{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Philip Bucher"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15749"],"description":["Insufficient functional T cell persistence impedes therapeutic success of chimeric antigen receptor (“CAR”) therapies. Here, we performed a CAR-adapted base editing screen of PIK3CD, a key regulator of T cell function, metabolism, and fate. We identified point mutations that beneficially modulate CAR T cell profiles in 4-1BBz and 28z CAR T cells, respectively. Remarkably, point mutations with differing effects on PI3Kδ signaling activity were advantageous in distinct CAR contexts: The PI3Kδ-activating mutation E81K enhanced proliferation, metabolic fitness and effector function in 4-1BBz CARs, promoting long-term functional persistence and enhanced therapeutic efficacy in vivo. Conversely, the PI3Kδ-attenuating mutation L32P improved T cell memory formation and functionality in 28z CAR T cells. Together, our approach of Rational Optimization of Activation-dependent Signaling via Targeted Allelic Reprogramming (ROADSTAR) illustrates the importance of CAR design-specific fine-tuning of tailoring intrinsic T cell signaling and demonstrates the potential of base editing for next-generation cellular therapies. Raw data files not provided due to data sensitivity and privacy concerns."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - CAR T cells were cultured in RMPI-1640 supplemented with IL7/IL15 before stimulation. TRBC1/2 stop mutation and PIK3CD E81K point mutations were induced with AncBE4max base editor mRNA introduced via electroporation. \\\"mock\\\" refers to TRBC1/2 stop mutation carrying 19BBz CAR T cells, \\\"E81K\\\" refers to TRBC1/2 stop mutation with additional PIK3CD E81K point mutation in 19BBz CAR T cells. 19BBz CAR T cells were harvested either unstimulated or after twice weekly stimulations with Nalm6 cells (stimulated). Four days after the last stimulation, no Nalm6 cells were detectable in the culture as determined by flow cytometry. All cells were washed twice with ice-cold PBS.","Nucleic Acid Extraction - RNA was directly extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions in addition with RNase-Free DNase Set (Qiagen).","Sequencing - Libraries were sequenced in paired-end mode on an Illumina sequencing platform. Sequencing type: RNA-seq.","Sample Treatment - see sample collection protocol","Library Construction - RNA-seq libraries prepared with the NEBNext Ultra II Directional RNA mRNA UMI Kit (New England Biolabs), according to manufacturer’s instructions.","Growth Protocol - see sample collection protocol"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Downstream analysis was performed with the Nextflow-based rnadeseq (version 2.2.0) pipeline (https://github.com/qbic-pipelines/rnadeseq). This workflow integrates the R package DESeq2 (version 1.40.2) for differential expression analysis used in the R language (version 4.3.1). Genes with a p-adjusted value ≤0.05 were considered differentially expressed and no cut-off in the logFold change was applied during assessment of differential expression analysis.","Sequence Alignment - Quality control, read mapping, and counting was performed using the Nextflow-based nf-core/rnaseq (version 3.12.0) pipeline (https://nf-co.re/rnaseq). Quality control assessment of the raw data was performed using FastQC (version 0.11.9) and RSeQC (version 3.0.1). Reads were mapped to the reference genome (GRCh38) using the STAR aligner (version 2.6.1d)"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["CAR-adapted PIK3CD base editing enhances T cell anti-tumor potency"],"pubmed_authors":["Philip Bucher","Philip Bucher, Nadine Brückner, Jule Kortendieck, Melanie Grimm, Jan T. Schleicher, Karlotta Bartels, Steffen Hardy, Martina Rausch, Hannah Wurzer, Meike Thiemann, Celina May, Mara Mitstorfer, Dennis Letzgus, Julia Quach, Carolin Schneider, Denis A. Ispan, Irene Gonzalez-Menendez, Nayan Jain, Yu-Jui Ho, Jiangqing Chen, Francisco J. Sánchez-Rivera, Jie Sun, Leticia Quintanilla-Martinez, Christoph Trautwein, Bettina Weigelin, Manfred Claassen, Michel Sadelain, Josef Leibold & Judith Feucht"],"additional_accession":[]},"is_claimable":false,"name":"CAR-adapted PIK3CD base editing enhances T cell anti-tumor potency","description":"Insufficient functional T cell persistence impedes therapeutic success of chimeric antigen receptor (“CAR”) therapies. Here, we performed a CAR-adapted base editing screen of PIK3CD, a key regulator of T cell function, metabolism, and fate. We identified point mutations that beneficially modulate CAR T cell profiles in 4-1BBz and 28z CAR T cells, respectively. Remarkably, point mutations with differing effects on PI3Kδ signaling activity were advantageous in distinct CAR contexts: The PI3Kδ-activating mutation E81K enhanced proliferation, metabolic fitness and effector function in 4-1BBz CARs, promoting long-term functional persistence and enhanced therapeutic efficacy in vivo. Conversely, the PI3Kδ-attenuating mutation L32P improved T cell memory formation and functionality in 28z CAR T cells. Together, our approach of Rational Optimization of Activation-dependent Signaling via Targeted Allelic Reprogramming (ROADSTAR) illustrates the importance of CAR design-specific fine-tuning of tailoring intrinsic T cell signaling and demonstrates the potential of base editing for next-generation cellular therapies. Raw data files not provided due to data sensitivity and privacy concerns.","dates":{"release":"2025-11-06T00:00:00Z","modification":"2025-11-06T14:48:48.88Z","creation":"2025-10-15T11:28:44.323Z"},"accession":"E-MTAB-15749","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}