Posted in Malaria, Resource

Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine

Figure highlighting that subjects with increased expression of genes involved in formation of the immunoproteasome complex after RTS,S vaccination are associated with increased protection from malaria challenge. Specific genes involved highlighted in red. Source from MT Vahey, JID, 2010.

The RTS,S is a subunit recombinant vaccine expressed in yeast that represents the central repeat and C-terminal portion of the Plasmodium falciparum circumsporozoite protein (CSP) covalently linked with the S antigen of hepatitis B virus. The overall protective efficacy of RTS,S/ASO1B in malaria-naive adults is ∼50%.

The differences in the spectrum of the protective responses to adjuvanted RTS,S, and the ability to do an experimental challenge with the mosquito-borne falciparum malaria, offers an opportunity to decipher the host genomic mechanisms involved in vaccine efficacy against malaria.

In this study by MT Vahey et al., 2010, 39 vaccine recipients were assessed at study entry, on the day of the third vaccination, at 24 h, 72 h, and 2 weeks after vaccination, and on day 5 after challenge. Of 39 vaccine recipients, 13 were protected and 26 were not.

Most DEGs were detected at day 1 post vaccination, with the majority of these transcripts associated with proinflammatory responses. Most of these responses resolve at day 3 post-vaccination.

After day 5 of malaria challenge, prediction analysis of microarray (PAMR) identified 393 genes that are differentially expressed in subjects who are protected and unprotected. Most of these genes are related to apoptosis and cell cycle.

At 2 weeks after the third vaccination but before malaria challenge, 32 genes belonging to the proteasome degradation pathway separated protected vs unprotected subjects. Examples include PSME2 (a component of the 11S regulator), and PSMA4, PSMB6, and PSMB9 which forms the immunoproteasome involved in processesing of peptides for presentation to the MHC complex.

This study may highlight the critical role of T-cells as correlate of protection against malaria. Data deposited at Gene Expression Omnibus, with accession number GSE18323.

Posted in influenza, Resource

Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection

Figure describing the 8 distinct clusters of genes that are temporally modulated (0-108hrs) in the symptomatic (Sx) and the asymptomatic (Asx) volunteers after challenge with influenza virus. Source: Yongsheng H et al., PLOS Genetics, 2011.

A deep understanding of the molecular underpinnings underlying severe viral disease outcome in humans is critical for the development of drugs and therapeutics. Controlled human infection studies, in which volunteers are intentionally infected with a pathogen, can advance our understanding of disease pathogenesis as the incubation time, time-course of disease progression, symptomatic rates and immune responses can be closely monitored. In this manuscript published by Yongsheng H et al., PLOS Genetics, 2011, the authors investigated how the transcripts are differentially modulated in the symptomatic and asymptomatic subjects after challenge with the live influenza (H3N2/Wisconsin) strain

17 healthy adults were inoculated with live influenza (H3N2/Wisconsin) strain at 3 different doses (1∶10, 1∶100, 1∶1000, 1∶10000). 9 subjects were symptomatic whereas 8 were asymptomatic. Changes in host peripheral blood gene expression measured at -12, 0, 12, 21, 29, 36, 45, 53, 60, 69, 77, 84, 93, 101 and 108 hrs. 

Increasing doses of virus does not correlate with increased symptomatic outcome. This finding is congruent with our previous findings showing vaccine viremia does not influence symptomatic rates (Chan et al., JCI insight, 2017). In contrast, gene signature patterns were strongly associated with disease severity.

Using EDGE with false discovery rate (FDR) significance level (q-value)<0.01, 5,076 genes were temporally changed, comparing between symptomatic and asymptomatic phenotypes. Self-organizing maps (SOM) identified eight distinct classes with differential expression dynamics (See figure above).

Cluster 3 reveal genes that are uniquely increased in symptomatic subjects. These include PRR genes such as Toll-like receptor 7 (TLR7), the RNA helicases (RIG-I), and interferon induced with helicase C domain 1 (IFIH1). In addition, 11 genes from the TLR signaling pathway, including MyD88, TRAF6, and STAT1. NOD1, RIPK2, NOD2, NLPR3, and CASP5 and CASP1 and IL1b were increased in symptomatic subjects but not in the asymptomatic subjects.

Cluster 6 genes identified genes that are uniquely increased in the asymptomatic subjects. Enriched pathways were enriched are related to cellular response to oxidative stress. These include superoxide dismutase (SOD1) and serine/threonine kinase 25 (STK25 or SOK1), which have been linked to anti-oxidant/stress response and reduced concentration of ROS. This cluster also contain genes related to ribosomal synthesis, suggesting that protein biosynthesis could be protective against severe disease.

Both raw and normalized gene expression data are available at GEO (GSE30550).