RNA-Seq profiling of blood and jejunal samples from subclinical Holstein cattle naturally infected with Mycobacterium avium subsp. paratuberculosis revealed host transcriptional adaptations to a latent MAP infection
Bovine paratuberculosis (PTB), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic granulomatous intestinal disease that leads to substantial economic losses in the global dairy industry. Current diagnostic tests have limited sensitivity, as they can reliably detect only animals that have advanced stages of disease characterized by diffuse lesions and with the presence of clinical signs, but fail to identify those in earlier or subclinical stages, with focal or multifocal lesions in gut tissues. Previous studies have suggested that multifocal granulomas prevent lesions progression, but the molecular mechanisms involved in the establishment and maintenance of a chronic MAP infection are not fully understood. This study aimed to compare the whole transcriptomic profiles of peripheral blood (PB), jejunum (JE), and jejunal lymph node (JELN) samples from Holstein cattle with multifocal lesions and those without lesions in gut tissues. Total RNA was extracted from samples from 11 cows with multifocal lesions and 4 control cows without lesions. RNA libraries were prepared using 250 ng of RNA with the Illumina NEBNext Ultra Directional RNA library preparation kit and sequenced on an Illumina NovaSeq sequencer. On average, 34.08, 33.85, and 36.92 million raw reads were sequenced from the PB, JE and JELN samples, respectively. In cows with multifocal lesions compared to controls, 1,272 differentially expressed (DE) genes were identified in PB, mainly linked to translation, RNA splicing, and mRNA processing. In JE, 7 genes were DE and related to metabolic processes, oxidative stress response, and granulocyte migration. In JELN, 18 genes were DE and associated with the mTOR signaling, response to reactive oxygen species and hypoxia, and regulation of autophagy. The protein-to-protein interaction (PPI) analysis revealed that several differentially expressed genes are highly interconnected and associated with pathways related to splicing and translation inhibition, as well as activation of a robust innate immune response in peripheral blood. Overall, this study demonstrates that MAP persistence with multifocal granulomas results from a complex interplay of host innate immune activation and regulation, autophagy suppression, translational reprogramming, and metabolic adaptation, providing new insights into MAP pathogenesis and identifying potential biomarkers or therapeutic targets. Overall design: RNA-Seq libraries prepared from peripheral blood (PB), jejunum (Ty), and jejunal lymph node (Tg) samples from Holstein cattle with multifocal lesions (N = 11) and without lesions in gut tissues (N = 4).