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E-GEOD-33601

ABSTRACT: Human transcriptome pattern of primary cutaneous lesions from patients with localized cutaneous leishmaniasis and mucosal leishmaniasis

OTHER RELATED OMICS DATASETS IN: PRJNA148519

PROVIDER: E-GEOD-33601 | ExpressionAtlas | 2019-05-14

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-33601-analysis-methods.tsv	Tabular
	E-GEOD-33601-analytics.tsv	Tabular
	E-GEOD-33601-analytics.tsv.undecorated	Tabular
	E-GEOD-33601-analytics.tsv.undecorated.unrounded	Tabular
	E-GEOD-33601-analytics.tsv.unrounded	Tabular

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Homo sapiens

Project description:Human transcriptome pattern of primary cutaneous lesions from patients with localized cutaneous leishmaniasis and mucosal leishmaniasis

| PRJNA148519 | ENA

Human transcriptome pattern of primary cutaneous lesions from patients with localized cutaneous leishmaniasis and mucosal leishmaniasis

Project description:We evaluated the trancriptome of primary cutaneous leisions caused by infection with Leishmania braziliensis. mRNA-seq technique was used to study the trancriptome of both host and parasite. A total of 10 samples was obtained from primary skin ulcers of two extreme clinical forms of American tegumentary leishmaniasis: (i) individuals that after antimonial treatment cured completely (localized cutaneous leishmaniasis - LCL, n=5) and (ii) individuals that developed mucosal lesions in naso and oropharynx areas long after initial healing of the cutaneous lesion (mucosal leishmaniasis - ML, n=5). The sequencing generated an average of 13+ 5 million reads per samples. The reads were aligned to Homo sapiens (USCS - hg19) and to Leishmania braziliensis (Wellcome Trust Sanger Institute - V2_29072008) genomes. Approximately, 15,000 human genes could be detected in the samples. Low amount of L. braziliensis reads did not allow the evaluation of parasite gene expression. LCL and ML samples showed different patterns of gene expression, indicating a more robust immune response in LCL individuals. In summary, this study demonstrated that next-generation sequencing can be used for identification of potentially important biological pathways and drug targets in the host-response to L. braziliensis infection and for characterization of a gene expression signature that could be used to predict the disease outcome. Moreover, we also showed the ability of this technique in, simultaneously, sequence host and pathogen mRNA. Examination of 10 fragments of cutaneous lesions: 5 from localized cutaneous leishmaniasis patients and 5 from mucosal leishmaniasis patients.

2012-10-24 | E-GEOD-33601 | biostudies-arrayexpress

Lack of human papilloma virus transcriptional activity in cutaneous squamous cell carcinoma stratified by histological grade and host immune status

Project description:Human Papilloma Virus (HPV) infection is known to contribute to mucosal (m)SCC, but its role in cutaneous (c)SCC progression remains unclear, especially in lesions determined to be at high-risk for metastasis. We hypothesized that histologically high grade cSCCs in immunosuppressed patients would display increased transcriptional activity of HPV when compared to low histologic grade lesions in otherwise healthy patients. To assess the role of viruses in cSCC pathogenesis we utilized high throughput RNA sequencing across risk-stratified lesions. Skin excisions classified as high grade in immunocompromised patients, low grade in otherwise healthy patients, and normal skin were used for detection of any non-human RNA. Reads were aligned to known viral transcriptomes using our recently developed Microbiome Coverage Profiler. While approximately two-thirds of all samples tested positive for HPV gDNA, no skin sample had detectable expression of HPV RNA.

2021-03-02 | GSE111354 | GEO

Genomic profiling of human Leishmania braziliensis lesions identifies transcriptional modules associated with cutaneous immunopathology

Project description:The host immune response plays a critical role not only in protection from human leishmaniasis, but also in promoting disease severity. Although candidate gene approaches in mouse models of leishmaniasis have been extremely informative, a global understanding of the immune pathways active in lesions from human patients is lacking. To address this issue, genome-wide transcriptional profiling of Leishmania braziliensis-infected cutaneous lesions and normal skin controls was carried out. A signature of the L. braziliensis skin lesion was defined that includes over 2,000 differentially regulated genes. Pathway-level analysis of this transcriptional response revealed key biological pathways, as well as specific genes, associated with cutaneous pathology, generating a testable 'metapathway' model of immune-driven lesion pathology, and providing new insights for treatment of human leishmaniasis. Thirty-five skin biopsies were analyzed, including 10 normal skin biopsies (2 from North America and 8 from non-endemic area in Brazil), and 25 skin lesion biopsies (8 early cutaneous lesions, 17 late cutaneous lesions) obtained from Leishmania brazilensis-infected patients presenting at the Corte de Pedra Health Post in Corte de Pedra, Bahia, Brazil.

2014-03-07 | E-GEOD-55664 | biostudies-arrayexpress

The cGAS-STING pathway drives type I IFN immunopathology in COVID-19

Project description:we profiled the inflammatory transcriptome of ten COVID-19 skin manifestations from patients with moderate-to-severe disease and compared the resultant signatures with those obtained from skin lesions of patients with cutaneous lupus erythematosus.

2022-01-07 | GSE193068 | GEO

Human transcriptome pattern of primary cutaneous lesions from patients with localized cutaneous leishmaniasis and mucosal leishmaniasis

2012-10-24 | GSE33601 | GEO

Single-cell RNAseq profiling in a patient with discordant primary cutaneous B and T cell lymphoma reveals micromilieu-driven immune skewing

Project description:Background: Primary cutaneous lymphomas comprise a heterogeneous group of B and T cell malignancies which often show an indolent course, but can progress to aggressive disease in a subset of patients. Diagnosis is often delayed due to clinical and histopathological similarities with benign inflammatory conditions. Especially during early disease, cancer cells are present at relatively low percentages in comparison to the inflammatory infiltrate, an interplay that is currently only insufficiently understood. Objectives: To improve diagnostics and perform molecular characterization of a complex type of primary cutaneous lymphoma. Methods: Single-cell RNA sequencing (scRNA-seq) combined with T and B cell receptor sequencing. Results: We were able to diagnose a patient with concurrent mycosis fungoides (MF) and primary cutaneous follicle center lymphoma (PCFCL), appearing in mutually exclusive skin lesions. Profiling of tumor cells and the tissue microenvironment revealed a type-2 immune skewing in MF, most likely guided by the expanded clone that also harbored upregulation of numerous pro-oncogenic genes. By contrast, PCFCL lesions exhibited a more type-1 immune phenotype, consistent with its indolent behavior. Conclusions: These data not only illustrate the diagnostic potential of scRNA-seq, but also allow the characterization of specific clonal populations shaping the unique tissue microenvironment in clinically distinct types of lymphoma skin lesions.

2021-05-25 | GSE173820 | GEO

Molecular signatures of anthroponotic cutaneous leishmaniasis in the lesions of patients infected with Leishmania tropica

Project description:In this study employed a systems analysis approach to study molecular signatures of cutaneous leishmaniasis (CL) caused by Leishmania tropica (L. tropica) in the skin lesions of ulcerativeCL (UCL) and non-ulcerative CL( NUCL) patients. Results from RNA-seq analysis determined shared and unique functional transcriptional pathways in the lesions of the UCL and Nucl patients. Several transcriptional pathways involved in inflammatory response were positively enriched in the CL lesions. These results enhance our understanding of human skin response to CL caused by L. tropica.

2022-11-01 | GSE216638 | GEO

Transcription profiling of human cutaneous primary melanomas in an independent population of 17 patients

Project description:Validation of genomics characteristics of human cutaneous primary melanoma in an independnat population of 17 patients.

2007-04-01 | E-TABM-2 | biostudies-arrayexpress

Ruxolitinib cream in the treatment of cutaneous lichen planus: A prospective, open-label study

Project description:Ruxolitinib is a Janus kinase 1/2 inhibitor (JAK1/2) that blocks signal transduction of interferon-gamma, a critical cytokine involved in the pathogenesis of cutaneous lichen planus (LP). In this prospective phase II study, we investigated the efficacy of topical ruxolitinib in cutaneous LP and performed transcriptomic analysis pre- and post-therapy. Twelve patients with cutaneous LP applied topical ruxolitinib twice daily for 8 weeks. Primary endpoints were change in total lesion count and modified Composite Assessment of Index Lesion Severity (mCAILS) score in index treated and untreated index control lesions at week 4. Total lesion count decreased by a median of 50 lesions (interquartile range 25, 723; p<0.001). mCAILS scores decreased by a mean difference of 7.6 (standard deviation 8.8, p=0.016) between index treated and control lesions. Type I and II interferon pathways were enriched in LP and responsive disease displayed downregulation of interferon-stimulated genes (ISGs). In this small pilot study, topical ruxolitinib was highly effective in the treatment of cutaneous LP. Transcriptomic analysis confirmed LP as an interferon-driven disease and downregulation of ISGs correlated with disease response.

2022-01-13 | GSE193351 | GEO

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