Abstract B006: Dissecting metabolic alterations of clear cell renal cell carcinomas one cell at a time
Authors: Salas Lucas A. , Zhang Ze , Perreard Laurent , Kolling Fred W. , Pettus Jason R. , Christensen Brock C. 
Published: August 2023

Pseudohypoxia-related metabolic alterations are known to exist in clear-cell renal cell carcinoma (ccRCC). Here we characterized single-cell metabolic pathways with the 10Xmultiome assay comparing metabolic and compositional shifts in tumor vs. normal-adjacent samples. We analyzed 57 tumor and 6 normal-adjacent samples from the Dartmouth Renal Tumors Biobank collected between 1994-2009. Samples were enzymatically disassociated and stored at -80 C until 10X multiome processing. RNA counts were extracted using Seurat, cell types were deconvolved using Azimuth, and 85 KEGG metabolic pathways were interrogated using scMetabolism scores. Linear mixed-effects models compared the metabolic scores in 10 cell lineages (juxtaglomerular apparatus, glomeruli, proximal tubule system, nephron loop, distal tubules, collecting ducts, lymphoid, myeloid, endothelia, and other stroma cells) between tumor and normal adjacent adjusting for sex, patient age, stage and grade as fixed-effects and donor, and year of collection, as random-effects. P-values were calculated using Satterthwaite's method. The mean age at diagnosis was 61.7 yrs (SD: 12.5), and 67% were stages I/II. 79,804 tumor and 5,967 normal-adjacent cells were analyzed. 34,318 cells were nephron epithelia (juxtaglomerular, glomeruli, renal tubules), 5,947 were collecting ducts, 18,959 were immune, 13,445 were endothelial, and 13,112 were other stromal cells. Out of 85 KEGG metabolic pathways, nine were prioritized based on the kidney cancer literature; glycolysis, oxidative phosphorylation, TCA cycle, fatty acid biosynthesis, glutamine/glutamate, arachidonic acids, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and glutathione. When comparing vs. the corresponding normal adjacent cell type, in tumor cells: 1) glutamine/glutamate expression increased in lymphoid, endothelial, and stromal cells; 2) fatty acid biosynthesis increased in myeloid and reduced in lymphoid, collecting ducts-like, and nephron loop-like cells, 3) glutathione and glycolysis increased in glomeruli-like and nephron loops-like, 4) glycolysis increased in collecting ducts-like and endothelial, 5) oxidative phosphorylation and TCA cycle genes decreased in distal tubules-like, collecting ducts-like, and endothelia, 6) arachidonic acid metabolism increased in nephron loops-like and glomeruli-like, and 7) phenylalanine, tyrosine, and tryptophan biosynthesis decreased in nephron loops-like, distal tubules-like, and collecting ducts-like cells. Cell-specific metabolic shifts were observed between tumor and normal adjacent samples that cannot be explained only by sample heterogeneity or cell lineages. Oxidative phosphorylation and TCA cycle modifications were observed in tumor endothelia and cells resembling distal tubules and collecting ducts. Similarly, glutamate and fatty acid alterations were focused on tumor microenvironment immune cells. Further dissecting these findings will provide additional therapeutic avenues for newer targets, such as glutaminase inhibitors and combinations with current therapies.

Citation Format: Lucas A. Salas, Ze Zhang, Laurent Perreard, Fred W. Kolling, Jason R. Pettus, Brock C. Christensen. Dissecting metabolic alterations of clear cell renal cell carcinomas one cell at a time [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B006.