High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment

An Integrated Study of Aberrant Gene Copy Number and Gene Expression in GIST and LMS

Increased chromosomal instability that alters the gene copy numbers throughout the genome is known to have a role in molecular pathogenesis of tumors. The impact of gene dosage effect to the expression levels of genes in GIST and LMS is unknown. In this paper, we used a combination of array comparative genomic hybridization (aCGH) and gene expression data to gain insights into the interplay of structural and functional changes of the genome in GIST and LMSs. We identified specific target genes that change their expression due to the gene dosage effect. Statistical analysis identified four chromosomal regions, 1p, 14q, 15q, and 22q, where both copy number and mRNA expression were significantly different between the tumor types. Multi-dimensional scaling (MDS) analysis showed that the gene expression profiles of these four regions accurately distinguish GIST and LMS. In addition, the gene dosage sensitive genes in these regions are differently involved in several tumor growth promoting pathways, implying that there are different mechanisms underlying the GIST and LMS carcinogenesis. Integration of aCGH and gene expression data has not only provided insights into how DNA copy number variations affect the gene expression patterns in these cancers, but also proves to be a promising method to choose biologically relevant biomarkers. </jats:p

Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression

Understanding of molecular events in cancer requires proteome-level characterisation. Here, proteome profiling of patient samples representing primary and progressed prostate cancer enables the authors to identify pathway alterations that are not reflected at the genomic and transcriptomic levels