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UMich Team Links Mutations in MED12, CNVs to Rare Type of Breast Cancer

NEW YORK (GenomeWeb) – Researchers from the University of Michigan have used targeted next-generation sequencing to uncover gene mutations linked to a rare form of breast cancer.

As they reported in Molecular Cancer Research today, researchers led by the Michigan Center for Translational Pathology's Scott Tomlins performed targeted next-generation sequencing on an archival set of 15 phyllodes tumors, representing benign, malignant, and borderline tumors.

Nearly all the phyllodes tumors, they reported, had mutations in the mediator complex subunit 12 (MED12) gene, while copy-number alterations and mutations in p53, retinoblastoma, and neurofibromin 1 were mostly limited to malignant tumors, suggesting that personalized treatments may be possible.

"We know little about the biology of phyllodes tumors. In part, they have not been studied much because it's difficult to accumulate a large number of samples," Tomlins said in a statement. "Using these new sequencing techniques, we were able to study archived tissue samples, which allowed us to identify enough samples to perform a meaningful analysis."

Phyllodes tumors are rare epithelial tumors that account for some 1 percent of breast tumors. While most phyllodes tumors are benign, they can be malignant and those that become metastatic are difficult to treat, Tomlins and his colleagues said.

The researchers gathered a set of 15 formalin-fixed, paraffin-embedded phyllodes tumors that included five benign, five malignant, and five borderline tumors, as determined by histological analysis.

They analyzed this set of tumors using a multiplexed PCR-based custom Ion Torrent AmpliSeq panel that included more than 2,400 amplicons targeting 126 genes that were then sequenced using the Ion PGM.

Those 126 genes included known oncogenes, tumor suppressor genes, and genes known to harbor high levels of copy-number alterations.

From this, Tomlins and his colleagues uncovered 26 high-confidence non-synonymous or splice site-changing point mutations and indels as well as 16 high-level copy-number alterations.

In 10 samples out of the 15 samples in the study, the researchers noted a mutation in MED12, whose protein product is part of a complex that is a co-activator of RNA polymerase II transcription. They confirmed these MED12 mutations using bidirectional Sanger sequencing.

All the MED12 mutations in these samples were localized to an exon 2 hotspot region near residue G44, which the researchers said has been reported to be recurrently mutated in uterine leiomyomas and benign breast fibroadenomas. As fibroadenomas and phyllodes tumors also share morphological features, the researchers suggested that this additional mutational relatedness might indicate that the two tumor types have similar molecular origins.

Further, as these MED12 mutations are shared across phyllodes tumors — no matter how they've been classified histologically — Tomlins and his colleagues said this could mean that MED 12 mutations in the breast are early changes that don't relate to malignancy. Malignant phyllodes tumors, then, might evolve from less aggressive phyllodes tumors or fibroadenomas by the additional loss of tumor suppressors, the researchers added.

The researchers also reported observing loss-of-function mutations in TP53, RB1, and NF1.

Copy-number alterations, Tomlins and his colleagues reported, were more common in malignant tumors — affecting all five studied — but such copy-number changes were also seen in two borderline samples and one benign sample.

CNVs affected EGFR, IGF1R, and CDKN2A, findings the researchers confirmed using qPCR. As treatments already exist that target EGFR and IGF1R, these genes could also represent potential therapeutic targets for malignant phyllodes tumors, the researchers said.

"Even though phyllodes tumors are rare, it's important to have good treatment options for the aggressive cases," Tomlins said.