Introduction: Breast cancer stem cells are suspected to be responsible for tumour recurrence, metastasis formation as well as chemoresistance. Consequently, great efforts have been made to understand the molecular mechanisms underlying cancer stem cell maintenance. In order to study these rare cells in-vitro, they are typically enriched via mammosphere culture. Here we developed a mammosphere-based negative selection shRNAi screening system suitable to analyse the involvement of thousands of genes in the survival of cells with cancer stem cell properties. Methods: We describe a sub-population expressing the stem-like marker CD44⁺/CD24^-/low in SUM149 that were enriched in mammospheres. To identify genes functionally involved in the maintenance of the sub-population with cancer stem cell properties, we targeted over 5000 genes by RNAi and tested their ability to grow as mammospheres. The identified candidate ATG4A was validated in mammosphere and soft agar colony formation assays. Further, we evaluated the influence of ATG4A expression on the sub-population expressing the stem-like marker CD44⁺/CD24^low. Next, the tumorigenic potential of SUM149 after up- or down-regulation of ATG4A was examined by xenograft experiments. Results: Using this method, Jak-STAT as well as cytokine signalling were identified to be involved in mammosphere formation. Furthermore, the autophagy regulator ATG4A was found to be essential for the maintenance of a sub-population with cancer stem cell properties and to regulate breast cancer cell tumourigenicity in vivo. Conclusion: In summary, we present a high-throughput screening system to identify genes involved in cancer stem cell maintenance and demonstrate its utility by means of ATG4A.

Significance: Recent success of T cell-based cancer immunotherapies highlights the importance of further understanding molecular mechanisms in the regulation of T cell responsiveness. Here, we performed a genome-wide CRISPR screen to identify genes that regulate T cell activation upon anti-T cell receptor (TCR) stimulation. Our screen confirmed many of the known regulators in proximal T cell signaling. Moreover, we identified a previously uncharacterized gene named FAM49B, which acts as a negative regulator in T cell activation. Our study suggests that genome-wide CRISPR screening is a powerful means to identify key regulators of TCR signaling. The same strategy could be applied to CD28-mediated costimulatory signaling or PD-1–mediated coinhibitory signaling. The unbiased approach presented here may allow us to identify new therapeutic targets for cancer immunotherapy.