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Clonotypic heterogeneity in cutaneous T-cell lymphoma (mycosis fungoides) revealed by comprehensive whole exome sequencing

ABSTRACT: Clonotypic heterogeneity in cutaneous T-cell lymphoma (mycosis fungoides) revealed by comprehensive whole exome sequencing

PROVIDER: PRJNA558096 | ENA |

REPOSITORIES: ENA

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Clonotypic heterogeneity in cutaneous T-cell lymphoma (mycosis fungoides) revealed by comprehensive whole exome sequencing

Project description:Clonotypic heterogeneity in cutaneous T-cell lymphoma (mycosis fungoides) revealed by comprehensive whole exome sequencing

| PRJNA558097 | ENA

Mycosis fungoides

Project description:Mycosis fungoides

| PRJNA430861 | ENA

Mycosis fungoides

Project description:Mycosis fungoides (MF) is the most common and best studied of cutaneous T-cell lymphoma (CTCL). Three clinical cutaneous stages have been described (patch, plaque and tumor) as the disease progress developing also the disease lymph node, peripheral blood or systemic involvement in late stages. Clinical and pathologic diagnosis of early MF stages (patch and plaque) is difficult as its morphologic similarity to inflammatory dermatoses and low proportion of tumoral cells.

2018-06-21 | GSE109421 | GEO

Clonotypic heterogeneity in cutaneous T-cell lymphoma (mycosis fungoides) revealed by comprehensive whole-exome sequencing.

Project description:Mycosis fungoides (MF), the most common type of cutaneous T-cell lymphoma, is believed to represent a clonal expansion of a transformed skin-resident memory T cell. T-cell receptor (TCR) clonality (ie, identical sequences of rearranged TCRα, TCRβ, and TCRγ), the key premise of this hypothesis, has been difficult to document conclusively because malignant cells are not readily distinguishable from the tumor-infiltrating reactive lymphocytes that contribute to the TCR clonotypic repertoire of MF. Here, we have successfully adopted targeted whole-exome sequencing (WES) to identify the repertoire of rearranged TCR genes in tumor-enriched samples from patients with MF. Although some of the investigated MF biopsies had the expected frequency of monoclonal rearrangements of TCRγ corresponding to that of tumor cells, the majority of the samples presented multiple TCRγ, TCRα, and TCRβ clonotypes by WES. Our findings are compatible with the model in which the initial malignant transformation in MF does not occur in mature memory T cells but rather at the level of T-lymphocyte progenitors before TCRβ or TCRα rearrangements. We have also shown that WES can be combined with whole-transcriptome sequencing in the same sample, which enables comprehensive characterization of the TCR repertoire in relation to tumor content. WES/whole-transcriptome sequencing might be applicable to other types of T-cell lymphomas to determine clonal dominance and clonotypic heterogeneity in these malignancies.

| S-EPMC6457216 | biostudies-literature

RNAseq of the skin of patients with Mycosis fungoides

Project description:We performed transcriptome analysis and multimodal data integration of the transcriptome and the microbiome of the skin of Mycosis fungoides Patients.

2023-12-01 | GSE221148 | GEO

Transcription profiling of human cutaneous B-cell lymphoma skin punch biopsies, mycosis fungoides (MF) and 3 normal skin biopsies

Project description:We studied gene expression profiles of 17 cutaneous B-cell lymphomas that were collected with 4-6 millimeter skin punch biopsies. We also included tissue from 2 cases of mycosis fungoides (MF), 3 normal skin biopsies and 3 tonsils to create a framework for further interpretation. A hierarchical cluster algorithm was applied for data analysis. Our results indicate that small amounts of skin tissue can be used successfully to perform microarray analysis and result in distinct gene expression patterns. Duplicate specimens clustered together demonstrating a reproducible technique. Within the cutaneous B-cell lymphoma specimens two specific B-cell differentiation stage signatures of germinal center B-cells and plasma cells could be identified. Primary cutaneous follicular and primary cutaneous diffuse large B-cell lymphomas had a germinal center B-cell signature while a subset of marginal zone lymphomas demonstrated a plasma cell signature. Primary and secondary follicular B-cell lymphoma of the skin were closely related, despite previously reported genetic and phenotypic differences. In contrast primary and secondary cutaneous diffuse large B-cell lymphoma were less related to each other. This pilot study allows a first glance into the complex and unique microenvironment of B-cell lymphomas of the skin and provides a basis for future studies, that may lead to the identification of potential histologic and prognostic markers as well as therapeutic targets.

2005-10-07 | E-SMDB-1798 | biostudies-arrayexpress

ALTERATIONS IN THE SKIN MICROBIOTA ARE ASSOCIATED WITH SYMPTOM SEVERITY IN MYCOSIS FUNGOIDES

Project description:We identified skin microbiota signatures related to different symptoms, i.e. pain, pruritus, in patients with Mycosis Fungoides.

2022-04-11 | GSE186083 | GEO

CD8+ T lymphocytes in hypopigmented mycosis fungoides: malignant cells or reactive clone?

Project description:We used targeted single cell RNA sequencing using a gene set composed of the BD Rhapsody Human Immune Response Panel, TCR panel, and a custom panel of 61 malignancy-associated genes and T/B cell receptor sequencing to characterize single cell populations in hypopigmented mycosis fungoides (HMF). Using a reference mapping model built on publically deposited classic mycosis fungoides single cell RNA sequencing datasets, we identified a predicted malignant cell population independent from the clonal T cell population in HMF.

2023-10-17 | GSE212146 | GEO

The Skin Microbiome of Mycosis fungoides

Project description:The Skin Microbiome of Mycosis fungoides

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Genetic characterization of tumor-stage mycosis fungoides

Project description:Mycosis fungoides patients who develop tumors or extracutaneous involvement usually have a poor prognosis with no curative therapy available so far. In the present EORTC multicenter study, the genomic profile of 41 skin biopsies from tumor-stage mycosis fungoides was analyzed using a high-resolution oligo-array comparative genomic hybridization platform. Seventy-six percent of cases showed genomic aberrations. The most common imbalances were gains of 7q33.3q35 followed by 17q21.1, 8q24.21, 9q34qter and 10p14 and losses of 9p21.3 followed by 9q31.2, 17p13.1, 13q14.11, 6q21.3, 10p11.22, 16q23.2 and 16q24.3. Three specific chromosomal regions, 9p21.3, 8q24.21 and 10q26qter were defined as prognostic markers exhibiting a significant correlation with overall survival (P= .042, P= .017 and P= .022, respectively). Moreover, we have established two MFt genomic subgroups distinguishing a stable group (0-5 DNA aberrations) and an unstable group (> 5 DNA aberrations), showing that the genomic unstable group had a shorter overall survival (P=.05). We therefore conclude that specific chromosomal abnormalities, such as gains of 8q24.21 (MYC) and losses of 9p21.3 (CDKN2A, CDKN2B and MTAP), and 10q26qter (MGMT and EBF3) may play an important role in prognosis. In addition, we describe the MFt genomic instability profile. Forty-one MFt were studied by arrayCGH using the Human Genome CGH 44K microarrays (G4410B and G4426B, Agilent Technologies, Palo Alto, CA, USA). In each microarray experiment, DNA obtained from a 20x10 um sections snap frozen samples from tumoral MF lesions was compared with commercial pools of healthy female DNA (Promega, Madison, WI, USA).

2010-05-06 | E-GEOD-18098 | biostudies-arrayexpress

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