When does the term transcriptome come in case of the cancer cells cultured in vitro? If we are thinking for similarity determination of the cancer cells in comparison to original tumor tissue from which it has been derived the early passage, cells are considered for studying NGS data because there is some common hypothesis and prove for some cancer cell lines that after some passages (5-15) genomic and transcriptomic alteration occurs. I am not sure in between the early passages, which passage will be utmost suitable because NGS run is always associated with high costs.
tl;dr: qRT-PCR first to see if contaminating cells are gone
If I am reading your question correctly, I'd suggest that you profile a cell line derived from a primary tumor at the earliest passage possible where you no longer have contaminating (stromal cells, immune cells, etc.) cells also in the culture.
Even a small amount of contaminating cell infiltrate will have highly abundant gene products that will complicate your classification against different tissues when comparing after your NGS run (I assume we are talking RNA-seq here).
Experimental suggestion: if you are taking a skin cancer biopsy that should only contain epidermal keratinocytes (the cell of origin for squamous cell carcinoma, let's say), design some qRT-PCR primers for genes exclusively found in an immune system cell, a pigmented melanocyte cell, and others in the skin. When the detection of these genes has fallen significantly from your original culture, I'd say you are ready to sequence the transcriptome for a relatively pure, early passage cell line.
As mentioned above 'contaminating' non-tumor cells will significantly alter transcriptome measures. A flow sort can be used to purify your cancer cell population and nearly eliminate stromal and lymphocytic cells. So assuming elimination of these cells, do transcriptomes of established cell lines and primary tumors differ? Yes. Cell lines typically have increased p16 expression and activation of associated pathways. However beyond this it depends on the system you are studying. Andrew South has demonstrated that transcriptomes of squamous cell skin cancer cell lines are quite similar to primary tumors. Others have shown considerable differences between established cell lines and similar primary tumors.
One key factor to consider is whether the genomic architecture and heterogeneity of architectures within the populations being studied are similar. If you have the resources to do the experiments, making trancriptomic comparisons between cell lines and primary tumors is always very welcomed data especially if data such as ploidy, whole genome sequence, and/or cytogenetics are included.
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