ArticleNature communications2023
Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- Senescent-Like Neutrophils Shape Angiogenic Immunosuppressive Niches in Colorectal Cancer Liver Metastasis.Cancer discovery · 2026Article
- Lactate metabolism and protein lactylation in inflammatory and tumor microenvironments.Molecular biomedicine · 2026Review
- Atomic elementary flux modes explain the steady state flow of metabolites in large-scale flux networks.Cell reports methods · 2026Article
- miR-146a-5p mediates atherogenic signalling from immune to vascular cells.Cardiovascular research · 2026Article
- Concordant and Discordant Transcriptomic Signatures of Twin Placentas in the Setting of Preeclampsia.Hypertension (Dallas, Tex. : 1979) · 2026Article
- Metabolic characterization of the tumor microenvironment orchestrates therapeutic strategies and clinical outcomes in pancreatic cancer.Nature communications · 2026Article
- Spatially-Resolved Multiomic Atlas of Leiomyosarcoma Identifies Two Clinically Relevant Epigenetically-Driven Cell States.bioRxiv : the preprint server for biology · 2026Article
- Single-cell and machine learning reveal ROS-associated heterogeneity in hepatocellular carcinoma for precision medicine.BMC cancer · 2026Article
- Machine learning integration of multi-omics data develops a sarcomatoid-related renal cell carcinoma score (SARS) for prognosis stratification and guiding therapy.Translational andrology and urology · 2026Article
- Not so cold after all: tumor infiltrating CD8+ T cells in EBV-positive Burkitt lymphoma are quiescent, not exhausted.bioRxiv : the preprint server for biology · 2026Article
- Macrophage metabolic exhaustion and PANoptotic cell death drive chronic tissue inflammation in rheumatoid arthritis.Immunity · 2026Article
- Mitochondrial transfer to granulocytic myeloid-derived suppressor cells augments immunosuppressive activity.Cell reports · 2026Article
- Cell-specific isotope labeling identifiesbioRxiv : the preprint server for biology · 2026Article
- Integrative analyses of dicarbonyls and advanced glycation end-products with multiomic profiles across tissue, plasma and stool samples reveal methylglyoxal accumulation in colon cancer.Free radical biology & medicine · 2026Article
- Simulated Microgravity Recapitulates Aspects of Biological Aging in Humans.bioRxiv : the preprint server for biology · 2026Article
- Targeting organelle function in T cells for cancer immunotherapy.Nature reviews. Immunology · 2026Review
- Sepsis and the immunometabolic inflammatory response.npj metabolic health and disease · 2026Review
- Flux sampling and context-specific genome-scale metabolic models for biotechnological applications.Trends in biotechnology · 2026Review
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- SLC7A7 Downregulation in Monocytes Drives Immunosuppression and Osteosarcoma Progression.International journal of genomics · 2026Article
22 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
Cells often alter metabolic strategies under nutrient-deprived conditions to support their survival and growth. Characterizing metabolic reprogramming in the tumor microenvironment (TME) is of emerging importance in cancer research and patient care. However, recent technologies only measure a subset of metabolites and cannot provide in situ measurements. Computational methods such as flux balance analysis (FBA) have been developed to estimate metabolic flux from bulk RNA-seq data and can potentially be extended to single-cell RNA-seq (scRNA-seq) data. However, it is unclear how reliable current methods are, particularly in TME characterization. Here, we present a computational framework METAFlux (METAbolic Flux balance analysis) to infer metabolic fluxes from bulk or single-cell transcriptomic data. Large-scale experiments using cell-lines, the cancer genome atlas (TCGA), and scRNA-seq data obtained from diverse cancer and immunotherapeutic contexts, including CAR-NK cell therapy, have validated METAFlux's capability to characterize metabolic heterogeneity and metabolic interaction amongst cell types.
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