The initial interaction between a microbial pathogen and the host immune response influences the outcome of the battle between the host and the foreign invader. Leprosy, caused by the obligate intracellular pathogen
Mycobacterium leprae
, provides a model to study relevant human immune responses. Previous studies have adopted a targeted approach to investigate host response to
M
.
leprae
infection, focusing on the induction of specific molecules and pathways. By measuring the host transcriptome triggered by
M
.
leprae
infection of human macrophages, we were able to detect a host gene signature 24–48 hours after infection characterized by specific innate immune pathways involving the cell fate mechanisms autophagy and apoptosis. The top upstream regulator in the
M
.
leprae
-induced gene signature was
NUPR1
, which is found in the
M
.
leprae
-induced cell fate pathways. The induction of
NUPR1
by
M
.
leprae
was dependent on the production of the type I interferon (IFN), IFN-β. Furthermore, NUPR1 mRNA and protein were upregulated in the skin lesions from patients with the multibacillary form of leprosy. Together, these data indicate that
M
.
leprae
induces a cell fate program which includes
NUPR1
as part of the host response in the progressive form of leprosy.