Single cell RNA-sequencing identifies a metabolic aspect of apoptosis in Rbf mutant

Abstract

The function of Retinoblastoma tumor suppressor (pRB) is greatly influenced by the cellular context, therefore the consequences of pRB inactivation are cell-type-specific. Here we employ single cell RNA-sequencing (scRNA-seq) to profile the impact of an Rbf mutation during Drosophila eye development. First, we build a catalogue of 11,500 wild type eye disc cells containing major known cell types. We find a transcriptional switch occurring in differentiating photoreceptors at the time of axonogenesis. Next, we map a cell landscape of Rbf mutant and identify a mutant-specific cell population that shows intracellular acidification due to increase in glycolytic activity. Genetic experiments demonstrate that such metabolic changes, restricted to this unique Rbf mutant population, sensitize cells to apoptosis and define the pattern of cell death in Rbf mutant eye disc. Thus, these results illustrate how scRNA-seq can be applied to dissect mutant phenotypes.

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics

“…To validate and further extend our cell type annotations, we used a publicly available Drop‐seq data set from the eye disc containing 11,500 single‐cell profiles with ~ 1× cellular coverage (Ariss et al , ) and a median of 517 genes detected per cell (Appendix Fig S3A and B). Using Seurat's label transferring, we mapped the cell types annotated by Ariss et al to our data set (and vice versa) and found that both annotations agreed (Fig D, Appendix Fig S3C–E).…”

“…Seurat (v3.0.1) was also used for transferring cluster labels between the eye disc data set from Ariss et al () and this data (and vice versa). Brain cells from our data set were not included in the analysis, resulting in a data set with 3,232 cells and 8,744 genes, and the eye disc data set from Ariss et al was filtered to keep cells with more than 1,000 UMI counts and 500 genes expressed, resulting in a data set with 5,630 cells and 7,801 genes.…”

“…Main spatial compartments in the eye‐antennal disc are annotated. tSNE representation of the scRNA‐seq data (with 3,531 cells). tSNE colored by the standardized gene expression of known cell type markers in the eye‐antennal disc. In each plot, three marker genes are shown, using RGB encoding. tSNE annotated by label transfer with Seurat v3 (Stuart et al , ) using the scRNA‐seq eye disc data set from Ariss et al (). Cell‐to‐regulon heatmap showing the standardized enrichment or area under the curve (AUC) from SCENIC (Aibar et al , ) for each selected regulon based on RSS in each cell. Top enriched motifs for representative regulons are shown below.…”

A single-cell transcriptome atlas of the adult muscle precursors uncovers early events in fiber-type divergence inDrosophila

“…Tissue was dissociated into single cell suspension as in (Ariss et al, 2018). Briefly, wandering third instar larvae were harvested.…”

NatB regulates Rb mutant cell death and tumor growth by modulating EGFR/MAPK signaling through the N-end rule pathways

“…Interestingly, inactivation of tsc2 or axin, in conjunction with rbf inactivation, promoted synergistic cell death mediated by deregulated TORC1 and E2F1 activity that induced excessive cellular stress including metabolic stress and DNA damage stress [18,19,20]. In support of the idea that metabolic alteration contributed to rbf mutant cell death, a recent single cell RNA sequencing (scRNA-seq) study of rbf mutant eye discs revealed that the altered metabolic activity with increased glycolysis and increased intracellular acidification contributed to the rbf mutant cell death near the MF [21].…”