Question: p53 upregulated in cancer cell line
0
gravatar for bharata1803
3.8 years ago by
bharata1803420
Japan
bharata1803420 wrote:

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 yoour experience. Thank you.

 

p53 rna-seq gene • 2.2k views
ADD COMMENTlink written 3.8 years ago by bharata1803420
1

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.

ADD REPLYlink written 3.8 years ago by roy.granit790

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

ADD REPLYlink written 3.8 years ago by bharata1803420

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. 

ADD REPLYlink written 3.8 years ago by Jautis270

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

ADD REPLYlink written 3.8 years ago by bharata1803420
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
ADD REPLYlink written 3.8 years ago by Manvendra Singh2.0k
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