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The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma [scVDJ-seq]

ABSTRACT: The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma [scVDJ-seq]

PROVIDER: PRJNA759182 | ENA |

REPOSITORIES: ENA

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The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma [scVDJ-seq]

Project description:Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by diverse cell types and cell states in the tumor microenvironment (TME). However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL cell states and ecosystems. Using this approach, we identified five cell states of malignant B cells that vary in prognostic associations and differentiation status. We also identified striking variation in cell states for 12 other lineages comprising the TME and forming cell-state interactions in stereotyped ecosystems. While cell-of-origin subtypes have distinct TME composition, DLBCL ecosystems capture clinical heterogeneity within existing subtypes and extend beyond cell-of-origin and genotypic classes. These results resolve the DLBCL microenvironment at unprecedented resolution and identify opportunities for therapeutic targeting (https://ecotyper-stanford-edu.stanford.idm.oclc.org/lymphoma).

2021-09-30 | GSE182435 | GEO

The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma [scRNA-seq]

2021-09-30 | GSE182434 | GEO

Spatial transcriptomics characterization of ecosystems in the immune tumor microenvironment of diffuse large B-cell lymphoma

Project description:This dataset comprises spatial transcriptomic profiles from 10 tissue samples of Diffuse Large B-cell Lymphoma (DLBCL) the most common subtype of non-Hodgkin’s lymphoma and secondary lymphoid organ controls (SLO). The diffuse nature of DLBCL challenges the analysis of cellular organization within the immune tumor microenvironment (TME). We employed spatial transcriptomics to map spatially-resolved gene expression patterns. The analysis led to the identification of six cellular ecosystems (Cell-Eco) that differ in cellular composition, functional patterns, and neighborhood characteristics. The spatially-resolved Cell-Eco signatures provided prognostic scores that stratified patients with different overall survival rates. We also found that C1q+ tumor-associated macrophages are the primary cells interacting with malignant B cells and influencing the spatial architecture of the TME. This resource offers valuable insights into the spatial complexity of the DLBCL microenvironment and its potential prognostic significance.

2026-04-29 | GSE276542 | GEO

The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma

Project description:The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma

| PRJNA756263 | ENA

The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma [scRNA-seq]

Project description:The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma [scRNA-seq]

| PRJNA756265 | ENA

The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma.

Project description: Not available

| S-EPMC9205168 | biostudies-literature

The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-09-30 | GSE182436 | GEO

Spatial transcriptomics characterization of ecosystems in the immune tumor microenvironment of diffuse large B-cell lymphoma

Project description:Spatial transcriptomics characterization of ecosystems in the immune tumor microenvironment of diffuse large B-cell lymphoma

| PRJNA1157819 | ENA

The prognostic value of hydroxybutyrate dehydrogenase in diffuse large B-cell lymphoma

Project description:<p>In our investigation, we examined biochemical parameters and identified hydroxybutyrate dehydrogenase (HBDH) as a significant predictor for diffuse large B-cell lymphoma (DLBCL) patients. A group of 100 patients was used to explore potential biomarkers related to progression-free survival (PFS). Subsequently, an independent cohort of 404 patients from a separate hospital was recruited to validate our findings. Our results revealed a strong association between elevated HBDH levels and poor PFS. Furthermore, while overexpression of LDHB, but not LDHA, was notably linked to poorer outcomes, HBDH expression emerged as a more robust predictor of clinical prognosis compared to LDH expression. Our investigations, which included metabolic and genetic pathway enrichment analyses, indicated that patients exhibiting heightened HBDH expression were characterized by distinct pathways related to energy metabolism and lymphoma progression. In conclusion, elevated HBDH levels were correlated with adverse survival and might serve as an independent parameter for evaluating patient outcomes.</p>

2024-09-02 | MTBLS10446 | MetaboLights

Diffuse large B-cell lymphoma

Project description:Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumors. Using DNA microarrays, we have conducted a systematic characterization of gene expression in B-cell malignancies. Here we show that there is diversity in gene expression among the tumors of DLBCL patients, apparently reflecting the variation in tumor proliferation rate, host response and differentiation state of the tumor. We identified two molecularly distinct forms of DLBCL which had gene expression patterns indicative of different stages of B-cell differentiation. One type expressed genes characteristic of germinal center B cells ('germinal center B-like DLBCL'); the second type expressed genes normally induced during in vitro activation of peripheral blood B cells ('activated B-like DLBCL'). Patients with germinal center B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL. The molecular classification of tumors on the basis of gene expression can thus identify previously undetected and clinically significant subtypes of cancer. This study is described more fully in Alizadeh AA et al.(2000) Nature 403:503-11

2002-06-27 | E-GEOD-60 | biostudies-arrayexpress

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