Leukemia-intrinsic determinants of CAR-T response revealed by iterative in vivo genome-wide CRISPR screening.
Azucena RamosCatherine E KochYunpeng Liu-LupoRiley D HellingerTaeyoon KyungKeene L AbbottJulia FröseDaniel GouletKhloe S GordonKeith P EidellPaul LeclercCharles A WhittakerRebecca C LarsonAudrey J MuscatoKathleen B YatesJuan DubrotJohn G DoenchAviv RegevMatthew G Vander HeidenMarcela V MausRobert T MangusoMichael E BirnbaumMichael T HemannPublished in: Nature communications (2023)
CAR-T therapy is a promising, novel treatment modality for B-cell malignancies and yet many patients relapse through a variety of means, including loss of CAR-T cells and antigen escape. To investigate leukemia-intrinsic CAR-T resistance mechanisms, we performed genome-wide CRISPR-Cas9 loss-of-function screens in an immunocompetent murine model of B-cell acute lymphoblastic leukemia (B-ALL) utilizing a modular guide RNA library. We identified IFNγR/JAK/STAT signaling and components of antigen processing and presentation pathway as key mediators of resistance to CAR-T therapy in vivo; intriguingly, loss of this pathway yielded the opposite effect in vitro (sensitized leukemia to CAR-T cells). Transcriptional characterization of this model demonstrated upregulation of these pathways in tumors relapsed after CAR-T treatment, and functional studies showed a surprising role for natural killer (NK) cells in engaging this resistance program. Finally, examination of data from B-ALL patients treated with CAR-T revealed an association between poor outcomes and increased expression of JAK/STAT and MHC-I in leukemia cells. Overall, our data identify an unexpected mechanism of resistance to CAR-T therapy in which tumor cell interaction with the in vivo tumor microenvironment, including NK cells, induces expression of an adaptive, therapy-induced, T-cell resistance program in tumor cells.
Keyphrases
- genome wide
- nk cells
- acute myeloid leukemia
- acute lymphoblastic leukemia
- crispr cas
- poor prognosis
- bone marrow
- dna methylation
- induced apoptosis
- genome editing
- electronic health record
- end stage renal disease
- cell therapy
- multiple myeloma
- big data
- transcription factor
- type diabetes
- gene expression
- copy number
- single cell
- chronic kidney disease
- computed tomography
- immune response
- weight loss
- ejection fraction
- metabolic syndrome
- allogeneic hematopoietic stem cell transplantation
- mesenchymal stem cells
- cell death
- combination therapy
- artificial intelligence
- high throughput
- skeletal muscle
- drug induced
- diabetic rats
- insulin resistance
- oxidative stress
- image quality
- high glucose
- smoking cessation
- pi k akt
- free survival