Probing dermal immunity to mycobacteria through a controlled human infection model

Cutaneous mycobacterial infections cause substantial morbidity and are challenging to diagnose and treat. An improved understanding of the dermal immune response to mycobacteria may inspire new therapeutic approaches. We conducted a controlled human infection study with ten participants who received 2x10^6 colony forming units of Mycobacterium bovis Bacillus Calmette-Guerin (BCG) (Tice strain) intradermally and were randomized to receive isoniazid or no treatment. Peripheral blood was collected at multiple timepoints for bulk RNA-seq and other assays. RNA isolation from whole blood cryopreserved in Tempus blood RNA Tubes (Thermo Fisher Scientific) was performed according to manufacturer's instructions using the Tempus spin RNA Isolation kit (Thermo Fisher Scientific). Globin depletion from total RNA from whole blood was performed according to manufacturer's instructions using the GLOBINclear-Human Kit (Thermo Fisher Scientific). Stranded poly-adenylated (polyA) mRNA-seq libraries were generated from 50ng of globin depleted whole blood RNA using the Advanta RNA-seq XT NGS library prep kit with unique dual indices (Standard Biotools) using the 48-Atlas Integrated Fluidic chip on the Juno Instrument (Standard Biotools) according to the manufacturer's instructions and sequenced on the Illumina Novaseq6000 sequencing platform (Illumina).