Full project title:
Biomarkers for early detection of leprosy using comparative transcriptomics

Project coordination
ICMR-National Institute of Research in Tribal Health

Partner
National Hansen's Disease Program (USA)

Aim: This project aimed to better understand how some infected people can resist an infection with the leprosy bacteria while others develop the disease.

Final project summary
Leprosy diagnosis is mainly guided by clinical symptoms (loss of sensation due to nerve damage) and positive smear from lesions, which is usually a late stage until when the transmission continues to other healthy contacts and community members. Microbial pathogens possess specific virulence factors which in combination with other molecules (called Pathogen Associated Molecular Patterns or PAMPs), elicit a characteristic gene-expression pattern (referred as transcriptional profile) that determines a differential outcome (disease or clearance) of an infection in different hosts. The main research quest is to understand “how some infected people can resist M. leprae infection while others progress to disease?”

Laboratory diagnosis of leprosy is challenging due to complex factors related to host genetics. The nine-banded armadillo is the only available animal model to study leprosy progression and pathogenesis with defined duration and dose of M. leprae infection. Interestingly, armadillos also exhibit differential susceptibility to leprosy, with ~20% animals being able to resist experimental inoculation of M. leprae. Thus, in the present study, the research team has used armadillo model for identifying the biomarkers of leprosy progression by comparing the gene expression profiles of leprosy-susceptible and -resistant animals after experimental infection of leprosy bacilli. Peripheral blood mononuclear cells (PBMCs) collected and cryo-preserved at the 4th and 18th month after infection from the leprosy-resistant and -susceptible animals were revived and stimulated with M. leprae antigens and their transcriptome profiles were compared using RNA-Seq & bioinformatics tools. This analysis has identified differentially expressed genes (DEGs). It was noticed that these gene-expression profiles were able to differentiate the animals according to their differential susceptibility to leprosy, including one animal which has an intermediate level of susceptibility and indeed clustered separately between the groups of the resistant and susceptible animals. Bioinformatic analysis and comparison of differentially expressed genes by literature mining was performed. In addition, the gene expression pattern observed at the 4th month time-point had remarkable similarities with that observed at the 18th month time-point, indicating that the gene-expression profiles can potentially predict the disease even during the pre-symptomatic stages of leprosy, and thus can serve as valuable biomarkers for early detection of the disease.

In this study, the researchers have identified a list of candidate pathways and genes (IDO-1, C-X-C motif chemokine ligand CXCL9/CXCL10, CD34 andIL10 etc.) which could be playing important role in leprosy pathogenesis and progression. Particularly, the IDO1 has been associated with immunosuppressive activity and may be linked to the poor cell-mediated immunity observed in lepromatous leprosy cases. The results were also confirmed using quantitative-PCR. Many of these genes have been previously implicated in leprosy pathogenesis (such as C-X-Cmotif chemokine ligand CXCL9 /CXCL10, myelin protein zero MPZ etc.) and have been found to be differentially expressed upon infection in different studies using clinical samples or cell-line based experiments. A significant number of DEGs and pathways are involved in host innate immunity and neurological processes, consistent with leprosy pathogenesis and neuro-predilection of M. leprae. The analysis of the affected pathways has revealed gene networks which are associated with leprosy pathogenesis and disease progression in a susceptible host which can be potentially useful for early detection of leprosy, particularly in form of a point-of-care diagnostics, considering theirrobustness in different clinical specimens.

Impact

Sharma, M., & Singh, P. (2022). Advances in the diagnosis of leprosy. Frontiers in Tropical Diseases, 3, 893653.

Avanzi, C., Lécorché, E., Rakotomalala, F. A., Benjak, A., Rapelanoro Rabenja, F., Ramarozatovo, L. S., ... & Cole, S. T. (2020). Population genomics of Mycobacterium leprae reveals a new genotype in Madagascar and the Comoros. Frontiers in microbiology, 11, 711.

Schaub, R., Avanzi, C., Singh, P., Paniz-Mondolfi, A., Cardona-Castro, N., Legua, P., ... & de Thoisy, B. (2020). Leprosy transmission in Amazonian countries: current status and future trends. Current Tropical Medicine Reports, 7, 79-91.

Sharma, M., & Singh, P. (2022). Repurposing drugs to combat drug resistance in leprosy: A review of opportunities. Combinatorial Chemistry & High Throughput Screening, 25(10), 1578-1586.

Sharma, M., & Singh, P. (2022). Role of tlyA in the biology of uncultivable mycobacteria. Combinatorial Chemistry & High Throughput Screening, 25(10), 1587-1594.

Sharma, M., Gupta, Y., Dwivedi, P., Kempaiah, P., & Singh, P. (2021). Mycobacterium lepromatosis MLPM_5000 is a potential heme chaperone protein HemW and mis-annotation of its orthologues in mycobacteria. Infection, Genetics and Evolution, 94, 105015.