 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 17, 2023 |
| Title |
The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation [Ago2 HITS-CLIP] |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, many intracellular bacteria and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a novel non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 also play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and T cell memory. Comparative Argonaute-2 high throughput sequencing of crosslinking immunoprecipitation (Ago2 HITS-CLIP, or AHC) combined with gene expression profiling in normal and miR-15/16-deficient T cells revealed a large network of several hundred direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, the long non-coding RNA Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak in T cells. This binding site was also among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16 binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of IL-2 and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long noncoding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.
|
| |
|
| Overall design |
Comparative Ago2 HITS-CLIP (High Throughput Sequencing following Crosslinking Immuno-Precipitation) was performed on Ago2 HITS-CLIP data from primary mouse CD8+ T cells isolated from the spleens of naive mice. T cells were stimulated for 72 hours with anti-CD3 and anti-CD28 antibodies followed by 2 days resting in IL-2 supplemented media. Cells from mice lacking the miR-15/16 binding site in Malat1, Malat1scr/scr; Bl6/J WT; and mir-15/16 deleted by CD4-cre, miR-15/16Δ/Δ were used.
|
| |
|
| Contributor(s) |
Wheeler BD, Ansel KM, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Simeonov D, Li Z, Marson A, Spitzer M, Wong SK, Debarge R |
| Citation(s) |
36993421, 38127070 |
| |
| Submission date |
Oct 25, 2022 |
| Last update date |
Jan 02, 2024 |
| Contact name |
Karl Mark Ansel |
| E-mail(s) |
mark.ansel@ucsf.edu
|
| Organization name |
University of California, San Francisco
|
| Department |
Microbiology
|
| Street address |
500 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94122 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (12)
|
| GSM6679263 |
CD8 T cells, miR-15/16 KO, ID 2-2 |
| GSM6679264 |
CD8 T cells, Malat1-scr, ID 1-1 |
| GSM6679265 |
CD8 T cells, Malat1-scr, ID 1-2 |
| GSM6679266 |
CD8 T cells, Malat1-scr, ID 2-1 |
| GSM6679267 |
CD8 T cells, Malat1-scr, ID 2-2 |
| GSM6679268 |
CD8 T cells, WT, ID 1-1 |
| GSM6679269 |
CD8 T cells, WT, ID 1-2 |
| GSM6679270 |
CD8 T cells, WT, ID 2-1 |
| GSM6679271 |
CD8 T cells, WT, ID 2-2 |
|
| Relations |
| BioProject |
PRJNA894227 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE216565_TargetScan_sums_Ansel_Wheeler.csv.gz |
4.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...