RASA2 deletion rescues immune synapse dysfunction, enhancing CAR T cell efficacy against DMGs
Methods: We compared the efficacy of B7-H3 CAR T-cells between SJ-DIPGX7c (DMG) and U87-MG (adult glioblastoma) patient-derived cell lines and showed impaired efficacy both in vitro and in vivo. We performed live-cell imaging and single-cell RNA sequencing to investigate deficiencies in immune synapse (IS) formation between CAR T-cells and DMGs. Lastly, we genetically deleted RASA2, a negative regulator of T cell activation, and evaluated the resulting impact on IS formation and quality, as well as in vitro and in vivo functionality. Sample preparation and sequencing For single cell RNA sequencing, two sets of co-culture arrays were prepared: (1) 2.5×106 Ctrl T cells were co-cultured with 2.5×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG) and (2) 1×106 CAR T-cells were co-cultured with 4×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG). Both co-culture arrays were incubated at 37°C 5% CO2 for 16 hours. Co-cultures were enzymatically digested with Accutase (Thermofisher; A1110501) for 10 min at room temperature, and cells were filtered by using Miltenyi dead cell removal kit (Miltenyi; 130-090-101). Highly viable cells were recovered and prepared using the Fixation Kit (PARSE Bioscience) according to manufacturer ‘s protocol. After fixation, the cell count was determined by using a Neubauer hemocytometer. A total of 1.14×105 cells from 12 coculture conditions were used, resulting in approximately 9.5×104 cells per condition. These cells were subjected to the Single Cell Whole Transcriptomic kit v2 (PARSE Bioscience) for library construction. Libraries were subsequently sequenced using the Illumina NovaSeq 6000 platform, generating paired-end 200 bp reads.
- 03/07/2026
- 2 samples
- DAC: EGAC50000001043
- Technology: Illumina NovaSeq 6000
- Archive: European Genome-phenome Archive (EGA)
RASA2 deletion rescues immune synapse dysfunction, enhancing CAR T cell efficacy against DMGs
This policy is affiliated to the open access datasets archived at the EGA. Datasets are not subject to controlled access and, as a result, may be distributed without the requirement of a data access application.
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS50000001918 | RNASeq |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Quality Report |
Located in
i
|
|---|---|---|---|---|
| EGAF50000910626 | fastq.gz | 12.2 GB |
|
|
| EGAF50000910627 | fastq.gz | 7.9 GB |
|
|
| EGAF50000910628 | fastq.gz | 12.0 GB |
|
|
| EGAF50000910629 | fastq.gz | 12.3 GB |
|
|
| EGAF50000910630 | xlsm | 925.5 kB |
|
|
| EGAF50000910631 | xlsm | 920.1 kB |
|
|
| EGAF50000910632 | fastq.gz | 8.9 GB |
|
|
| EGAF50000910633 | fastq.gz | 15.5 GB |
|
|
| EGAF50000910634 | fastq.gz | 2.2 GB |
|
|
| EGAF50000910635 | fastq.gz | 1.7 GB |
|
|
| EGAF50000910636 | fastq.gz | 15.8 GB |
|
|
| EGAF50000910637 | fastq.gz | 1.7 GB |
|
|
| EGAF50000910638 | fastq.gz | 2.1 GB |
|
|
| EGAF50000910639 | fastq.gz | 15.5 GB |
|
|
| EGAF50000910640 | fastq.gz | 15.7 GB |
|
|
| EGAF50000910641 | fastq.gz | 15.5 GB |
|
|
| EGAF50000910642 | fastq.gz | 15.6 GB |
|
|
| EGAF50000910643 | fastq.gz | 1.7 GB |
|
|
| EGAF50000910644 | fastq.gz | 1.5 GB |
|
|
| EGAF50000910645 | fastq.gz | 12.0 GB |
|
|
| EGAF50000910646 | fastq.gz | 12.3 GB |
|
|
| EGAF50000910647 | fastq.gz | 1.7 GB |
|
|
| EGAF50000910648 | fastq.gz | 1.5 GB |
|
|
| EGAF50000910649 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910650 | fastq.gz | 998.9 MB |
|
|
| EGAF50000910651 | fastq.gz | 8.7 GB |
|
|
| EGAF50000910652 | fastq.gz | 8.8 GB |
|
|
| EGAF50000910653 | fastq.gz | 1.4 GB |
|
|
| EGAF50000910654 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910655 | fastq.gz | 8.7 GB |
|
|
| EGAF50000910656 | fastq.gz | 8.9 GB |
|
|
| EGAF50000910657 | fastq.gz | 1.5 GB |
|
|
| EGAF50000910658 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910659 | fastq.gz | 10.2 GB |
|
|
| EGAF50000910660 | fastq.gz | 1.4 GB |
|
|
| EGAF50000910661 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910662 | fastq.gz | 10.0 GB |
|
|
| EGAF50000910663 | fastq.gz | 10.3 GB |
|
|
| EGAF50000910664 | fastq.gz | 903.6 MB |
|
|
| EGAF50000910665 | fastq.gz | 904.2 MB |
|
|
| EGAF50000910666 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910667 | fastq.gz | 7.6 GB |
|
|
| EGAF50000910668 | fastq.gz | 9.6 GB |
|
|
| EGAF50000910669 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910670 | fastq.gz | 9.5 GB |
|
|
| EGAF50000910671 | fastq.gz | 9.6 GB |
|
|
| EGAF50000910672 | fastq.gz | 1.7 GB |
|
|
| EGAF50000910673 | fastq.gz | 2.1 GB |
|
|
| EGAF50000910674 | fastq.gz | 1.8 GB |
|
|
| EGAF50000910675 | fastq.gz | 1.5 GB |
|
|
| EGAF50000910676 | fastq.gz | 11.9 GB |
|
|
| EGAF50000910677 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910678 | fastq.gz | 984.9 MB |
|
|
| EGAF50000910679 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910680 | fastq.gz | 985.1 MB |
|
|
| EGAF50000910681 | fastq.gz | 8.7 GB |
|
|
| EGAF50000910682 | fastq.gz | 9.9 GB |
|
|
| EGAF50000910683 | fastq.gz | 10.2 GB |
|
|
| EGAF50000910684 | fastq.gz | 1.3 GB |
|
|
| EGAF50000910685 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910686 | fastq.gz | 10.0 GB |
|
|
| EGAF50000910687 | fastq.gz | 10.7 GB |
|
|
| EGAF50000910688 | fastq.gz | 10.9 GB |
|
|
| EGAF50000910689 | fastq.gz | 1.3 GB |
|
|
| EGAF50000910690 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910691 | fastq.gz | 10.8 GB |
|
|
| EGAF50000910692 | fastq.gz | 1.4 GB |
|
|
| EGAF50000910693 | fastq.gz | 10.6 GB |
|
|
| EGAF50000910694 | fastq.gz | 1.3 GB |
|
|
| EGAF50000910695 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910696 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910697 | fastq.gz | 10.7 GB |
|
|
| EGAF50000910698 | fastq.gz | 10.8 GB |
|
|
| EGAF50000910699 | fastq.gz | 8.0 GB |
|
|
| EGAF50000910700 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910701 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910702 | fastq.gz | 8.1 GB |
|
|
| EGAF50000910703 | fastq.gz | 8.0 GB |
|
|
| EGAF50000910704 | fastq.gz | 8.1 GB |
|
|
| EGAF50000910705 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910706 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910707 | fastq.gz | 8.0 GB |
|
|
| EGAF50000910708 | fastq.gz | 8.1 GB |
|
|
| EGAF50000910709 | fastq.gz | 925.7 MB |
|
|
| EGAF50000910710 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910711 | fastq.gz | 961.7 MB |
|
|
| EGAF50000910712 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910713 | fastq.gz | 7.9 GB |
|
|
| EGAF50000910714 | fastq.gz | 7.9 GB |
|
|
| EGAF50000910715 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910716 | fastq.gz | 1.0 GB |
|
|
| EGAF50000910717 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910718 | fastq.gz | 7.9 GB |
|
|
| EGAF50000910719 | fastq.gz | 7.9 GB |
|
|
| EGAF50000910720 | fastq.gz | 7.9 GB |
|
|
| EGAF50000910721 | fastq.gz | 893.8 MB |
|
|
| EGAF50000910722 | fastq.gz | 7.6 GB |
|
|
| EGAF50000910723 | fastq.gz | 7.6 GB |
|
|
| EGAF50000910724 | fastq.gz | 1.1 GB |
|
|
| EGAF50000910725 | fastq.gz | 889.8 MB |
|
|
| EGAF50000910726 | fastq.gz | 7.6 GB |
|
|
| EGAF50000910727 | fastq.gz | 7.6 GB |
|
|
| EGAF50000910728 | fastq.gz | 1.0 GB |
|
|
| EGAF50000910729 | fastq.gz | 7.4 GB |
|
|
| EGAF50000910730 | fastq.gz | 7.6 GB |
|
|
| EGAF50000910731 | fastq.gz | 944.9 MB |
|
|
| EGAF50000910732 | fastq.gz | 7.5 GB |
|
|
| EGAF50000910733 | fastq.gz | 1.0 GB |
|
|
| EGAF50000910734 | fastq.gz | 7.5 GB |
|
|
| EGAF50000910735 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910736 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910737 | fastq.gz | 9.5 GB |
|
|
| EGAF50000910738 | fastq.gz | 9.7 GB |
|
|
| EGAF50000910739 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910740 | fastq.gz | 1.2 GB |
|
|
| EGAF50000910741 | fastq.gz | 988.6 MB |
|
|
| EGAF50000910742 | fastq.gz | 1.0 GB |
|
|
| EGAF50000910743 | fastq.gz | 7.3 GB |
|
|
| EGAF50000910744 | fastq.gz | 7.4 GB |
|
|
| EGAF50000910745 | fastq.gz | 7.4 GB |
|
|
| EGAF50000910746 | fastq.gz | 9.5 GB |
|
|
| EGAF50000910747 | fastq.gz | 1.3 GB |
|
|
| 122 Files (662.5 GB) | ||||