High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

RNA interference (RNAi) screening is a state-of-the-art technology that enables the dissection of biological processes and disease-related phenotypes. The commercial availability of genome-wide, short hairpin RNA (shRNA) libraries has fueled interest in this area but the generation and analysis of these complex data remain a challenge. Here, we describe complete experimental protocols and novel open source computational methodologies, shALIGN and shRNAseq, that allow RNAi screens to be rapidly deconvoluted using next generation sequencing. Our computational pipeline offers efficient screen analysis and the flexibility and scalability to quickly incorporate future developments in shRNA library technology

The Cancer Research UK Stratified Medicine Programme as a model for delivering personalised cancer care

Genomic screening is routinely used to guide the treatment of cancer patients in many countries. However, several multi-layered factors make this effort difficult to deliver within a clinically relevant timeframe. Here we share the learnings from the CRUK-funded Stratified Medicine Programme for advanced NSCLC patients, which could be useful to better plan future studies

CM-Path Molecular Diagnostics Forum-consensus statement on the development and implementation of molecular diagnostic tests in the United Kingdom.

BACKGROUND: Pathology has evolved from a purely morphological description of cellular alterations in disease to our current ability to interrogate tissues with multiple 'omics' technologies. By utilising these techniques and others, 'molecular diagnostics' acts as the cornerstone of precision/personalised medicine by attempting to match the underlying disease mechanisms to the most appropriate targeted therapy. METHODS: Despite the promises of molecular diagnostics, significant barriers have impeded its widespread clinical adoption. Thus, the National Cancer Research Institute (NCRI) Cellular Molecular Pathology (CM-Path) initiative convened a national Molecular Diagnostics Forum to facilitate closer collaboration between clinicians, academia, industry, regulators and other key stakeholders in an attempt to overcome these. RESULTS: We agreed on a consensus 'roadmap' that should be followed during development and implementation of new molecular diagnostic tests. We identified key barriers to efficient implementation and propose possible solutions to these. In addition, we discussed the recent reconfiguration of molecular diagnostic services in NHS England and its likely impacts. CONCLUSIONS: We anticipate that this consensus statement will provide practical advice to those involved in the development of novel molecular diagnostic tests. Although primarily focusing on test adoption within the United Kingdom, we also refer to international guidelines to maximise the applicability of our recommendations

Telomere maintenance in human cells : implications in cancer and ageing diseases

Telomeres are protective structures at the end of eukaryotic chromosomes essential for indefinite cell proliferation. Their disruption causes activation of DNA repair pathways, growth arrest and/or cell death. In normal cells telomere shortening during cell division has been proposed to act as a tumor suppressor mechanism to block the proliferation of cells at risk of undergoing malignant transformation. Overcoming this proliferative block by activating a mechanism to maintain telomeres is a necessary requirement for unlimited proliferation and tumor progression. Human cells have two mechanisms for telomere maintenance: a more common one based on telomerase and a rarer one based on recombination called ALT.Here we report the isolation of an immortal human cell line that maintains short telomeres in the absence of biologically active telomerase and key features of active ALT. Our results suggest that the mechanisms of telomere maintenance in human cells may be more diverse than previously thought and have important implications for the development of anti-cancer strategies based on the inhibition of telomere maintenance.Due to widespread distribution of telomerase in human tumors and its absence in most normal cells, telomerase is the main target of these anti-cancer strategies. However, targeting telomerase per se or in combination with anti-cancer drugs is not sufficient to trigger rapid cell death of tumor cells. On the other hand, disturbances in telomere capping do not require telomere shortening to induce growth arrest and may act more quickly. Our goal was to investigate the feasibility of a new approach based on the combination of telomere destabilization and chemotherapeutic drugs. Our results show that interfering with telomere maintenance enhances the susceptibility of human tumor cells to anti-cancer drugs independently of their telomere lengths and mechanisms to maintain them.Finally, given the involvement of telomeres in maintaining genomic stability, we investigated the mechanism by which mutations in the telomerase RNA subunit contribute to autosomal dominant dyskeratosis congenita, a premature ageing disease associated with mutations in the telomerase holoenzyme. Our data strongly indicate that the clinical manifestations of this disease may be caused by telomere shortening due to haploinsufficiency of telomerase activity and provide a direct correlation between disturbances in telomere length maintenance and human disease

In vitro low propensity to form nucleosomes of four telomeric sequences

The structural aspects of nucleosome assembly on telomeres are largely unknown. We analyzed by competitive reconstitution the affinities for the histone octamer of telomeric sequences from four different eukaryotic groups, Arabidopsis thaliana, mammals, Tetrahymena, and Saccharomyces cerevisiae, All telomeres reconstitute in nucleosomes with lower association constants than average nucleosomal DNA. DNase I digestion analysis suggests a multiple translational positioning and the lack of rotational positioning, probably due to telomeric repeats length (in most cases 6-8 bp), out of phase with the DNA helical repeat on the nucleosome (10.2 bp). These results could partly explain the lack of nucleosomes on lower eukaryote telomeres, and suggest a high in vivo mobility of telomeric nucleosomes