhCMV/TB vector using a prime-boost strategy. Two modified CMV vectors were used in this study, including 68-1 RhCMV/TB-6Ag (encoding 6 Mtb protein immunogens, including Ag85A, ESAT-6, Rv3407, Rv2626, Rpf A, and Rpf D) and its attenuated variant, 68-1 RhCMV/Δpp71-TB-6Ag (a cell-to-cell spread-deficient vaccine vector lacking the Rh110 gene encoding the pp71 tegument protein). Bulk mRNA sequencing, differential gene expression, and functional enrichment analyses showed that these RhCMV/TB vaccines induce the innate and adaptive immune responses with specific transcriptomic signatures, including the IL-15-induced protective gene signature previously defined to be linked with protection against simian immunodeficiency virus (SIV) by the 68-1 RhCMV/SIV vaccine. While both vectors exhibited a transcriptomic response of the IL-15 protective signature in whole blood, we show that lack of pp71 does not maintain induction of the protective signature for the full duration of the study compared to the parental non-attenuated vector. Our observations indicate that RhCMV vector vaccines induce a transcriptomic response in whole blood that include a conserved IL-15 signature of which vector-encoded pp71 is an important component of response durability that upon future Mtb challenge may define specific vaccine protection outcomes against Mtb infection.

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Project description:The 68-1 rhesus cytomegalovirus (RhCMV) vector which expresses Simian Immunodeficiency Virus (SIV) genes (Gag/Tat/Nef/5-Pol) is effective in controlling and clearing SIV in rhesus macaques and the human ortholog vector is a vaccine candidate for the prevention of HIV. Currently the RhCMV/SIV vaccine is only effective in ~55% (referred to as protected animals) of Rhesus Macaques. A previous study by Barrenäs et al., 2021, showed that significant gene expression changes in a key set of IL-15 linked genes was correlated with a protection outcome. To further our understanding of the transcriptomic state if cells in protected animals and mechanisms of protection induced by the RhCMV vaccine we performed single cell RNA-sequencing on PBMCs from protected, non-protected and unvaccinated animals at longitudinal time points post SIV challenge. We identified monocytes, CD8 T cells and NK cells were primarily responsible for expression of genes in the IL-15 enriched protective signature. Myeloid cells were transcriptionally distinct 1) from all other cell types, 2) between nonprotected and protected vaccinated RMs and 3) between protected and unvaccinated SIV-infected animals. Specifically, transcriptomics indicated that myeloid cells were more activated and mature in protected animals by the vaccine at pre-challenge and post-challenge time points. This suggests that the transcriptional state of myeloid cells is essential in eliciting a protection outcome and could be used to determine whether an animal will be protected after vaccination.

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Project description:RhCMV/SIV strain 68-1 vector vaccination in RhCMV+ and RhCMV- rhesus macaques

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Bulk RNA sequencing study of female rhesus macaques given Modified versions of the RhCMV/SIV vector-based vaccines.

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