44 Y chromosome genes found in breast cancer cell line AU-565

[Stephen Rocca]

Hello,

I'm studying common gene copy number alterations found in 4 cell lines that are sensitive to a drug we are testing.

The lines are:

MV411, AML from a male patient

Hep3b2.1-7, liver cancer from a male patient

CAPAN1, pancreatic cancer from a male patient, and

AU-565, HER2 + breast cancer from a female patient.

We found 50 common genes with copy number alterations in these 4 lines. In order to weed out possible genes that may not have any connection to the sensitivity, I looked at TTTY genes, of which there were 12. In researching these, I found that they are all on the Y chromosome, which was puzzling as they were even present in the female line. Looking more in depth, I found that 44 out of the 50 genes were from Y chromosome. 

I looked at other breast cancer lines, (8 total, from female patients): MDA-MB-231, MDA-MB-157, MCF7, BT-20, HCC1419, HCC1954, and HCC1569. We also checked  5 ovarian lines: OVCAR3, OVCAR4, OVCAR5, OVCAR8, and SKOV3. All had multiple TTTY genes that with CNAs, (all deep deletions).

I was hoping you could shed some light on this. Any information or ideas you could share with me would be greatly appreciated.

Two ideas that we discussed were:

Contamination with a male cell line, but this seemed unlikely to have happened to so many lines.

Misidentification of the genes, as they were deep deleted and may have identified a short sequence of an analogous female gene.

Also, do you have access to the original sequencing data files that you could share with us?

Thanks for any assistance you can provide.

Sincerely,

Steve Rocca

[Pieter Lukasse]

Hi Steve,

Thanks for reaching out, sorry for the late reply. Deep deletions reported on Y chromosome genes might be common in female samples, since all these genes could be seen as missing by the algorithm. This could perhaps happen if the algorithm does not take gender into account when making the calls. I'll reach out to someone in the team to check if something like this might actually be happening here and whether there is a way to remove such cases from our database.

Best,

Pieter

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[Stephen Rocca]

Hi Pieter,

Thanks very much. That actually makes sense. I appreciate your help.

Sincerely,

Steve Rocca

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From: Pieter Lukasse <pie...@se4.bio>
Sent: Tuesday, July 29, 2025 9:22 AM
To: Stephen Rocca <stephe...@aprea.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>; Molly Hansbarger <molly.ha...@aprea.com>; Teresa Lee <teres...@aprea.com>
Subject: Re: [cbioportal] 44 Y chromosome genes found in breast cancer cell line AU-565