CRISPR4ALL - Lentiviral Arrays for the Indexed Activation, Deletion, and Silencing of All Human Genes

CRISPR-mediated genomic screens have been instrumental and widely applied to study fundamental biological phenomena. Recently, we developed two human genome-wide CRISPR libraries, that enable the manipulation of individual genes in human cells. To support the global research community, we have launched CRISPR4ALL with the support of swissuniversities. Through this initiative, we distribute our libraries to researchers around the world, offer training, protocols, and computational resources for using our libraries effectively, and start a FAIR-compliant CRISPR screen community.

Arrayed CRISPR libraries extend the screening territory of phenotypic CRISPR screens to cell non-autonomous, biochemical and morphological phenotypes. We have generated two human genome-wide arrayed plasmid libraries: “T.spiezzo” (gene ablation, 19,936 plasmids) and “T.gonfio” (gene activation and epigenetic silencing, 22,442 plasmids). Each library contains 116 non-targeting plasmids for control and is organized into thematic sublibraries. The libraries and the APPEAL cloning method are described in our recent paper in Nature Biomedical Engineering (Yin et al. 2024, in press). In order to use our libraries with primary human cells and human induced pluripotent stem cells, we have repackaged them into lentiviral vectors.

With CRISPR4ALL we enable the access of the global research community to these toolsets and to the research data generated therefrom 1) by generating lentiviruses from our library plasmids and providing them to the research community; 2) by providing practical training, protocols and standards to interested users, and 3) by creating a community of users adopting robust FAIR-compliant computational tools for collaborative research and data sharing.

Through CRISPR4ALL, we are enabling the global research community to access these toolsets and the research data they generate by:
1) generating lentiviruses from our library plasmids and providing them to the research community;
2) providing practical training, protocols and standards to interested users;
3) creating a community of users adopting robust FAIR-compliant computational tools for collaborative research and data sharing.

This project is still ongoing at the time of writing (July 2024). After conducting a call for project proposals for the dissemination of our libraries, we have provided access to them to more than 15 labs in Europe and the USA, concluded the training of several researchers hosted in our lab in Zurich, organized a CRISPR-themed retreat for CRISPR4ALL beneficiaries, which will take place in September 2024, and visited more than 30 labs to disseminate our libraries and their use.

In the next months, in addition to fulfilling more requests for reagents and hosting more researchers for trainings in our lab, we will deposit 100 highly-characterized plasmids to Addgene and publish a detailed protocol for large-scale arrayed library generation and screens. In parallel, we are working on the computational and data-analysis part of this project, and we will continue to update our website to include links to repositories where relevant data and results can be found, relevant papers and protocols, and incorporate an interactive database for our CRISPR libraries.

We believe that Open Science practices are not limited to digital data and resources, but also extend to sharing tangible resources and practical experience. Unlike the well-established electronic data sharing schemes within the research community, there is no mature scheme that can be adapted to share large amounts of physical resources and their associated information and (meta)data. In addition, given the increasing interest in genomic screens and the fact that relevant experience is lacking in many laboratories, we believe that sharing our practical experience with interested scientists, complemented by computational resources for data analysis, is a very important aspect of upholding and applying Open Science principles.