Shared pathways up in disease blood and tissue relative to healthy blood (scRNA-seq)

Question

[Lucy]

Hi,

We have performed scRNA-seq on blood and tissue from a cohort of disease patients. Unfortunately our scRNA-seq dataset doesn't include any healthy controls. We are interested in pathways that are upregulated in both the blood and tissue of disease patients relative to blood from healthy controls i.e. what are common disease-associated pathways?

Does anyone have any thoughts as to how we could look at this?

Best wishes,
Lucy

Answer 1

[ATpoint]

I will answer generally since this applies to pretty much all OMICS experiments and since there is no details on disease and setup: OMICS is mostly relative, so you can compare what is in your dataset. No healthy controls mean no comparison to this group. What is often done with disease-only samples is to try and define subsets and categories of disease, that might benefit from different diagnostic and treatment regimens. You might also analyse the blood vs tissue comparison to learn whether the local niche and stroma has any interesting effect on gene expression. There must be a reason why this cohort was analysed and why no controls were added. Talk to the clinicians and find out what the most pressing unanswered questions for this disease are. THen try to address that with the data at hand.