Cancer, Hypoxia, and Metabolism

Bhlhe40 limits proliferation and prevents excessive angiogenesis in mouse embryoid bodies under hypoxia

Pharmacological Ascorbate Induces Transient Hypoxia Sensitizing Pancreatic Ductal Adenocarcinoma to a Hypoxia Activated Prodrug

This study shows that pharmacological ascorbate induces transient hypoxia in pancreatic ductal adenocarcinoma, enhancing the efficacy of the hypoxia-activated prodrug evofosfamide in some tumor models.

Whole genome profiling of short-term hypoxia induced genes and identification of HIF-1 binding sites provide insights into HIF-1 function in Caenorhabditis elegans

The paper identifies HIF-1 binding sites and hypoxia-responsive genes in C. elegans using gene expression and ChIP-seq analyses, revealing their roles in metabolism and stress response.

NADPH composite index analysis quantifies the relationship between compartmentalized NADPH dynamics and growth rates in cancer cells

The paper quantifies the relationship between compartmentalized NADPH dynamics and cancer cell growth rates using a composite index analysis and identifies key transporters involved in this relationship.

BET inhibition induces GDH1-dependent glutamine metabolic remodeling and vulnerability in liver cancer

This study shows BET inhibition in liver cancer reduces proliferation by inducing GDH1-dependent glutamine metabolic changes, suggesting a therapeutic strategy combining BET and OXPHOS inhibitors.

Transcriptome analyses describe the consequences of persistent HIF-1 over-activation in Caenorhabditis elegans

The paper examines the gene expression changes in C. elegans mutants with persistent HIF-1 over-activation, revealing shared pathways and functional overlaps with DAF-16 in stress responses.

Metabolic Symbiosis between Oxygenated and Hypoxic Tumour Cells: An Agent-based Modelling Study

This paper uses agent-based modeling to study metabolic cooperation between oxygenated and hypoxic tumor cells, finding that aerobic glycolysis provides an overall advantage and that blocking glucose transporters is more effective than lactate transporters in reducing tumor growth.

Amino Acid and Glucose Fermentation Maintain ATP Content in Mouse and Human Malignant Glioma Cells

This study shows that malignant glioma cells rely on amino acid and glucose fermentation for ATP production, not oxidative phosphorylation, and that glutamine is essential for maintaining ATP content and viability.

Expression profiles of hypoxia-related genes of cancers originating from anatomically similar locations using TCGA database analysis

The paper analyzes hypoxia-related gene expression in cancers from anatomically similar locations using TCGA data to identify prognostic hub genes and functional enrichments.

Lactiplantibacillus plantarum K8 lysates regulate hypoxia-induced gene expression

This study shows that Lactiplantibacillus plantarum K8 lysates suppress hypoxia-induced gene expression by reducing HIF1 accumulation and its target genes.

Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer

The paper identifies metabolic reaction modules driving metastatic transitions in ovarian cancer and validates oseltamivir as a non-cytotoxic drug to disrupt spheroidal morphologies.

Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer.

This study uses TCGA transcriptomics data to analyze metabolic shifts in 11 cancer subtypes and their adjacent normal tissues, revealing patterns in glucose uptake, glycolysis, TCA cycle, and glutaminolysis.

Identification and characterization of metabolic subtypes of endometrial cancer using systems-level approach

This study identifies two metabolic subtypes of endometrial cancer using transcriptomics and metabolic modeling, linking them to clinical outcomes and genomic alterations.

Discovery of multi-state gene cluster switches determining the adaptive mitochondrial and metabolic landscape of breast cancer

The paper introduces a method to identify metabolic switches in breast cancer transcriptomes, revealing gene clusters associated with mitochondrial and metabolic states and their clinical implications.

Hybrid computational modeling highlights reverse Warburg effect in breast cancer-associated fibroblasts

This paper develops a hybrid computational model of breast cancer-associated fibroblasts to identify HIF-1 as a driver of the reverse Warburg effect.

A systematic study of HIF1A cofactors in hypoxic cancer cells

This study identifies 201 potential HIF1A cofactors in hypoxic cancer cells, with 30 validated and 21 matching known cofactors from public databases.

Epithelial-mesenchymal transition is the main driver of intrinsic metabolism in cancer cell lines

The paper profiles the metabolome of 180 cancer cell lines and identifies two major metabolic types linked to epithelial-mesenchymal transition (EMT).

Development and validation of glycolysis-cholesterol synthesis genes in lung adenocarcinoma

The paper identifies 13 prognostic genes related to MPC1/2 in LUAD and develops a model to predict patient outcomes.

Identification of subgroups and development of prognostic risk models along the glycolysis-cholesterol synthesis axis in lung adenocarcinoma

The paper identifies metabolic subgroups in LUAD using glycolysis and cholesterol synthesis genes and develops a prognostic risk model based on these subgroups.

Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer

The paper uses computational modeling and transcriptomic data to show that cancer cell phenotypes can be explained by Fenton reaction-driven proton production and reprogrammed metabolisms.

Hypoxia classifier for transcriptome datasets

The paper develops hypoxia classifiers using decision trees from a meta-analysis of RNA-seq data, achieving high accuracy in identifying hypoxic samples across diverse datasets.

Nuclear Hormone Receptor NHR-49 controls a HIF-1-independent hypoxia adaptation pathway in Caenorhabditis elegans

The paper identifies a HIF-1-independent hypoxia response pathway in C. elegans mediated by NHR-49, showing its role in hypoxia survival and gene regulation.

Regulation of Chromatin Accessibility by hypoxia and HIF

This study shows hypoxia and HIF regulate chromatin accessibility through locus-specific changes, which are reversible and can be mimicked by HIF stabilisation.

Identification of biological processes and signaling pathways in lactate-treated cancer cells

The paper analyzes RNA-seq data from lactate-treated prostate cancer cells to identify significant biological processes and signaling pathways.

Gene expression is a poor predictor of the metabolite abundance in cancer cells

The paper evaluates the ability to predict metabolite levels from gene expression in cancer cell lines and finds that gene expression is a poor predictor.

Elucidating Tumor-stromal Metabolic Crosstalk in Colorectal Cancer through Integration of Constraint-Based Models and LC-MS Metabolomics

This study investigates tumor-stromal metabolic interactions in colorectal cancer by integrating constraint-based models with metabolomics data, revealing how cancer-associated fibroblasts reprogram tumor cell metabolism.

Crosstalk in oxygen homeostasis networks: SKN-1/NRF inhibits the HIF-1 hypoxia-inducible factor in Caenorhabditis elegans

The paper identifies crosstalk between SKN-1/NRF and HIF-1 in C. elegans, showing SKN-1 inhibits HIF-1 through EGL-9 regulation.

Multi-omic meta-analysis of transcriptomes and the bibliome uncovers novel hypoxia-inducible genes

This study identifies novel hypoxia-inducible genes through a meta-analysis of transcriptomes and bibliome data, revealing previously uncharacterized genes like G protein-coupled receptor 146.

The Hypoxia Response Pathway Promotes PEP Carboxykinase Expression And Gluconeogenesis

The paper shows HIF-1 promotes gluconeogenesis by upregulating PCK-1 in C. elegans, revealing a new role for HIF-1 beyond glycolysis.

Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors

The paper develops a bioinformatics pipeline to integrate multi-omics data into personalized genome-scale metabolic models, identifying redox metabolism targets in radiation-resistant tumors.