Journal: Genes & Development

Article Title: Aneuploidy generates enhanced nucleotide dependency and sensitivity to metabolic perturbation

doi: 10.1101/gad.352512.124

Figure Lengend Snippet: Net gain aneuploidy is associated with metabolic phenotypes and is prognostic for response to DNA-damaging chemotherapy in cancer. ( A ) Volcano plot showing metabolite log 2 fold change (log 2 FC) ( X -axis) and −log 10 ( P -value) ( Y -axis) in net gain aneuploid HMECs compared with diploid HMEC controls under steady-state conditions. Log 2 FC capped at minimum −3 and maximum 3. ( B ) Volcano plot showing linear regression coefficient ( X -axis) and corresponding −log 10 ( P -value) ( Y -axis) of metabolite levels compared with net gain aneuploidy levels across cancer cell lines. ( C ) Volcano plot showing linear regression coefficient ( X -axis) and corresponding −log 10 ( P -value) ( Y -axis) of metabolite levels compared with net gain aneuploidy levels across a cohort of human breast cancer samples (aneuploidy levels inferred from matched RNA-seq data). ( D ) Heat map of differentially essential gene sets associated with net gain aneuploidy across DepMap cancer cell line CRISPR screen data ( right column) showing a pattern similar to that of the aneuploidy epistasis profile of HMECs ( left column). Gene set enrichment analysis (KEGG gene sets) was performed on a gene list ranked by the correlation of effect scores with net gain aneuploidy levels. HMEC data are summarized from CRISPR screens in . ( E ) Gene effect scores of mitochondrially localized genes are mostly negatively correlated with net gain aneuploidy levels across cancer cell lines. ( F ) Gene set enrichment plots showing all mitochondrially localized genes ( top ) or just oxidative phosphorylation genes ( bottom ) using the gene ranking in D . ( G ) Overall survival across a 5 year time frame of breast cancer patients from the TCGA cohort with aneuploid tumors classified as either “net gain” or “net loss,” treated with DNA-damaging/antinucleotide/antimetabolite chemotherapeutics ( left panel) or without chemotherapy ( right panel). Hazard ratios and associated P -values were calculated from Cox proportional hazards regression models. ( H ) Diagram depicting a net gain aneuploidy nucleotide insufficiency model and putative therapeutic vulnerability. Increased nucleotide pool requirements render net gain aneuploid cells sensitive to nucleotide pool stress caused by nucleotide synthesis inhibitors or DNA damage. This nucleotide pool stress cannot be fully rescued by uridine salvage and results in p53 activation and cell cycle arrest, whereas diploid cells can replicate efficiently using salvage alone.

Article Snippet: Six hours prior to metabolite isolation, the cells were treated with Lonza HMEC medium containing 10 mM 13 C 4 -aspartate (Sigma), and the pH was adjusted to 7.4 with the relevant treatments.

Techniques: RNA Sequencing, CRISPR, Phospho-proteomics, Activation Assay