Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications.

Advances in genomic and transcriptome sequencing are revealing the massive scale of previously unrecognised alterations occurring during neoplastic transformation. Breast cancers are genetically and phenotypically heterogeneous. Each of the three major subtypes [ERBB2 amplified, estrogen receptor (ESR)-positive and triple-negative] poses diagnostic and therapeutic challenges. Here we show, using high-resolution next-generation transcriptome sequencing, that in all three breast cancer subtypes, but not matched controls, there was significant overexpression of transcripts from intronic and untranslated regions in addition to exons from specific genes, particularly amplified oncogenes and hormone receptors. For key genes ERBB2 and ESR1, we demonstrate that overexpression is linked to the production of highly modified and truncated splice variants in tumours, but not controls, correlated with tumour subtype. Translation of these tumour-specific splice variants generates truncated proteins with altered subcellular locations and functions, modifying the phenotype, affecting tumour biology, and targeted antitumour therapies. In contrast, tumour suppressors TP53, BRCA1/2 and NF1 did not show intronic overexpression or truncated splice variants in cancers. These findings emphasize the detection of intronic as well as exonic changes in the transcriptional landscapes of cancers have profound therapeutic implications.

siRNA knockdown of ribosomal protein gene RPL19 abrogates the aggressive phenotype of human prostate cancer.

We provide novel functional data that posttranscriptional silencing of gene RPL19 using RNAi not only abrogates the malignant phenotype of PC-3M prostate cancer cells but is selective with respect to transcription and translation of other genes. Reducing RPL19 transcription modulates a subset of genes, evidenced by gene expression array analysis and Western blotting, but does not compromise cell proliferation or apoptosis in-vitro. However, growth of xenografted tumors containing the knocked-down RPL19 in-vivo is significantly reduced. Analysis of the modulated genes reveals induction of the non-malignant phenotype principally to involve perturbation of networks of transcription factors and cellular adhesion genes. The data provide evidence that extra-ribosomal regulatory functions of RPL19, beyond protein synthesis, are critical regulators of cellular phenotype. Targeting key members of affected networks identified by gene expression analysis raises the possibility of therapeutically stabilizing a benign phenotype generated by modulating the expression of an individual gene and thereafter constraining a malignant phenotype while leaving non-malignant tissues unaffected.

Primer: tissue fixation and preservation for optimal molecular analysis of urologic tissues.

Appreciation of the different methods of tissue handling is a prerequisite to obtaining accurate and biologically relevant tissue-based information. When a tissue sample is removed from its environment, biological changes are induced within its constituent cell population. It is inevitable that artefacts will be induced through obtaining and processing tissues, irrespective of whether the samples comprise a few cells derived by fine-needle aspiration or larger specimens obtained surgically. Depending upon the level of sophistication of the analytical methods subsequently employed, such changes might be irrelevant, or might result in acquisition of spurious data. While even brief ischemia alters expression of some genes, detectable by appropriate molecular techniques, the same changes might make no appreciable difference to tissue histomorphology. Furthermore, the phenotype of viable cells is known to change during tissue collection and handling. For example, transitional epithelial cells voided in urine are not phenotypically identical to those retained within the urothelium. Such phenotypic changes are temporary and might be of little consequence to subsequent analyses. Surprisingly, many cells in tissues preserved in an ischemic state can remain viable for several hours, and are believed to remain genotypically stable in the short term.