Anne Dumaine

Genetic ancestry shapes context-dependent immune regulation across Indigenous South American populations

The paper generates a single-cell transcriptional atlas of Indigenous South American populations and shows genetic ancestry influences immune gene expression, particularly after stimulation.

Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients

This study identifies gene-environment interactions influencing immune response to SARS-CoV-2 in hospitalized patients using single-cell RNA-sequencing and eQTL analysis.

Adaptive immune responses to vaccination reflect social status at first exposure in female rhesus macaques

This study shows that social status at first exposure, but not secondary exposure, influences antibody responses and gene expression in vaccinated female rhesus macaques.

Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts

The paper identifies chromatin accessibility QTLs (caQTLs) in immune cells and finds they colocalize more with GWAS loci than eQTLs, but often lack downstream gene expression effects.

Reply to Barton et al: signatures of natural selection during the Black Death

The paper addresses statistical concerns about detecting natural selection during the Black Death using ancient genomic data, reaffirming findings related to immune loci and the ERAP2 variant.

Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV

The paper investigates how HIV and antiretroviral therapy affect the transcriptional and epigenetic response of alveolar macrophages to Mycobacterium tuberculosis.

Gene activation precedes DNA demethylation in response to infection in human dendritic cells

The paper shows that gene expression changes precede DNA demethylation in human dendritic cells during infection with Mycobacterium tuberculosis.

Widespread shortening of 3’ untranslated regions and increased exon inclusion are evolutionarily conserved features of innate immune responses to infection

The paper identifies widespread changes in RNA processing, including shorter 3’ UTRs and increased exon inclusion, in innate immune responses across humans and non-human primates.

Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans.

The paper identifies a Neandertal haplotype at the OAS locus that affects innate immune responses by altering OAS gene expression and splice variants in humans.

Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells

This study shows that bacterial infection rapidly alters DNA methylation in human dendritic cells, affecting enhancer elements and gene expression related to immune responses.