Is it suitable for lung cancer scRNA-seq analysis?

[wisRen]

We know that lung cancer may contain lung cancer cells, TME cells, including immuno-cells, how should I select the tissue types? tissue = "Lung" # e.g. Immune system,Pancreas,Liver,Eye,Kidney,Brain,Lung,Adrenal,Heart,Intestine,Muscle,Placenta,Spleen,Stomach,Thymus tissue = "Immune system" # e.g. Immune system,Pancreas,Liver,Eye,Kidney,Brain,Lung,Adrenal,Heart,Intestine,Muscle,Placenta,Spleen,Stomach,Thymus

Above, we used Lung or Immune system, they final figure give different cell type annoation. There are some cell type overlap, and an unknown cell type with [tissue = "Lung"] was annoated with [tissue = "Immune system"], which I think this was correction, however, there are some cell types was annoated differently, how can I be sure which annoation was correct? Or if we can use [`tissue = c("Immune system", "lung")] to use both markers? Please see the attached figures.

using tissue immune system: https://drive.google.com/file/d/1Tja4EH9YPJXNwGq4ewlXWZbvPD5uTXIY/view?usp=sharing using tissue lung: https://drive.google.com/file/d/1zx1ER9ay9jxqWZ6o8VYyeqMliMrsDGY9/view?usp=sharing

[IanevskiAleksandr]

If you are analyzing lung tissue, it is recommended to use the lung annotation dataset. In some cases, certain cell clusters in "Lung-based" annotations may be marked as "Immune system" cells. In these instances, you can reannotate the cells using the tissue = "Immune system" parameter to gain deeper resolution.

When dealing with a large unknown cell type, it can be challenging to determine the appropriate ScType annotation. To address this, you should identify the most differentially expressed genes (DEGs) for this cluster (or its subclusters) and search the literature to determine their potential cell type. If after checking DEGs, this large cluster cells express T-cell markers, it is appropriate to use tissue = "Immune system" annotations. However, it is important to avoid mixing annotations and strictly use correspondind cell type annotations.

Could those be cancer cells as well? Try running CopyKat or other similar tools.

We also had our own function to determine malignant/healthy cells. Even though, this feature (SNV calling) was initially available, it was later disabled due to variations in BAM input file formats which made it difficult to create a versatile function. However, a new function is currently being developed that will be more flexible and ask only for scRNA-seq expression matrix as input. We estimate that this new function for malignant/healthy cell annotations will be ready in 2-3 months.

BR, Aleksandr

[wisRen]

That's very kind of you. Thanks for your response.