Type 1 reaction leprosy patients display distinct immune-regulatory capacity before onset of symptoms

Leprosy is a chronic disease of the skin and peripheral nerves caused by Mycobacterium leprae . A major public health and clinical problem are leprosy reactions, which are inflammatory episodes that often contribute to nerve damage and disability. Type I reversal reactions (T1R) can occur after microbiological cure of leprosy and affect up to 50% of leprosy patients. Early intervention to prevent T1R and, hence, nerve damage, is a major focus of current leprosy control efforts. In a prospective study, we enrolled and collected samples from 32 leprosy patients before the onset of T1R. Whole blood aliquots were challenged with M. leprae sonicate or media and total RNA was extracted. After a three-year follow-up, the transcriptomic response was compared between cells from 22 patients who remained T1R-free and 10 patients who developed T1R during that period. Our analysis focused on differential transcript (i.e. isoform) expression and usage. Results showed that, at baseline, cells from T1R-destined and T1R-free subjects had no main difference in their transcripts expression and usage. However, the cells of T1R patients displayed a transcriptomic immune response to M. leprae antigens that was significantly different from the one of cells from leprosy patients who remained T1R-free. Transcripts with significantly higher upregulation in the T1R-destined group, compared to the cells from T1R-free patients, were enriched for pathways and GO terms involved in response to intracellular pathogens, apoptosis regulation and inflammatory processes. Similarly, transcript usage analysis pinpointed different transcript proportions in response to the in-vitro challenge of cells from T1R-destined patients. Hence, transcript usage in concert with transcript expression suggested a dysregulated inflammatory response including increased apoptosis regulation in the peripheral blood cells of T1R-destined patients before the onset of T1R symptoms. Combined, these results provided detailed insight into the pathogenesis of T1R. Author Summary The prevention and clinical management of type 1 reactions (T1R) remain an important unmet need to reduce nerve damage in leprosy patients. It is not known why 30-50% of leprosy patients will develop T1R. This knowledge gap underlies the need for a better mechanistic understanding of T1R that could lead to biomarker candidates to identify leprosy patients who are at high risk of developing T1R. Here, we used a prospective design in which leprosy patients were enrolled before the onset of T1R.Whole blood samples were obtained at enrollment, aliquots were left unstimulated or were stimulated M. leprae antigens and total RNA was extracted. Patients were followed for three years at which time 10 out of 32 participants had developed T1R. Subsequent transcript expression and usage analyses revealed that groups differed little in their isoform landscape at baseline. Following stimulation, transcriptomic response differences became pronounced. Transcripts with higher response in T1R group preferentially involved genes of intracellular defense and inflammatory pathways. Among these transcripts, non-coding ones had higher frequency in T1R. Our study provided new insights into the T1R pathogenesis by suggesting a role for non-coding transcripts into the immune dysregulations of T1R and providing additional candidate genes and their isoforms to be further investigated. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Yes ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study received approval from the regulatory authorities of Ho Chi Minh City, Vietnam (So3813/UB-VX and 4933/UBND-VX) and the Research Ethics Board of the Research Institute at McGill University Health Centre in Montreal, Canada (REC98-041). Informed consent was obtained for all subjects participating in the study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes RNA-seq raw sequences and corresponding estimated expression matrices analyzed in this work are being submitted to NCBI’s Gene Expression Omnibus repository and will be available at the time of publication.