Use of cryopreserved cell aliquots in the high-throughput screening of small interfering RNA libraries

Identification of modulators of autophagic flux in an image-based high content siRNA screen

Autophagy is the primary process for recycling cellular constituents through lysosomal degradation. In addition to nonselective autophagic engulfment of cytoplasm, autophagosomes can recognize specific cargo by interacting with ubiquitin-binding autophagy receptors such as SQSTM1/p62 (sequestosome 1). This selective form of autophagy is important for degrading aggregation-prone proteins prominent in many neurodegenerative diseases. We carried out a high content image-based siRNA screen (4 to 8 siRNA per gene) for modulators of autophagic flux by monitoring fluorescence of GFP-SQSTM1 as well as colocalization of GFP-SQSTM1 with LAMP2 (lysosomal-associated membrane protein 2)-positive lysosomal vesicles. GFP-SQSTM1 and LAMP2 phenotypes of primary screen hits were confirmed in 2 cell types and profiled with image-based viability and MTOR signaling assays. Common seed analysis guided siRNA selection for these assays to reduce bias toward off-target effects. Confirmed hits were further validated in a live-cell assay to monitor fusion of autophagosomes with lysosomes. Knockdown of 10 targets resulted in phenotypic profiles across multiple assays that were consistent with upregulation of autophagic flux. These hits include modulators of transcription, lysine acetylation, and ubiquitination. Two targets, KAT8 (K[lysine] acetyltransferase 8) and CSNK1A1 (casein kinase 1, α 1), have been implicated in autophagic regulatory feedback loops. We confirmed that CSNK1A1 knockout (KO) cell lines have accelerated turnover of long-lived proteins labeled with (14)C-leucine in a pulse-chase assay as additional validation of our screening assays. Data from this comprehensive autophagy screen point toward novel regulatory pathways that might yield new therapeutic targets for neurodegeneration.

Cell-based screening: extracting meaning from complex data

Unbiased discovery approaches have the potential to uncover neurobiological insights into CNS disease and lead to the development of therapies. Here, we review lessons learned from imaging-based screening approaches and recent advances in these areas, including powerful new computational tools to synthesize complex data into more useful knowledge that can reliably guide future research and development.

Tales from an academic RNAi screening facility; FAQs

RNAi technology is now a well-established and widely employed research technique that has been adopted by many researchers for use in large-scale screening campaigns. Here, we offer our experience of genome-wide siRNA screening from the perspective of a facility providing screening as a service to a wide range of researchers with diverse interests and approaches. We have experienced the emotional rollercoaster of screening from the exuberant early promise of a screen, the messy reality of the data through to the recognition of screen data as a potential information goldmine. Here, we use some of the questions we most frequently encounter to highlight the initial concerns of many researchers embarking on a siRNA screen and conclude that an informed view of what can be reasonably expected from a screen is essential to the most effective implementation of the technology. Along the way, we suggest that for this area of research at least, either centralization of the resources or close and open collaboration between interested parties offers distinct advantages.