Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer

ABSTRACT: Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer

PROVIDER: PRJNA798619 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR17660983.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer [Human tumor]

Project description:Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer [Human tumor]

| PRJNA798625 | ENA

Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer [cell lines]

Project description:Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer [cell lines]

| PRJNA798626 | ENA

Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer [Human tumor]

Project description:Intratumoral heterogeneity underlies cancer treatment resistance, but approaches to neutralize it remain elusive. Here, we recast heterogeneity in a systems perspective that considers cancer cell functional tasks inherited from cells of origin. We apply Archetype Analysis to bulk transcriptomics data from small cell lung cancer (SCLC), which forms tumors composed of neuroendocrine (NE) and non-neuroendocrine (non-NE) transcriptional subtypes. SCLC subtypes fit well in a 5-dimensional polytope whose vertices optimize tasks reminiscent of pulmonary NE cells, the SCLC normal counterpart, and include injury repair, slithering, and chemosensation. SCLC cells near a vertex are specialists for a task, while more distant cells are generalists, bearing gene signatures of multiple archetypes. Evolutionary theory and dynamical systems modeling suggest a division of labor strategy for adaptation to treatment, based on task trade-offs amongst specialists and generalists. Cell Transport Potential, a metric derived from single-cell RNA velocity, uncovers plasticity trends from specialists to generalists, and NE to non-NE subtypes. Transcription factor network simulations indicate that MYC overexpression increases plasticity by de-stabilizing NE subtypes. Framing heterogeneity in archetype space provides insights into transformative cancer treatments aimed at tumor cell plasticity.

2022-07-05 | GSE193960 | GEO

Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer [cell lines]

2022-07-05 | GSE193959 | GEO

Archetype tasks link intratumoral heterogeneity to plasticity in recalcitrant small cell lung cancer

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

2022-07-05 | GSE193961 | GEO

Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer.

Project description:Small cell lung cancer (SCLC) tumors comprise heterogeneous mixtures of cell states, categorized into neuroendocrine (NE) and non-neuroendocrine (non-NE) transcriptional subtypes. NE to non-NE state transitions, fueled by plasticity, likely underlie adaptability to treatment and dismal survival rates. Here, we apply an archetypal analysis to model plasticity by recasting SCLC phenotypic heterogeneity through multi-task evolutionary theory. Cell line and tumor transcriptomics data fit well in a five-dimensional convex polytope whose vertices optimize tasks reminiscent of pulmonary NE cells, the SCLC normal counterparts. These tasks, supported by knowledge and experimental data, include proliferation, slithering, metabolism, secretion, and injury repair, reflecting cancer hallmarks. SCLC subtypes, either at the population or single-cell level, can be positioned in archetypal space by bulk or single-cell transcriptomics, respectively, and characterized as task specialists or multi-task generalists by the distance from archetype vertex signatures. In the archetype space, modeling single-cell plasticity as a Markovian process along an underlying state manifold indicates that task trade-offs, in response to microenvironmental perturbations or treatment, may drive cell plasticity. Stifling phenotypic transitions and plasticity may provide new targets for much-needed translational advances in SCLC. A record of this paper's Transparent Peer Review process is included in the supplemental information.

| S-EPMC9615940 | biostudies-literature

Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma

Project description:Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma

| PRJNA616343 | ENA

Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma [Array]

Project description:Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma [Array]

| PRJNA616347 | ENA

Large B-cell lymphoma microenvironment archetype profiles (LymphoMAPs). [macrophage]

Project description:Large B-cell lymphomas (LBCL) are clinically and biologically heterogeneous lymphoid malignancies with complex microenvironments that are central to disease etiology. Here we have employed single-nucleus multiome profiling of 232 tumor and control biopsies to characterize diverse cell types and subsets that are present in LBCL tumors, effectively capturing the lymphoid, myeloid, and non-hematopoietic cell compartments. Cell subsets co-occurred in stereotypical Lymphoma Microenvironment Archetype Profiles (LymphoMAPs) defined by; (i) a sparsity of T-cells and high frequencies of cancer-associated fibroblasts and tumor-associated macrophages [FMAC]; (ii) lymph node architectural cell types with naïve and memory T-cells [LN]; or (iii) activated macrophages and exhausted CD8 T-cells [TEX]. Divergent patterns of cell-cell communication underpinned the transcriptional phenotypes of archetype-defining cell subsets resulting in exclusion, support or suppression of T-cells, respectively. Consistent with this, LymphoMAPs were associated with significantly different clinical outcomes following CD19 CAR T-cell therapy.

2025-05-27 | GSE297979 | GEO

Large B-cell lymphoma microenvironment archetype profiles (LymphoMAPs). [tonsil frc]

2025-05-27 | GSE297982 | GEO