scRNAseq vs snRNAseq in cancer

Question

[MCH]

my question is about phagocytosis as response to cancer. It is known that cytotoxic T cell may kill a cancer cell and sends cytokines to phagocytes like macrophage or dendritic cell to engulf and digest the killed cancer cell. From this, my questions: 1) can one assume that mRNAs of the cancer cells can be captured and sequenced along with those of the phagocyte by scRNAseq? In this case, the phagocyte should show a hybrid expression profile 2) if 1 holds (that I have observed in practice), can snRNAseq show a similar result? I ask this because in snRNAseq we deal with nuclei not the entire cell. However, I have observed hybrid expression profiles in phagocytes analyzed by snRNASeq.

Answer 1

[LChart]

Unfortunately, hybrid expression profiles may be a result of contamination (see https://www.biorxiv.org/content/10.1101/791699v2); and the extent of background signal is certainly higher in snRNAseq than scRNAseq as the nucleus allows cDNA to leak out at a faster rate (just take a look at any data using Split&Pool multiplexed barcoding -- the background is insane compared to droplet).

While it is of course possible for phagocyte-ingested mRNA to make its way into the nucleus; I should think it more likely that the hybrid expression profile you observe in snRNA-seq is due to background contamination. You could apply CellBender or SoupX and see if that makes a significant difference.

[MCH]

thank you for the your reply. The result was after applying cellbender.