Hello everyone,
I have thawed primary tumor cells and performed FACS. There were EpCAM positive cells among them. Then I cultured them as organoids and did another FACS. Again, they were EpCAM positive. I also send organoids to pathology for IHC. Results showed they expressed EpCAM, EGFR, and pan CK. But to my surprise, the Ampli LowPass sequencing results showed they had a balanced profile like normal cells. How could that be explained? Any help (comments, papers, ...) is appreciated.
Thank you.
Tumor cells do have different genetic and epigenetic profiles compared to normal cells, to say the least. One explanation of your results could be that the input DNA used for sequencing contains high percentage of normal cells DNA. This could substantially dilute signals from altered DNA below detection limits.
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To the best of my knowldge primary tumor cell lines have abnormal genetic profiles and usually show DNA aneuploidy.
In my opinion, the primary cells you obtained could comprise of several different cluster of cells. Together, they contributed to a balanced profile. You may consider sorting them first before continuing with FACS. Good luck with your work.
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