p53 upregulated in cancer cell line

Question

[bharata1803]

Hello all,

So, I found a strange data from my RNA-seq analysis. I found that p53 is upregulated in cancer cell line compare to normal cell line. I found this is really strange because usually p53 is down regulated in cancer cell line. Is it possible I messed up with my DESeq function call? Comparing to another gene, I think other gene expression result is normal. Is it biologically explainable? I'm thinking probably the upregulation is caused by a drug. Maybe you can share your experience. Thank you.

[roy.granit]

It is often observed that a mutant form of p53 is up-regulated in cancer cells and acts as a 'dominant' negative. Which cell line did you use? you might be able to validate your findings in the CCLE database.

[bharata1803]

Thank you for your suggestion. The cell is liver and the disease is intrahepatic cholangiocarcinoma. I will check the database after this.

[Jautis]

Even if it doesn't show up in the database, you could also check the sequence and see if the version you see expressed is likely functional.

[bharata1803]

Now, I plan to do some variation detection workflow and I will verify what kind of mutation happened. Thank you.

[Manvendra Singh]

It's completely okay, p53 has been shown to be unregulated in variious cancer types, p53 is dna damage respondent tumor suppressor gene, which could get unregulated, if cells undergo apoptosis, senescence or if dna breaks are there. In the case of L1 retrotransposition p53 is up, and in many cancer types l1 is undergoing retrotransposition