Experimental Study of Human Expressed Sequences Newly Identified in Silico as Tumor Specific

Abstract

In our previous studies, we used global computational differential display of ESTs that belong to UNIGENE clusters and identified human sequences differentially expressed in human tumors, as well as a considerable amount of transcripts represented only in tumor-derived cDNA libraries. Most of the tumor-specific EST clusters are derived from the plurality of the tumor types originated in tissues of both ectodermal and mesodermal origin. We found that many of such tumor-specific ESTs do not contain long open reading frames and cannot be classified as protein-encoding genes. To experimentally assess patterns of expression of these EST clusters, we studied four of them in PCR experiments on Clontech MTC panels. The experimental data confirm the results obtained by in silico screening, i.e. tumor specificity of their expression. We suggest that a significant increase in the expression of non-coding RNA is a fundamental feature of cancer cells, and that such transcripts could serve as markers for the diagnosis or monitoring of human malignancies.

Evolutionarily new sequences expressed in tumors

“…Experimental data confirmed the results obtained in silico , i.e., the tumor-specificity of expression of these sequences [4]. …”

“…133294 includes an alternatively spliced isoform of the IQGAP3 gene that arises by retention of its 672-nt intron. Earlier [4], we demonstrated that this isoform is characterized by broad tumor-related and embryonal expression, thus representing a new carcinoembryonic transcript.…”

“…For this cluster, we used PCR primers specific to sequences located on chromosome 2. According to our experimental data [4], this sequence is expressed in carcinomas only. This sequence has not been found in any sequenced mammalian genome except rhesus and chimpanzee, with similarity levels of 88% and 99%, respectively ([see Additional file 2], Table 2).…”

“…Clusters very often do not mark a specific transcript, but a set of transcripts whose genome mapping regions are often neighboring but may be not overlapping. Therefore, we selected ESTs which were used for primer design in our previous investigations [3,4] and followed the history of their sequences in UniGene.…”

The Human T-Box Mesodermal Transcription Factor Brachyury Is a Candidate Target for T-Cell–Mediated Cancer Immunotherapy

“…In the present work, we have used a computer-based differential display (CDD) analysis tool, designated HSAnalyst, to conduct global comparison of expressed sequence tag (EST) clusters belonging to the human Unigene database (6,7). Among a list of various genes highly represented in tumorderived libraries and rarely observed in normal tissue-derived libraries was the Unigene cluster Hs.389457, which contains the complete mRNA sequence of human Brachyury, a homologue of the mouse Brachyury gene (8).…”