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Christoph Bock Lab @ CeMM & MedUni Vienna

@bocklab.bsky.social
1.4K followers 343 following 128 posts

Technology-driven biomedical research at CeMM Research Center for Molecular Medicine & MedUni Vienna #cancer #immunology #bioinformatics #AI #singlecell #CRISPR

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 21/09/2026
We are recruiting PhD students in ML/AI methods & biomedical applications via the @ellis.eu PhD Program (ellis.eu/news/ellis-p...). Keywords: Perturbation modeling, generative AI, synthetic biology, cancer immunotherapy, precision medicine. Details: medical-epigenomics.org/files/PhD_St...
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 08/03/2026
CellWhisperer can now run on your laptop. Talk to your cells! And check out our paper: www.nature.com/articles/s41...
nature.com
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 09/02/2026
Additional information about our research: cemm.at/research/gro... | bocklab.org | med-ai.org Full job posting: cemm.at/fileadmin/im... Further details & application portal: cemm.at/postdoc-prog... & cemm.onlyfy.jobs/job/7k2624z5
bocklab.org
Medical Epigenomics | Bock Lab at CeMM & MedUni Vienna
Led by Christoph Bock, the Medical Epigenomics Lab pursues technology-driven biomedical research for cancer, immunology, and precision medicine.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 09/02/2026
Maybe get some inspiration from our recent papers and consider proposing a project idea or research direction (as part of your application's cover letter) that connects your and our research expertise. Be ambitious & creative!
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 09/02/2026
What excites you? What expertise do you bring from your PhD? What do you envision your future independent research group to focus on (or the start-up company you will found)? What could be a truly exciting & impactful postdoc project?
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 09/02/2026
3. Cancer: Epigenetic tumor heterogeneity (nature.com/articles/s41...) 4. Technology: High-content CRISPR screening for causality at scale (nature.com/articles/s43...) 5. Biomedical ML/AI: Chat-based single-cell data analysis with natural language (nature.com/articles/s41...)
nature.com
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 09/02/2026
Examples of our recent research: 1. Immunology: Immune regulation by non-immune cells (nature.com/articles/s41...) 2. Cell engineering: CRISPR-optimized CAR T cell immunotherapy (www.nature.com/articles/s41...)
nature.com
Structural cells are key regulators of organ-specific immune responses - Nature
Structural cells implement a broad range of immune-regulatory functions beyond their roles as barriers and connective tissues, and they utilize an epigenetically encoded potential for immune gene acti...
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 09/02/2026
We are open to purely wet-lab candidates (including organoids & mouse models), purely computational candidates (including ML/AI), and those who want to pursue a mix of wet-lab & computational work. We are a highly interdisciplinary & collaborative research group with ambitions in molecular medicine.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 09/02/2026
HIRING: We recruit postdocs via the CeMM Pre-ERC Postdoc Program (cemm.at/postdoc-prog...). Seeking 3 types of candidates: (1) experimental systems biology in immunity or cancer; (2) bioinformatics & biomedical ML/AI; (3) tech-dev & bioengineering (CRISPR, single-cell, spatial, cell programming).
cemm.at
PostDoc Program
CeMM Pre-ERC Postdoc Program
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 22/12/2025
Further details & application portal: apply.cemm.at Additional information about our research: cemm.at/research/gro... | bocklab.org | med-ai.org
bocklab.org
Medical Epigenomics | Bock Lab at CeMM & MedUni Vienna
Led by Christoph Bock, the Medical Epigenomics Lab pursues technology-driven biomedical research for cancer, immunology, and precision medicine.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 22/12/2025
What excites you? What could be a great PhD project? Please have a look at our recent publications and consider proposing an idea or research direction (as part of your application's cover letter) that you might want to pursue in our PhD. (4/5)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 22/12/2025
4. Technology: High-content CRISPR screening for causality at scale (nature.com/articles/s43...) 5. Biomedical ML/AI: Chat-based single-cell data analysis with natural language (nature.com/articles/s41...)
nature.com
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 22/12/2025
Examples of our recent research: 1. Immunology: Immune regulation by non-immune cells (nature.com/articles/s41...) 2. Cell engineering: CRISPR-optimized CAR T cell immunotherapy (www.nature.com/articles/s41...) 3. Cancer: Epigenetic tumor heterogeneity (nature.com/articles/s41...)
nature.com
Systematic discovery of CRISPR-boosted CAR T cell immunotherapies - Nature
CELLFIE, a CRISPR platform for optimizing cell-based immunotherapies, identifies gene knockouts that enhance CAR T cell efficacy using in vitro and in vivo screens.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 22/12/2025
HIRING: We recruit PhD students via the AITHYRA-CeMM PhD Program (cemm.at/phd-program). Seeking 3 types of candidates: (1) experimental systems biology in immunity or cancer; (2) bioinformatics & biomedical ML/AI; (3) tech-dev & bioengineering (CRISPR, single-cell, spatial, cell programming) (1/5)
cemm.at
CeMM PhD Program – Molecular Medicine Research in Vienna
Join the CeMM PhD Program in Vienna and pursue cutting-edge research in cancer, immunology, aging, and precision medicine. Applications open in 2025!
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 16/11/2025
Nice example of "garbage-in, garbage out" behavior of CellWhisperer. We could probably add checks to mark meaningless queries. But for now we rely on cooperative users, and CellWhisperer has a clear warning: "Please keep in mind that CellWhisperer is an AI system and may produce misleading results."
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Reposted by Christoph Bock Lab @ CeMM & MedUni Vienna
Nature Portfolio @natureportfolio.nature.com · 15/11/2025
A paper in Nature Biotechnology presents CellWhisperer, which uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data. go.nature.com/3XqzItR 🧬 🧪
This is figure 1, which gives an overview of the CellWhisperer multimodal AI for natural-language analysis of transcriptome data.
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Reposted by Christoph Bock Lab @ CeMM & MedUni Vienna
Nature Biotechnology @natbiotech.nature.com · 11/11/2025
Multimodal learning enables chat-based exploration of single-cell data - @bocklab.bsky.social @cemm.oeaw.ac.at @meduniwien.ac.at go.nature.com/3WPGJnW
go.nature.com
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🤝 Huge thanks to the team! Moritz Schaefer & Peter Peneder with Daniel Malzl, Salvo Lombardo, Mihaela Peycheva, Jake Burton, Anna Hakobyan, Varun Sharma, Thomas Krausgruber, Celine Sin, Jörg Menche, Eleni Tomazou, Christoph Bock. @cemm.oeaw.ac.at, @meduniwien.ac.at, @stanna-ccri.bsky.social (11/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🧬 CellWhisperer introduces a chat-based way to explore scRNA-seq data. By enabling natural language analysis, it bridges biologists and bioinformaticians—paving the way for AI-driven bioinformatics assistants. (10/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
Ready to talk to cells? 📖 Read the paper: doi.org/10.1038/s415... 🧬 Try the web app with public datasets: cellwhisperer.bocklab.org 🖥️ Analyze your own datasets: github.com/epigen/cellw... (9/11)
doi.org
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
📚 We trained on >1 million bulk & pseudo-bulk transcriptomes with textual annotations that we AI-curated from GEO & @CELLxGENE Census. Our training data is open source and useful for developing multimodal biomedical AI models and future bioinformatics research assistants. (8/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🪄 How does CellWhisperer work behind the scenes? We trained a multimodal AI that links transcriptomes and text, enabling free-text search and annotation of RNA profiles. And we connected this model to an LLM that we fine-tuned into a chat assistant for transcriptome data (7/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🚀 We also validated CellWhisperer’s chat-based analysis with conventional bioinformatics. CellWhisperer was >4x faster (and 10x cooler 😊). Our recommendation: Use CellWhisperer for dataset exploration – but statistics is still important to ensure rigor & reproducibility (6/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🆕 The CellWhisperer paper (doi.org/10.1038/s415...) includes several new analyses beyond our 2024 bioRxiv preprint (biorxiv.org/content/10.1...). For example, we used CellWhisperer for an AI-guided analysis of human organ development (5/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🔬 You can easily query large transcriptome datasets for your favorite biological process using CellWhisperer. Just open Tabula Sapiens (cellwhisperer.cemm.at/tabulasapiens/) or GEO (cellwhisperer.cemm.at/geo/) in CellWhisperer & type your query into the chat box – for example “infection” (4/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🔍 We investigate one of the identified cell clusters by selecting the cells & prompting CellWhisperer with ‘Describe these cells in detail’. This interactive workflow is enabled by seamless integration of the CellWhisperer AI chat box into a version of CELLxGENE Explorer (3/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
⚙️ To get started, let’s find cells by typing into the CellWhisperer chat box. For example ‘Show me structural cells with immune functions’. CellWhisperer scores each transcriptome by how well it matches this textual query and colors by query match (red: high, blue: low) (2/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
Ready to talk to cells? 📖 Read the paper: www.nature.com/articles/s41... 🧬 Try the web app with public datasets: cellwhisperer.bocklab.org 🖥️ Analyze your own datasets: github.com/epigen/cellw... (9/11)
nature.com
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
📚 We trained on >1 million bulk & pseudo-bulk transcriptomes with textual annotations that we AI-curated from GEO & CELLxGENE Census. Our training data is open source and useful for developing multimodal biomedical AI models and future bioinformatics research assistants. (8/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🪄 How does CellWhisperer work behind the scenes? We trained a multimodal AI that links transcriptomes and text, enabling free-text search and annotation of RNA profiles. And we connected this model to an LLM that we fine-tuned into a chat assistant for transcriptome data (7/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🚀 We also validated CellWhisperer’s chat-based analysis with conventional bioinformatics. CellWhisperer was >4x faster (and 10x cooler 😊). Our recommendation: Use CellWhisperer for dataset exploration – but statistics is still important to ensure rigor & reproducibility (6/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🆕 The CellWhisperer paper (doi.org/10.1038/s415...) includes several new analyses beyond our 2024 bioRxiv preprint (biorxiv.org/content/10.1...). For example, we used CellWhisperer for an AI-guided analysis of human organ development (5/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🔬 You can easily query large transcriptome datasets for your favorite biological process using CellWhisperer. Just open Tabula Sapiens (cellwhisperer.cemm.at/tabulasapiens/) or GEO (cellwhisperer.cemm.at/geo/) in CellWhisperer & type your query into the chat box – for example “infection” (4/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
🔍 We investigate one of the identified cell clusters by selecting the cells & prompting CellWhisperer with ‘Describe these cells in detail’. This interactive workflow is enabled by seamless integration of the CellWhisperer AI chat box into a version of CELLxGENE Explorer (3/11)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025
⚙️ To get started, let’s find cells by typing into the CellWhisperer chat box. For example ‘Show me structural cells with immune functions’. CellWhisperer scores each transcriptome by how well it matches this textual query and colors by query match (red: high, blue: low) (2/11)
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Reposted by Christoph Bock Lab @ CeMM & MedUni Vienna
CeMM @cemm.oeaw.ac.at · 11/11/2025
🗨️Chat with your cells, explore #CellWhisperer! CeMM PI Christoph Bock (@bocklab.bsky.social) together with @meduniwien.ac.at & @stanna-ccri.bsky.social have developed a new #AI tool that lets scientists explore single-cell data using plain English. ➡️ bit.ly/3JQqe87 📄 bit.ly/3WJCxGi
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
📑 Check out our paper titled “Systematic discovery of CRISPR-boosted CAR T cell immunotherapies” at @Nature (open access): www.nature.com/articles/s41.... Feedback & suggestions are very welcome. (13/13)
nature.com
Systematic discovery of CRISPR-boosted CAR T cell immunotherapies - Nature
CELLFIE, a CRISPR platform for optimizing cell-based immunotherapies, identifies gene knockouts that enhance CAR T cell efficacy using in vitro and in vivo screens.
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
🤝 This was a large project & great teamwork by: P. Datlinger*, E.V. Pankevich*, C.D. Arnold*, N. Pranckevicius, J. Lin, D. Romanovskaia, M. Schäfer, F. Piras, A.-C. Orts, A. Nemc, P. Biesaga, M. Chan, T. Neuwirth, A. Artemov, W. Li, S. Ladstätter, T. Krausgruber, C. Bock (12/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
⚕️ Our CELLFIE platform supports clinical translation of CRISPR-boosted CAR T cells. For example, to avoid the DNA double-strand breaks introduced by CRISPR knockout, we performed a tiling base-editing screen across RHOG and identified promising gRNA for clinical testing. (11/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
🔥 What’s next? Our discovery of strong combined effects for RHOG & FAS knockout underlines the potential of synergistic gene edits for boosting CAR T cell function. We thus integrated combinatorial screening into CELLFIE, using the Blainey lab’s CROPseq-multi method. (10/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
🔬 From a technical perspective, we are excited how our new in vivo CROP-seq method improves gRNA detection (reading from an mRNA transcript as in nature.com/articles/nme...) and reduces experimental noise (by using UMIs), which enables larger screens with fewer mice. (9/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
💪 We also observed prolonged survival for FAS knockout CAR T cells, likely because these cells are less effective at killing each other (“fratricide”). Combining RHOG & FAS knockout, we obtained more & better CAR T cells, which further improved survival in leukemic mice. (8/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
🔍 RHOG is a small GTPase involved in cell signaling. How does it influence CAR T cells ? We found that RHOG knockout increases the proliferative capacity of CAR T cells and helps them retain a highly functional state with reduced exhaustion and enhanced memory phenotype. (7/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
🐁 We performed extensive in vivo validations and found that RHOG knockout CAR T cells achieve strong reductions in cancer cell numbers and prolonged survival in an aggressive mouse model of human leukemia, with consistent results across different CARs and T cell donors. (6/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
🐭 But not everything that makes CAR T cells proliferate or kill better in vitro translates into more effective therapies. For scalable validation in mice, we conducted pooled in vivo CRISPR screening and observed strong positive effects of RHOG, PRDM1, and FAS knockouts. (5/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
💡 Conceptually, our CRISPR screens create a form of “artificial evolution” by which we optimize CAR T cells for their tasks as cancer therapeutics. This is important because CAR T cells are products of cell engineering and lack task-specific evolutionary optimization. (4/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
🩸 Using CELLFIE, we conducted 58 genome-wide CRISPR screens, with readouts for CAR T cell proliferation, target cell recognition, activation, apoptosis & fratricide, and exhaustion. The screens identified known genes (PD-1, CTLA4, TIM3, TIGIT etc.) and promising new hits. (3/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
⚙️ We developed CELLFIE (“cell engineering for immunotherapy enhancement”), a CRISPR platform to make & test gene-edited CAR T cells at scale. CELLFIE supports in vitro & in vivo screens with various clinically relevant readouts, plus combinatorial & base-editing screens. (2/13)
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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025
🧬 CAR T cells demonstrate the power of engineered cells as therapeutics. But they fail for most patients. Can CRISPR help here? Our new paper in Nature (www.nature.com/articles/s41...) presents a screening platform to optimize immunotherapies & discover boosters of CAR T cell function. (1/13)
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