Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lineage and ecology define liver tumor evolution in response to treatment

ABSTRACT: Lineage and ecology define liver tumor evolution in response to treatment

PROVIDER: PRJNA955805 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Lineage and ecology define liver tumor evolution in response to treatment

Project description:Single-cell transcriptome-based strategy to determine the evolutionary trajectories of longitudinal tumor biopsies from liver cancer patients by measuring cellular lineage and ecology. Our study provides a framework for monitoring tumor evolution in response to therapeutic intervention.

2023-12-22 | GSE229772 | GEO

Lineage and ecology define liver tumor evolution in response to treatment.

Project description:A tumor ecosystem constantly evolves over time in the face of immune predation or therapeutic intervention, resulting in treatment failure and tumor progression. Here, we present a single-cell transcriptome-based strategy to determine the evolution of longitudinal tumor biopsies from liver cancer patients by measuring cellular lineage and ecology. We construct a lineage and ecological score as joint dynamics of tumor cells and their microenvironments. Tumors may be classified into four main states in the lineage-ecological space, which are associated with clinical outcomes. Analysis of longitudinal samples reveals the evolutionary trajectory of tumors in response to treatment. We validate the lineage-ecology-based scoring system in predicting clinical outcomes using bulk transcriptomic data of additional cohorts of 716 liver cancer patients. Our study provides a framework for monitoring tumor evolution in response to therapeutic intervention.

| S-EPMC10897542 | biostudies-literature

MICROBIAL ECOLOGY AND SOIL EVOLUTION

Project description:MICROBIAL ECOLOGY AND SOIL EVOLUTION

| PRJEB79920 | ENA

CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE

Project description:CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE

2023-07-10 | GSE227943 | GEO

CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE

Project description:CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE

| PRJNA947553 | ENA

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

Project description:The evolution of human anatomical features likely involved changes in gene regulation during development. However, the nature and extent of human specific developmental regulatory functions remain unknown. We obtained a genome-wide view of cis regulatory evolution in human embryonic tissues by comparing the histone modification H3K27ac, which provides a quantitative readout of promoter and enhancer activity, during human, rhesus, and mouse limb development. Based on increased H3K27ac, we find that 13% of promoters and 11% of enhancers have gained activity on the human lineage since the human-rhesus divergence. These gains largely arose by modification of ancestral regulatory activities in the limb or potential co-option from other tissues and are likely to have heterogeneous genetic causes. Most enhancers that exhibit gain of activity in humans originated in mammals. Gains at promoters and enhancers in the human limb are associated with increased gene expression, suggesting they include molecular drivers of human morphological evolution. ChIP-Seq and RNA-Seq of autopod tissue of developing limb buds of Human (E33-E47), rhesus (E31-E36), and mouse (E10.5-E13.5). No raw data are provided for human samples. Human alignments were anonymized by removing sequence information and converting to bed format.

2013-07-02 | E-GEOD-42413 | biostudies-arrayexpress

Epigenetic evolution and lineage histories of chronic lymphocytic leukemia

Project description:Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer. In addition to genetic mutations, chronic lymphocytic leukemia (CLL) undergoes diversification through stochastic DNA methylation changes – epimutations. To measure the epimutation rate at single-cell resolution, we applied multiplexed reduced representation bisulfite sequencing (MscRRBS) to healthy donors B cells and CLL patient samples. We observed that the common clonal CLL origin results in consistently elevated epimutation rate (i.e., low cell-to-cell epimutation rate variability). In contrast, variable epimutation rates across normal B cells reflect diverse evolutionary ages across the B cell differentiation trajectory, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed high-resolution lineage reconstruction with single-cell data, applicable directly to patient sample. CLL lineage tree shape revealed earlier branching and longer branch lengths than normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. To validate the inferred tree topology, we integrated MscRRBS with single-cell transcriptomes and genotyping, which confirmed that genetic subclones map to distinct clades inferred solely based on epimutation information. Lastly, to examine potential lineage biases during therapy, we profiled serial CLL samples prior to and during ibrutinib-associated lymphocytosis. Lineage trees revealed divergent clades of cells preferentially expelled from the lymph node with ibrutinib therapy, marked by distinct transcriptional profiles. These data offer direct single-cell integration of genetic, epigenetic and transcriptional information in the study of leukemia evolution, providing deeper insight into its lineage topology and enabling the charting of its evolution with therapy.

2019-05-02 | GSE109085 | GEO

Functional characterization of enhancer evolution in the primate lineage

Project description:Functional characterization of enhancer evolution in the primate lineage

| PRJNA454716 | ENA

Endogenous retroviruses direct the evolution of lineage-specific imprinting

Project description:Endogenous retroviruses direct the evolution of lineage-specific imprinting

| PRJNA521704 | ENA

Epigenetic evolution and lineage histories of chronic lymphocytic leukemia

Project description:Epigenetic evolution and lineage histories of chronic lymphocytic leukemia

| PRJNA429620 | ENA