Comparison of single cell RNA sequencing in leprosy lesions from lepromatous and reversal reaction patients
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ABSTRACT:
PROVIDER: PRJNA636282 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11888084_1.fastq.gz | Fastqsanger.gz | |||
| SRR11888084_2.fastq.gz | Fastqsanger.gz | |||
| SRR11888085_1.fastq.gz | Fastqsanger.gz | |||
| SRR11888085_2.fastq.gz | Fastqsanger.gz | |||
| SRR11888086_1.fastq.gz | Fastqsanger.gz |
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Project description:Comparison of spatial sequencing in leprosy lesions from lepromatous and reversal reaction patients
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Project description:Effective innate immunity against many microbial pathogens requires macrophage programs that upregulate phagocytosis and direct antimicrobial pathways, two functions generally assumed to be coordinately regulated. Here the regulation of these key functions was investigated in human blood-derived macrophages. IL-10 induced the phagocytic pathway, including CD209 and scavenger receptors, resulting in phagocytosis of mycobacteria and oxLDL. IL-15 induced the vitamin D-dependent antimicrobial pathway and CD209, yet the cells were less phagocytic. The differential regulation of macrophage functional programs was confirmed by analysis of the spectrum of leprosy lesions: the macrophage phagocytosis pathway was prominent in the clinically progressive, multibacillary form, whereas the vitamin D-dependent antimicrobial pathway predominated in the self-limited form of the disease and in patients undergoing reversal reactions from the multibacillary to the self-limited form. These data indicate that macrophage programs for phagocytosis and antimicrobial responses are distinct and differentially regulated in innate immunity in bacterial infections. Experiment Overall Design: 7 LL lesions, 10 BT lesions, 7 RR lesions
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Project description:Here we report the data generated by short-read sequencing of mRNA (polyA) isolated from granuloma annulare and leprosy skin lesions. Our main aim was to identify putative mRNA biomarkers for distinguishing leprosy from other differential diagnoses. Additionally, we also explored the distinction between MB and PB by using differential expression analysis as well as training a penalized logistic regression to select important features. Our results showed that few genes are enough to differentiate leprosy lesions, including paucibacillary cases, from other morphological and histopathological similar skin diseases. Some of these genes have been replicated in a larger and more heterogeneous sample with RT-qPCR, validating their classification potential. We also suggest important novel gene candidates to improve our understanding of molecular differences between MB and PB lesions, which could either pinpoint new pathways and targets for host-based specialized adjuvant treatment for leprosy. Finally, this dataset has been used to explore the relationship between cornification and keratinocyte-related genes and TGFB-mediated epithelial-mesenchymal transition (EMT), which could indicate that in skin, M. leprae could be de-differentiating, directly or indirectly, other cell types into a progenitor/stem-like phenotype, facilitating mycobacterial survival and migration within the host. Alternatively, this could highlight which pathways are activated during granuloma formation and/or skin barrier assembly/disassembly.
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Project description:In this study, a comprehensive assessment of human mRNA was performed on leprosy skin lesions using DNA chip microarrays, which included the entire spectrum of the disease along with its reactional states. Sixty-six samples from leprotic lesions (10TT, 10BT, 10BB, 10BL, 4LL, 14R1, and 10R2) and nine skin biopsies from healthy individuals were used as controls (CC) (ages ranged from 06 to 83 years, 48 were male and 29 female). The evaluation identified differentially expressed mRNAs [Fold Change (FC)â¥2.0, p<0.05] in disease lesions versus healthy controls or between them. Some of these genes were validated by RT-PCR and/or immunohistochemistry. The sequence of events for this study followed the order below. Patients who were treated for leprosy were examined by leprologists and submitted to two biopsy procedures. One biopsy was processed for histopathological analysis, bacilloscopy and immunohistochemistry (IHC), the other was immediately stored in RNAlater® solution (Ambion) for further RNA extraction. Sixty-eight samples from leprotic lesions (10TT, 10BT, 10BB, 10BL, 4LL, 14R1, and 10R2) were selected for analysis. In addition, nine skin biopsies from healthy individuals were usedas controls (CC). Differentially expressed genes identified in the cDNA microarray assay were validated by quantitative RT-PCR and IHC.
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