{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/file_names.xlsx"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/7March21_uniprot-proteome_UP000005640_reviewed_yes.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/timsTOF2_4447_8-31-2023_Slot2-29_230823_TIMS02_LiMa_400ng_D15.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/timsTOF2_4451_8-31-2023_Slot2-32_230823_TIMS02_LiMa_400ng_C25.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/timsTOF2_4445_8-31-2023_Slot2-27_230823_TIMS02_LiMa_400ng_B15.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/timsTOF2_4449_8-31-2023_Slot2-30_230823_TIMS02_LiMa_400ng_A25.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/timsTOF2_4446_8-31-2023_Slot2-28_230823_TIMS02_LiMa_400ng_C15.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/timsTOF2_4450_8-31-2023_Slot2-31_230823_TIMS02_LiMa_400ng_B25.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/timsTOF2_4444_8-31-2023_Slot2-26_230823_TIMS02_LiMa_400ng_A15.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/timsTOF2_4452_8-31-2023_Slot2-33_230823_TIMS02_LiMa_400ng_D25.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD060508/Maxquant_output.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["ak.jayavelu@kitz-heidelberg.de"],"submitter":["Lianghao Mao"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"disease":["Acute Leukemia"],"software":[""],"submitter_keywords":["Cd4+ t-cells","Car-t therapy","Acute leukemia","Antitumor activity"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD060508"],"tissue":["T Cell","Blood"],"sample_protocol":["FACS-sorted CD4+ CART cells from the coculture condition were thoroughly washed in plain PBS, lysed in 1%SDC buffer (1%SDC, 100mM Tris pH8.5, 40mM CAA and 10mM TCEP), incubated on ice for 20 minutes, boiled at 95°C, sonicated for 5 mins on a Biorupter plus as described previously.43 Samples were digested with trypsin and LysC for 16 hours at 37°C. Digestion was stopped by adding 5X volumes of isopropanol/1% TFA and vortexing vigorously. The peptides were de-salted on equilibrated styrene divinylbenzene-reversed phase sulfonated (SDB-RPS) StageTips, washed with isopropanol/1% TFA and 0.2% TFA, and eluted with 60μl of elution buffer (1.25% Ammonia, 80% ACN). The dried elutes were resuspended in MS loading buffer (3% ACN, 0.3% TFA) and stored at -20°C until MS measurement."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["MS raw files were processed using Maxquant （version 1.5.5.2） supported by Andromeda search engine against the UniProt human reference fasta (version 2016). MaxQuant default settings were employed for identification and quantification, allowing a maximum of 2 missed cleavages. The minimal peptide length was set to 7. Label-free quantification (LFQ) was performed using the MaxLFQ algorithm implemented in MaxQuant, with the following settings: a minimal ratio count of 2 and fast LFQ enabled. The peptide and protein FDR was set to 1% to ensure high confidence in the identified peptides and proteins.  The protein group file generated from MaxQuant software was further analyzed in Perseus (version 2.0.7.0). Values were log2 transformed, and data were pre-cleaned by filtering out contaminants, reverse, and only identified by site modifications before statistical analysis. Enrichment analysis and keywords were performed by comparing the protein expressions between groups. Paired sample t-tests and multi-sample t-tests were used to compare between two groups with a permutation-based FDR cutoff of 5%."],"omics_type":["Proteomics"],"labhead":["Dr Ashok kumar Jayavelu"],"instrument_platform":[""],"labhead_affiliation":["Proteomics and Cancer Cell Signaling, DKFZ Heidelberg (lab head)"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["lianghao.mao@hotmail.com"],"publication":["42237537 Chen Q, Sedloev D, Yao H, Mao L, Depke D, Wang L, Scheller M, He B, Liu Y, Unglaub JM, Schmitt A, Jayavelu AK, Müller-Tidow C, Schmitt M, Sauer T. Depletion of CD8&lt;sup&gt;+&lt;/sup&gt; CART cells leads to superior anti-tumor efficacy of pure CD4&lt;sup&gt;+&lt;/sup&gt; CART cells against acute leukemias. Mol Ther. 2026 34(8):4687-4707 10.1016/j.ymthe.2026.05.027"],"submitter_affiliation":["German Cancer Research Center"],"submitter_country":["Germany"],"pubmed_abstract":["Chimeric antigen receptor T (CART) cell therapy has demonstrated clinical efficacy in hematologic malignancies; however, primary or secondary treatment failure remains a major obstacle to durable responses. Defining the optimal cellular composition of CART products therefore represents a critical unmet need. Here, we show that CARTs targeting acute leukemias achieve maximal efficacy when composed exclusively of CD4<sup>+</sup> T cells. Pure CD4<sup>+</sup> CARTs exhibit superior anti-tumor activity and proliferation compared with CD8<sup>+</sup>-containing CART products. To elucidate the molecular basis of this functional divergence, we applied a combinatorial exploratory approach integrating bulk RNA sequencing and quantitative proteomics. Transcriptomic analyses revealed that pure CD4<sup>+</sup> CARTs adopt a highly proliferative state characterized by a cytotoxic effector-like polarization. On the protein level, we are demonstrating coordinated loss of cell-cycle machinery and induction of apoptotic pathways in CD4<sup>+</sup> CART cells co-cultured together with CD8<sup>+</sup> CART cells, while pure CD4<sup>+</sup> CART cultures maintained a proliferative, cytotoxic phenotype. Using mechanistically discriminative co-culture systems, we demonstrate that CD8<sup>+</sup> CART-mediated impairment of CD4<sup>+</sup> CART functionality is primarily driven by competitive access to shared antigen. Collectively, these findings identify antigen competition between CART subsets as a previously unrecognized mechanism limiting CD4<sup>+</sup> CART efficacy and provide a framework for optimizing CART product composition to enhance therapeutic persistence and durability."],"pubmed_title":["Depletion of CD8&lt;sup&gt;+&lt;/sup&gt; CART cells leads to superior anti-tumor efficacy of pure CD4&lt;sup&gt;+&lt;/sup&gt; CART cells against acute leukemias."],"pubmed_authors":["Chen Qian Q, Sedloev David D, Yao Hao H, Mao Lianghao L, Depke Dominic D, Wang Lei L, Scheller Marina M, He Bailin B, Liu Yi Y, Unglaub Julia M JM, Schmitt Anita A, Jayavelu Ashok Kumar AK, Müller-Tidow Carsten C, Schmitt Michael M, Sauer Tim T"],"additional_accession":[]},"is_claimable":false,"name":"Superior Anti-tumor Efficacy of CD4+ CAR-T Cells against Acute Leukemias","description":"While chimeric antigen receptor T-cell (CART) therapy has shown impressive therapeutic efficacy in several hematologic malignancies, primary or secondary treatment failure remains a significant challenge driving investigators to explore opportunities to improve the functionality of CART products. In this context, we aimed to explore the optimal compostion of CARTs targeting acute leukemias with respect to the content of CD4+ and CD8+ T-cells. Our analysis demonstrated superior antitumor activity and proliferative capacity both in vitro and in vivo for pure CD4+ CARTs compared to products containing CD8+ CARTs. Despite the enhanced proliferation, our murine xenograft models did not suggest an increased risk of toxicity associated with pure CD4+ CART products. Mechanistically, the secretome of CD4+ CARTs, that contained higher levels of Th1 and Th2 cytokines, was more potent in stimulating the anti-leukemic activity of CARTs. Furthermore, the presence of CD4+ CARTs induced stronger proliferation of CD8+ CARTs leading to a decreasing CD4/CD8 ratio within in the products over time. However, we found that the physical interaction between CD4+ and CD8+ CARTs impaired the functionality of CD4+ CARTs through induction of apoptosis. Taken together, the results of our study highlight the potential of pure CD4+ CARTs to enhance the efficacy and persistence of CART products against hematologic malignancies and warrant further testing within early phase clinical 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