Elucidating the functional dynamics of DNASE1L2 intron retention in tuberculosis progression

Intron retention (IR) is an important biological process associated with disease development. However, the role of IR in the progression of tuberculosis (TB) remains unexplored. Therefore, this study aimed to characterize the dynamic IR landscape during TB progression and elucidate the role of DNASE1L2 -IR in this process.

We conducted a comprehensive high-throughput sequencing analysis using 1729 samples from 19 public datasets and identified candidate IR events associated with TB progression. We then validated these candidate IR events in three macrophage infection models by quantitative polymerase chain reaction and revealed the underlying molecular mechanisms by investigating the subcellular localization and functional roles of their associated isoforms.

In an analysis of 1729 clinical specimens, we found genome-wide intron-splicing reprogramming in host cells during TB progression. Notably, deoxyribonuclease 1 like 2 ( DNASE1L2, a gene encoding deoxyribonuclease)-IR exhibited striking differences among healthy controls, individuals with latent TB infection, and individuals with active TB ( Padj <0.05), particularly between progressors and nonprogressors ( Padj <0.0001). Similar differences were observed in Mycobacterium tuberculosis ( M. tuberculosis ) infection models in vitro ; as the stimulation increased in concentration or duration, IR initially increased but subsequently decreased. DNASE1L2 -IR generated two transcript isoforms: a long isoform ( DNASE1L2 -L) and a short isoform ( DNASE1L2 -S). Upon stimulation, DNASE1L2-L appeared in the cytoplasm, whereas DNASE1L2-S remained membrane-anchored. Deoxyribonuclease activity assays revealed that compared with DNASE1L2-S, DNASE1L2-L exhibited significantly greater enzymatic activity against plasmid and M. tuberculosis DNA substrates and more effectively suppressed the release of interleukin-1beta and tumor necrosis factor alpha, indicating isoform-specific functional divergence in inflammatory regulation.

These findings identify DNASE1L2 -IR splicing dynamics as a novel biomarker for monitoring TB progression and reveal a host-defense mechanism in which DNASE1L2 -IR regulates M. tuberculosis DNA degradation to modulate TB progression.