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🎉 Celebrating a decade of CRISPR screening: Back to 2018 🎉 Utilizing #CRISPRscreening, three 2018 publications  probe large-scale genetic and protein interactions, contributing to our understanding of cellular machines and complex cellular mechanisms. ▶ A team led by Michael Boutros reported the largest genetic network of cancer cells to date (Benedikt Rauscher et al, Mol Sys Biol 2018). Using a novel computational framework termed MINGLE, they integrated data from 85 screens to extract #syntheticlethal genetic interactions (GIs). These genetic interactions — where the loss of one gene exacerbates the loss of another — are crucial for uncovering disease vulnerabilities that could be therapeutically exploited. They explored more than 2 M gene-background relationships. The study significantly broadened our understanding of cancer-specific gene interactions and highlighted the complexity of genetic networks in cancer. Its findings serve as a resource for identifying potential drug targets and personalized cancer therapies. ▶ Yet another blueprint for mapping the human genetic landscape came from the teams of Jonathan Weissman and Luke Gilbert. They perturbed more than 220k gene pairs by combinatorial #CRISPRi which enabled GI mapping and identified hitherto unknown gene functions (Max Horlbeck et al, Cell 2018). Their work elucidated unexpected relations between pathways involved in cell growth, proliferation and differentiation, plus delivering a high-resolution view of gene function in human biology. ▶ Finally, a team around Cigall Kadoch focused on uncovering the structure and function of protein complexes using data derived from #CRISPR and #RNAi #screening in human cancer cells (Pan, Meyers et al, Cell Syst 2018). They devised functional similarity networks to provide critical insights how proteins function together. Besides reflecting known structures and functions, the networks also revealed new functional groups in complexes that were not yet structurally resolved. Again, the team utilized data from a large number of screens performed in hundreds of cancer cell lines. Then they integrated their functional networks with protein-protein-interaction information, leading to the discovery of novel protein complexes. This work established a new methodology to explore how proteins cooperate in multi-subunit complexes, paving the way for improved drug discovery and a deeper understanding of how molecular complexes function in cellular processes. 🚀 The collective impact of these publications lies in their contribution to creating high-resolution maps of GIs and cellular dependencies, offering powerful tools for basic research and therapeutic applications. They accelerated the use of CRISPR screens as a standard technique for dissecting complex genetic networks, identifying novel drug targets and developing #personalized #therapies, particularly in cancer.

🎉 Celebrating a decade of CRISPR screening: Back to 2018 🎉 Today, we highlight a review and a breakthrough highly relevant to advancing #crispr #screening capabilities. ▶ First the review – if you haven’t done so yet, the piece by John Doench in Nature Reviews Genetics titled “Am I ready for CRISPR? A user's guide to genetic screens” is a must read. It provides a step-by-step roadmap for scientists considering to use the power of #CRISPRscreening in their work, with practical considerations on design, execution and interpretation of CRISPR screening experiments, be it for understanding gene function, drug resistance or complex biological pathways. The review advises CRISPR novices, it demystifies the technical and conceptual aspects and offers critical advice on how to successfully apply #CRISPR #screening to a diverse set of research questions. ▶ Next, a 2018 technological breakthrough: In an editorial letter to Nature Methods, the teams of Luca Pinello and Daniel Bauer introduced CRISPR-SURF, a computational framework for deconvoluting data from CRISPR/Cas9 tiling screens that significantly advanced both functional genomics and regulatory element discovery (Jonathan Hsu et al, Nature Methods 2018). CRISPR-SURF is an abbreviation for Screening of Uncharacterized Region Function – referring to tiling screens that are designed to map and identify functional regulatory elements, e.g. enhancers and promoters, by creating systematic point mutations across large genomic regions. The framework provides a robust statistical framework for analyzing dense CRISPR tiling experiments across large genomic landscapes. It improves the signal to noise ratio by accounting for factors like target sequence properties and screen efficiency, increasing the confidence when discovering regulatory elements, thereby expanding the #searchspace of CRISPR screens to the #noncoding genome. Before this, most CRISPR screens were largely focused on protein-coding genes. CRISPR-SURF became a critical resource for research into complex biological systems and diseases. It paved the way for deeper biological insights into gene regulation, epigenetics and the underlying genetic mechanisms of disease.   Watch out for our next post, where we stay in 2018 and highlight gene interaction mapping to understand complex biology! #analysisiskey

A warm welcome to Simran Rastogi, who started as Associate Scientist at #Vivlion in beginning of October! Simran completed her master's training in molecular biosciences at Universität Heidelberg and DKFZ Deutsches Krebsforschungszentrum. She is specialized in molecular and cell biology and has extensive hands-on experience in different applications of #CRISPR-mediated genome editing. Through several longer internships at Broad Institute of MIT and Harvard, BioMed X Institute and National Center for Tumor Diseases (NCT) Heidelberg, she acquired a wide variety of technologies. Happy to have you on the team, Simran! #CRISPR #PRCISR #Screening #Startup

🎉 Celebrating a decade of CRISPR screening: Back to 2017 (again) 🎉 After highlighting two methodological innovations (CERES & CRISPR-UMI) yesterday, we will now dive into the ever-growing variety of biological applications of CRISPR screening. ▶ Screening for active lncRNA loci: In 2017, a team led by Feng Z. and Eric Lander shed light into the functions of long noncoding RNA (#lncRNA) loci by utilizing a CRISPR activation (#CRISPRa) screen (Joung et al, Nature 2017). Their screen was designed to target more than 10k transcriptional start sites for lncRNAs and identified 11 lncRNA loci to confer resistance to BRAF inhibitors in melanoma cells. Digging deeper into one of these loci, they were able to show how transcriptional activation of this lncRNA locus exerted a dose-dependent effect of four neighboring protein-coding genes, one of which was responsible for the resistance phenotype. This publication highlights how #CRISPRscreening enables the exploration of noncoding regions of the genome with direct implications for human diseases.    ▶ Understanding cancer immunotherapy response: A team around Nicholas Restifo, Shashank Patel and Neville Sanjana explored genetic factors that influence the efficacy of T cell immunotherapies in human cancer, particularly why some tumors resist treatment (Patel et al, Nature 2017). They utilized a genome-wide CRISPR library to mimic loss-of-function mutations occurring in human melanoma, and identified over 100 genes that are essential for the effector function of CD8  T cells. Amongst them were genes with prominent roles in antigen presentation and interferon-γ signaling. One significant and unexpected discovery was the identification of the apelin receptor (APLNR) as a gene mutated in therapy-refractory patient tumors, and the authors also deciphered the underlying molecular mechanism. Taken together, the study revealed how loss of certain genes, including APLNR, could impair the efficacy of immunotherapies. As such, it is a prominent example for how #CRISPR #screening significantly accelerates research into resistance mechanisms by mimicking diverse genetic backgrounds of tumors in a pooled experiment. The results of this and many similar studies since have guided preclinical efforts to enhance the effectiveness of cancer therapy.

🎉 Celebrating a decade of CRISPR screening: Back to 2017 🎉 From 2017 onwards, CRISPR screening saw multiple technological improvements and an ever-growing variety of applications. Hence, we have chosen to highlight a couple of major publications from 2017 – starting today with two major technological advancements. ▶ Breakthrough in mapping vulnerabilities: The teams of William Hahn and Aviad Tsherniak developed the computational tool CERES and thereby solved a critical issue related to the analysis of genetic dependencies (Meyers et al, Nature Genetics 2017). The tool helps to account for the effects of gene copy number variations (CNVs), which can confound results in CRISPR screens, by correcting for the background gene editing effects caused by these variations. By applying CERES to a dataset of genome-scale CRISPR-Cas9 essentiality screens across 342 cancer cell lines (originating from The Cancer Dependency Map Project), the authors were able to significantly decrease false positive results. This publication marked a milestone in the ability to map critical cancer vulnerabilities, offering a refined approach to identifying genes crucial for cancer proliferation and survival. ▶ Single-cell tracing in pooled CRISPR screens: A team led by Ulrich Elling improved the predictive power of pooled screens by devising the CRISPR-UMI methodology (Michlits et al, Nature Methods 2017). They utilized sgRNA libraries bearing unique molecular identifiers (UMIs) to enable cell lineage tracing. The authors proved the robustness of the new methodology in both negative and positive selection screens and were able to reliably measure genetic perturbations at a single-cell level. CRISPR-UMI thereby overcomes limitations of traditional pooled #CRISPR screens, where results are usually aggregated across populations of cells and confounding effects due to off-target edits can occur. Whilst Perturb-Seq – which was one of our 2016 highlights – focusses on the transcriptomic consequences of individual edits, CRISPR-UMI provides insights into how genetic #perturbations influence the fate of individual cells within a population over time. It can trace the cell’s evolutionary history and its response to genetic changes.   📣 Stay tuned until tomorrow, when we will highlight two novel biological applications of #crisprscreening!

The Initiative Gesundheitsindustrie Hessen (IGH) hosted a forum at the Hessian dependance in Brussels to promote Hesse as a location for biotechnology to drive innovation. #Vivlion contributed with a featured speech about the opportunity for Hesse to position itself as a leading location in the EU for advanced #CRISPRscreening for accelerated drug discovery. BioSpring GmbH, industry leader in nucleic acid manufacturing technology, also emphasized gene editing as future key technology, and highlighted the opportunities that lie in supporting beyond start-ups the growth acceleration of established SMEs. Technologieland Hessen can further strengthen its position as leading location for biotechnology if the opportunities are seized. #biotech #Innovationsmotor #Biotechnologie

🎉 Celebrating a decade of CRISPR screening: Back to 2016 🎉   In 2016, Perturb-seq emerged as a groundbreaking tool in functional genomics, revolutionizing the way how genetic screens are interpreted. Perturb-seq refers to the use of CRISPR-based pooled perturbations in combination with single-cell RNA sequencing (scRNA-seq), enabling the systematic modulation of genes whilst recording gene expression profiles at the single-cell level. The power of this approach lies in its ability to identify the mode of a gene’s action in a phenotype-unbiased manner, providing high-resolution insight into gene functions, gene-gene interactions and the regulatory networks governing cell behavior. Two pioneering studies that were published in the same issue of Cell kicked off this new era: In the first one, a team around Aviv Regev utilized Perturb-seq to analyze transcription factors that regulate the response of dendritic cells to lipopolysaccharide (Dixit et al, Cell 2016). They identified distinct gene expression signatures and proposed novel roles for regulators involved in differentiation, the antiviral response and mitochondrial function during immune activation. In the second study, a team around Ido Amit investigated immune system pathways using Perturb-seq (Jaitin et al, Cell 2016). They mapped regulatory circuits governing immune responses with high precision. In addition, they identified opposing roles for Cebpb and Irf8 in myeloid lineage differentiation and distinct functions for Rela and Stat1/2 in regulating monocytic and dendritic pathogen responses. Today, combining single-cell transcriptomic readouts with CRISPR screens is becoming more widely applied with scalability continuing to increase. In contrast to conventional bulk screening methods, scRNA-seq excels at capturing the variability of individual genotypes at single-cell resolution. It can provide powerful new insights into cellular heterogeneity, gene regulatory networks and complex biological systems, opening the door to improved target and drug discovery, disease modeling and personalized medicine approaches.

We are delighted to welcome Jessica Martyn as Scientific Project Manager to the Vivlion team! Jessica did her PhD in bacterial genetics at University of Oxford (UK), followed by a postdoctoral fellowship at Institut Pasteur Paris (France). With her extensive expertise in gene editing and molecular genetics, Jessica will be a valuable addition and further strengthen our clients’ support team. #CRISPR #PRCISR #Screening #Startup

🎉 Celebrating a decade of CRISPR screening: Back to 2015 🎉 For 2015, we chose to highlight a landmark publication by first author Traver Hart and the team around Jason Moffat from University of Toronto (Hart et al., Cell 2015). The publication stands out as the first comprehensive CRISPR screening using multiple contexts to study general cell fitness and synthetic lethal interactions. It opened avenues for the development of targeted therapies that can exploit cancer vulnerabilities, offering more effective and personalized treatment options for patients.   Summary of key findings and impact: ▶ Comprehensive gene mapping: Using high-resolution, genome-wide CRISPR screens, the first set of core essential fitness genes were identified. These are crucial for the survival of cells, and, today, serve as critical controls for most unbiased screens. These genes also represent potential targets for novel therapies, as inhibiting them could impair cancer cell growth without affecting healthy cells. ▶ Personalized therapeutic targets: The study's high-resolution approach also revealed genotype-specific cancer liabilities, or genetic weaknesses unique to particular cancer mutations. These findings underscored the importance of tailoring cancer treatments to a patient's specific genetic makeup, advancing the field of personalized medicine. ▶ Advancing drug discovery: Demonstrating the efficacy of CRISPR-Cas9 in large-scale genetic screens, the study underscored the transformative potential of gene editing technologies in functional genomics and therapeutic discovery. The team uncovered new therapeutic targets, which could be exploited in the development of cancer therapies. This approach was particularly important for addressing cancers that were resistant to conventional treatments.   In 2015, this study was a game changer, demonstrating the potential of #CRISPRscreening as a tool for dissecting the complex genetic dependencies of cancer cells. It did not only enhance our understanding of cancer biology, but also marked a crucial step towards the realization of precision oncology, offering hope for more targeted, less toxic therapies for cancer patients.

🎉 Celebrating a decade of CRISPR screening: Back to 2014 🎉 To the best of our knowledge, the first genome-wide screens utilizing CRISPR/Cas9 in human cells were published back-to-back by Feng Zhang (Shalem et al., Science 2014) and by Eric Lander and David Sabatini (Wang et al., Science 2014). The team around Zhang developed a genome-scale CRISPR-Cas9 knockout (GeCKO) library for lentiviral delivery and targeting over 18,000 human genes with 64,000 unique guide sequences. They showed that this innovative approach enables both negative and positive selection screening in human cells and demonstrated that CRISPR screening could overcome some of the limitations of RNAi, such as off-target effects and incomplete knockdown. The team successfully identified essential genes for cell viability in cancer and stem cells and uncovered genes linked to drug resistance in melanoma. They utilized their CRISPR screening data to infer genetic networks that underlie drug resistance mechanisms, providing a broader understanding of cellular response to treatment. Lander’s and Sabatini’s teams used a library with 73,000 gRNAs in a range of pooled screening approaches. They systematically identified and cataloged essential genes, which are fundamental to cell survival, identified novel tumor suppressors and new biological roles of known proteins in drug resistance, establishing CRISPR screening as a suitable tool for insights into gene function and drug resistance mechanisms. They also showed that certain sequence characteristics of sgRNAs can influence their effectiveness. These two publications mark a significant milestone in genetic research, setting the stage for widespread adoption of CRISPR/Cas9 as a standard technique for high-throughput functional genomics in the pre-clinical value chain. 🥂🚀