Chromosomal rearrangements and copy number abnormalities of TP63 correlate with p63 protein expression in lung adenocarcinoma

Abstract

The TP63 gene encodes a member of the p53 family of transcription factors. Although TP53 is a well-known tumor suppressor gene, the role of p63 in tumorigenesis is controversial. Our group recently identified novel chromosomal rearrangements involving TP63 in approximately 6% of peripheral T-cell lymphomas, which correlated with a p63 þ /p40 À immunohistochemical profile. As a subset of lung adenocarcinomas are p63 þ / p40 À , we undertook the current study to examine the presence of TP63 rearrangements and correlate with p63/ p40 expression. Next-generation sequencing was used to identify genomic rearrangements of TP63 in 37 adenocarcinomas. Confirmatory fluorescence in-situ hybridization (FISH) using a break-apart probe to the TP63 gene region and immunohistochemistry for p63 and p40 were performed on adenocarcinomas with TP63 rearrangements identified by mate-pair sequencing. Immunohistochemistry for p63 and p40 was performed on 45 additional adenocarcinomas, and FISH was performed on all adenocarcinomas with p63 positivity. TP63 rearrangement was identified in two adenocarcinoma specimens from a single patient. The rearrangement resulted in a complex rearrangement of 3q that fused B3GALNT1 at the 3 0 intron to TP63. FISH confirmed the rearrangement in both tumors. Immunohistochemistry staining for p63 was diffuse (480% cells þ ) and p40 was negative. Of the 44 additional adenocarcinomas, 13 (30%) showed p63 expression; p40 was negative in all cases. No case showed rearrangement of TP63 by a break-apart FISH. However, extra copies of the intact TP63 locus were seen in the p63-positive areas of all 12 cases, with copy numbers ranging from three to seven. We have identified a novel chromosomal rearrangement involving TP63 in a p63 þ /p40 À lung adenocarcinoma. Break-apart FISH testing can be used to diagnose this finding. Immunohistochemistry for p63 was not specific for this rearrangement, as nearly 33% of adenocarcinomas expressed p63. Additional copies of the intact TP63 locus were also a common finding and correlated with immunohistochemistry positivity for p63.

Expression of p63 protein in anaplastic large cell lymphoma: implications for genetic subtyping

“…In a previous study, we reported a p63 protein expression in a TP63 -rearranged lung adenocarcinoma and in non-rearranged cases with extra copies of the intact TP63 locus [16]. Therefore, we examined p63 expression and TP63 copy number in ALCL and found these to be correlated significantly.…”

“…We previously have demonstrated that p63 protein expression is associated with extra copies of the TP63 locus in lung adenocarcinomas [16]. Thus, we investigated whether this association was observed in ALCLs lacking TP63 rearrangements.…”

“…IHC for ΔNp63 (“p40”) was performed in a subset of cases with available tissue sections using a rabbit polyclonal antibody (Biocare) as previously described [16]. p63 expression was scored by decile for percentage of tumor cell nuclei with positive staining.…”

Anaplastic Large Cell Lymphomas

“…9); these rearrangements also can be seen in pcALCL, ALK-negative ALCL limited to mucosal sites, and lymphomatoid papulosis (LyP; see next section). [95][96][97] As discussed above, comparative genomic hybridization has shown copy-number differences between ALK-negative ALCL and ALK-positive ALCL, and differences between ALK-negative ALCL and PTCL, NOS also have been identified. However, other partners have been identified and the significance of the partner locus is unknown.…”

Cellular and molecular architecture of hematopoietic stem cells and progenitors in genetic models of bone marrow failure

“…To identify the spectrum of somatic mutations and affected genes, we analyzed DNA from phenotypical sorted GMP cells. DNA samples from 200 to 965 sorted GMPs were amplified by whole-genome amplification (REPli-G Mini Kit, QIAGEN) for 16 hours with adjustment of reagents to cell number as per the manufacturer's instructions and as previously described (72)(73)(74)(75).…”