title: PTEN transcript variants caused by illegitimate splicing in "aged" blood samples and EBV-transformed cell lines.
abstract: PTEN is one of the most frequently mutated tumor suppressor genes in human cancers. Mutations occur in either heritable or sporadic fashion. Sequencing of cDNA from patients and normal individuals often reveals splicing variants (SVs) of PTEN, some of which are non-mutation related. To investigate whether these SVs were the result of illegitimate splicing (a general decrease of fidelity in splicing site selection in "aged" samples), we tested "aged" blood from individuals who had normal PTEN transcripts in their "fresh" mononuclear cells. Blood from 20 normal individuals was collected and split into two aliquots. Total RNA and DNA were extracted immediately ("fresh") and 48 h later ("aged"), respectively. Using RT-PCR, subcloning and sequencing, we found seven types of SVs. No mutation was detected in the related intron-exon flanking region in genomic DNA in either "fresh" or "aged" samples. Some of the SVs were also consistently present in both the "fresh" and "aged" EBV-transformed lymphoblastoid cells from six normal individuals. Western blot data indicated that the PTEN protein level (in full length) was not altered in the "fresh" EBV-transformed lymphoblastoid cells with SVs. In conclusion, our data demonstrate that PTEN illegitimate splicing often occurs in "aged" blood and EBV-transformed lymphoblastoid cells. Therefore, it is critical to note the time point of RNA extraction when investigating for PTEN aberrant transcripts. We hope that our data will increase awareness about the sample status, because gene expression data may be potentially flawed from "aged" samples, particularly when dealing with clinical samples.
authors.affiliation: Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
authors.forename: Yunying
authors.initials: Y
authors.lastname: Liu
authors.forename: Priyangi
authors.initials: P
authors.lastname: Malaviarachchi
authors.forename: Marjorie
authors.initials: M
authors.lastname: Beggs
authors.forename: Peter D
authors.initials: PD
authors.lastname: Emanuel
mesh_terms: D017398:Alternative Splicing; D001793:Blood Preservation; D002461:Cell Line, Transformed; D004854:Herpesvirus 4, Human; D006801:Humans; D008214:Lymphocytes; D051059:PTEN Phosphohydrolase / Q000235:genetics*; D020033:Protein Isoforms; D012326:RNA Splicing; D013048:Specimen Handling
chemical_list: D020033:Protein Isoforms; D051059:PTEN Phosphohydrolase; C494929:PTEN protein, human