Question

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:

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
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

Yes, mRNAs from cancer cells could potentially be sequenced along with phagocyte's own mRNAs in scRNAseq if the sequencing occurs before complete digestion, resulting in a hybrid expression profile. The observation of hybrid profiles from snRNAseq suggests ingested mRNAs may be present within the phagocyte nucleus, though this is less common.

Step-by-step explanation:

You asked whether we can assume that mRNAs of cancer cells can be captured and sequenced along with those of the phagocyte by single-cell RNA sequencing (scRNAseq), leading to a hybrid expression profile. In phagocytosis, macrophages, dendritic cells, and neutrophils engulf and digest pathogens and potentially cancer cells. During this process, it is possible for remnants of the ingested material, including mRNAs, to be present within the phagocyte. If the sequencing occurs while this material is still intact within the phagocyte, you could indeed observe a hybrid expression profile from scRNAseq data.

As for your observation of a hybrid expression profile using single-nucleus RNA sequencing (snRNAseq), this is an interesting finding since snRNAseq typically sequences RNA found in the nucleus, not the entire cell. It is possible for mRNAs from ingested cancer cells to have been transported or retained in the nucleus of the phagocyte, which might explain the hybrid profiles seen in your snRNAseq data. However, this would be a less common event, as most mRNA from phagocytosed material wouldn't usually be localized to the phagocyte nucleus.Phagocytosis is an important immune response in which phagocytes like macrophages or dendritic cells engulf and digest particles, including cancer cells. The captured material can include mRNAs from the cancer cells. It is possible to capture and sequence the mRNAs of both the cancer cells and the phagocytes using single-cell RNA sequencing (scRNAseq), which provides information about gene expression in individual cells. Similarly, single-nucleus RNA sequencing (snRNAseq) can also be used to analyze gene expression profiles of phagocytes by focusing on the nuclei instead of the entire cell. Both techniques can reveal hybrid expression profiles in phagocytes, indicating the presence of genetic material from the engulfed cancer cells.