Gene expression profiling in pure neural leprosy: insights into pathogenesis and diagnostic biomarkers

Abstract

Introduction: Leprosy may affect skin and nerves, leading to permanent disabilities and deformities. Pure neural leprosy (PNL) lacks skin lesions, complicating diagnosis. Moreover there is no a specific treatment to control neural damage. Transcriptomic profiling may reveals unique gene expression changes in PNL nerves, shedding light on immune response and pathogenesis. These findings may guide early diagnosis and improve patient outcome.

Methods: In the present study, we investigated the gene profiling of nerve samples from patients with PNL and revealed significant transcriptomic alterations compared to non-leprosy controls.

Results: Principal Component Analysis (PCA) of the 500 most differentially expressed genes separated the groups, with 1,199 genes showing differential expression (|log₂FC| ≥ 1, FDR ≤ 0.1). Downregulated genes included GAS2L2, TRIM67, IL1RAPL1, MAP1LC3B2, and NTNG1, implicated in neuronal development and autophagy, while upregulated genes were linked to immune responses. Functional analyses highlighted inflammasome activation and autophagy impairment in PNL, correlating with nerve inflammation and architecture loss.

Discussion: We hope that our data will aid in identifying new markers, fostering strategies for early diagnosis, preventing disabilities, and improving the management of PNL patients.

Keywords: autophagy; immunopathogenesis; inflammasomes; pure neural leprosy; transcriptomic analysis.

Figure 1

Nerve fragments from PNL patients display a distinct transcriptomic profile to that of non-leprosy controls. (A) Principal component analysis (PCA) of the 500 most variable genes in PNL patients (PNL; red, n=6) compared to those that were non-leprosy controls (Vasculitis; blue, n=9). (B) Volcano plot analysis of differentially expressed genes in PNL vs. non-Leprosy controls. Differentially expressed genes are depicted in blue. (C) Heatmap showing the differentially expressed genes (DEG) in the nerve fragments from PNL (pure-neural-lep) patients over non-leprosy controls (vasculitis). In addition to comparing patients with PNL to the control group (vasculitis), the correlation of gene expression with the presence of neuritis, disability degree, AFB, qPCR, age and sex is presented, showing that gene expression is not influenced by these variables. Expression levels are represented by a scale of log₂FC from -3 (dark blue) to 3 (bright red). AFB, acid fast bacilli.

Figure 2

Biological processes enriched in the nerve fragments transcriptomics of patients experiencing PNL. Dotplot of enriched biological processes associated with (A) positively and (B) negatively regulated genes in PNL patients obtained by the overrepresentation analysis (ORA). Pathways are depicted in a hierarchy according to the enrichment ratio. Circle size (Count) and color indicate, respectively, the number of genes associated with the pathway and the adjusted P-value. The square color indicates the p.adjust value according to the scale.

Figure 3

Nerve fragments from PNL patients display a deficiency in the expression of autophagy genes and an increase in the inflammasome pathways. (A) Volcano plot analysis of differentially expressed genes in inflammasome and autophagy pathways by PNL vs. non-Leprosy controls. Differentially expressed genes are depicted in blue (FDR < 0,1 |log₂FC| > 1) and green (FDR < 0.1 |log₂FC| > 0.5). (B) Heatplot of enriched biological processes associated with positively regulated genes in the PNL patients obtained by over-representation analysis (ORA). Values of log₂FC are color-graded according to the scale.

Figure 4

The inflammasome components are increased in nerve fragments from PNL. (A, B) Expression of S100; (C, D) CD68; (E, F) ASC; (G, H) IL-1β; and (I, J) NLRP-1 was detected by immunohistochemistry. Epineurium (asterisk); Vessels (arrows). Representative images are shown. Bars: 50 µm.