Whole blood RNA signatures in leprosy patients identify reversal reactions before clinical onset: a prospective, multicenter study

Abstract

Early diagnosis of leprosy is challenging, particularly its inflammatory reactions, the major cause of irreversible neuropathy in leprosy. Current diagnostics cannot identify which patients are at risk of developing reactions. This study assessed blood RNA expression levels as potential biomarkers for leprosy. Prospective cohorts of newly diagnosed leprosy patients, including reactions, and healthy controls were recruited in Bangladesh, Brazil, Ethiopia and Nepal. RNA expression in 1,090 whole blood samples was determined for 103 target genes for innate and adaptive immune profiling by dual color Reverse-Transcription Multiplex Ligation-dependent Probe Amplification (dcRT-MLPA) followed by cluster analysis. We identified transcriptomic biomarkers associated with leprosy disease, different leprosy phenotypes as well as high exposure to Mycobacterium leprae which respectively allow improved diagnosis and classification of leprosy patients and detection of infection. Importantly, a transcriptomic signature of risk for reversal reactions consisting of five genes (CCL2, CD8A, IL2, IL15 and MARCO) was identified based on cross-sectional comparison of RNA expression. In addition, intra-individual longitudinal analyses of leprosy patients before, during and after treatment of reversal reactions, indicated that several IFN-induced genes increased significantly at onset of reaction whereas IL15 decreased. This multi-site study, situated in four leprosy endemic areas, demonstrates the potential of host transcriptomic biomarkers as correlates of risk for leprosy. Importantly, a prospective five-gene signature for reversal reactions could predict reversal reactions at least 2 weeks before onset. Thus, transcriptomic biomarkers provide promise for early detection of these acute inflammatory episodes and thereby help prevent permanent neuropathy and disability in leprosy patients.

Gene expression identifies patients who develop inflammatory arthritis in a clinically suspect arthralgia cohort

“…We studied a comprehensive set of genes with known functions using dcRT-MLPA. The candidate genes were selected based on their known role in inflammation or immunity and their previously reported identification as markers of progression in patients with other inflammatory disorders [ 8 ]. We have not used a hypothesis-free approach such as RNA sequencing in this set of 236 patients to avoid multiple testing and subsequent false-positive results.…”

“…RNA expression was determined for 133 genes of the innate and adaptive immune system by dcRT-MLPA (Additional file 1 ) and was performed as described previously [ 8 ]. Trace data were analyzed using GeneMapper software 5 (Applied Biosystems).…”

“…As previous reports suggest the involvement of immune response genes in RA pathology [ 4 – 7 ], we here hypothesize that the expression of genes related to immunity and inflammation are differently expressed in whole blood between patients who do and do not progress to inflammatory arthritis (IA). We studied RNA expression levels of a set of inflammatory and immune response genes that was previously compiled to identify markers of progression in other inflammatory conditions [ 8 , 9 ] and now used to identify markers of progression to clinical IA in patients with arthralgia.…”

Susceptibility and resistance in leprosy: Studies in the mouse model

“…88 The mechanisms that underlie and modulate the onset of leprosy reactions are not well understood but are likely manifestations of immunoregulatory changes, both systemically and in the microenvironment of the leprosy granulomas. Predicting and preventing reactional episodes would be of great benefit 89 as existing treatments often have side effects which limit application and effectiveness, especially when they must be administered long term.…”

“…94 Recently, studies using longitudinal analyses of leprosy patients before, during, and after type 1 reaction revealed an upregulation of IFNγ downstream genes 95 and identified a five-gene transcriptomic signature for onset type 1 reactions. 89…”