Using next-generation sequencing analysis of mate-pair DNA libraries, a group of researchers from the Center for Individualized Medicine recently identified novel chromosomal rearrangements involving TP63 in approximately 6% in peripheral T-cell lymphomas and demonstrated that these were associated with a poorer overall survival than lymphomas without these rearrangements. These rearrangements also were found in occasional B-cell lymphomas, but were not identified by RNA sequencing in a small series of carcinomas of the lung, breast, or head and neck. By immunohistochemistry, TP63 rearrangements were associated with a p63+/p40− profile in lymphomas. As a subset of lung adenocarcinomas has a p63+/p40− immunoprofile, we examined the presence of TP63 rearrangements and associated p63/p40 expression of lung adenocarcinomas.
Thirty seven lung adenocarcinomas were sequenced using the mate-pair break-point sequencing protocol. For this study, data were mined for TP63 genomic rearrangements. Fluorescence in-situ hybridization (FISH) and immunohistochemistry were used to further evaluate potential TP63 rearrangements. A validation study was performed on a separate cohort of 45 resected adenocarcinoma including immunohistochemistry for p63 and p40. All cases positive for p63 and negative for p40 and two cases negative for both were selected for further FISH studies. The diagnosis of adenocarcinoma was confirmed using the WHO classification and classified according to the new proposed classification of adenocarcinoma. The Mayo Clinic Institutional Review Board approved the study.
Of the 37 sequenced adenocarcinomas, a TP63 rearrangement was identified in two (5%) synchronous lung tumors from one patient. This patient underwent resection of two adenocarcinomas with a 5 months interval, the first from the right middle lobe and the second from the left lower lobe. Histologically, both tumors were mucinous adenocarcinoma and determined to be intrapulmonary metastasis through shared genomic break points. The TP63 fusion resulted from a complex rearrangement on the q-arm of chromosome 3 that fused the B3GALNT1 gene at locus 3q26.1a to TP63 at locus 3q28b.
The rearrangement predicted an inversion of the gene sequence in the third intron of B3GALNT1 transcript variant 1, which fused with a region in the first intron of TP63 transcript variant 1, positioning the promoter of B3GALNT1 in line with the TP63 coding unit from exon 2 onwards. PCR validation of the rearrangement using primers flanking the predicted fusion junction generated unique bands in both adenocarcinomas, which was absent in non-neoplastic lung tissue from the same patient and a mixed germline population control sample. Additional validation in germline DNA extracted from blood from that patient also confirmed the event as a novel somatic rearrangement. Sanger sequencing on DNA extracted from the PCR validation bands confirmed the fusion with precise positions at chromosome 3, 160,819,605 and 189,429,980, with an intermediate 11 nucleotides between these fusion positions of unknown origin. Immunohistochemistry staining for p63 was diffuse (>80% tumor cells+) and p40 was negative in both adenocarcinomas. Break-apart FISH confirmed rearrangement of TP63 in both samples.
Read the full published article here.
Tags: Biobank, biomarker, biomarkers, cancer, center for individualized medicine, DNA, DNA Sequencing, dna test, DNA Testing, gene sequencing, genetic, Genetics, genome, genome science, Genome Sequencing, Genomic, genomic medicine, genomics, individualized medicine, Individualized Medicine Clinic, mayo clinic, microbiome, personal genomics, personalized care, predictive medicine, Uncategorized, whole genome sequencing