Marcos Chiñas

B cells are central for immunity and immune-mediated diseases (IMD), but how distinct signaling pathways drive diverse activation responses over time is not comprehensively understood. Here, we obtain peripheral blood B cells from 27 female healthy donors for in vitro stimulation, profiling the response at multiple time points using RNA-seq, single-cell RNA-seq with surface protein markers (CITE-seq), and ATAC-seq. Using diverse stimuli including activation of the B cell receptor (BCR), Toll-like receptor 7 (TLR7), TLR9, CD40, and differentiation into double negative 2 (DN2) IgD ^– CD27 ^– CD11c ⁺ CD21 ^– B cells, our analyses uncover activation-dependent B cell states, stimulation-specific transcription factors and regulatory regions, the dynamic response of IMD-associated gene expression, and specific open chromatin regions associated with IMD genetic risk. Furthermore, we also identify a lupus risk variant in an enhancer regulating TNFSF4 expression. The analysis data can be accessed via an interactive browser: https://mgalab.shinyapps.io/bcellactivation . Our findings underscore how profiling the full breadth of B cell activation pathways may be important for understanding B cell biology in health and disease.

A quarter of humanity is estimated to have been exposed to Mycobacterium tuberculosis (Mtb) with a 5–10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n = 63) or did not progress to TB (controls, n = 63). Transcriptomic profiling of monocyte-derived DCs and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Four genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.

Bacillus thuringiensis svar. israelensis (Bti) larvicides are effective in controlling Aedes aegypti; however, the effects of long-term exposure need to be properly evaluated. We established an Ae. aegypti strain that has been treated with Bti for 30 generations (RecBti) and is still susceptible to Bti, but females exhibited increased susceptibility to Zika virus (ZIKV). This study compared the RecBti strain to a reference strain regarding: first, the relative transcription of selected immune genes in ZIKV-challenged females (F₃₀) with increased susceptibility detected in a previous study; then, the whole transcriptomic profile using unchallenged females (F₃₅). Among the genes compared by RT-qPCR in the ZIKV-infected and uninfected females from RecBti (F₃₀) and the reference strain, hop, domeless, relish 1, defensin A, cecropin D, and gambicin showed a trend of repression in RecBti infected females. The transcriptome of RecBti (F₃₅) unchallenged females, compared with a reference strain by RNA-seq, showed a similar profile and only 59 differentially expressed genes were found among 9202 genes analyzed. Our dataset showed that the long-term Bti exposure of the RecBti strain was associated with an alteration of the expression of genes potentially involved in the response to ZIKV infection in challenged females, which is an important feature found under this condition.