Leukemia-intrinsic determinants of CAR-T response revealed by iterative in vivo genome-wide CRISPR screening

Azucena Ramos; Catherine E Koch; Yunpeng Liu-Lupo; Riley D Hellinger; Taeyoon Kyung; Keene L Abbott; Julia Fröse; Daniel Goulet; Khloe S Gordon; Keith P Eidell; Paul Leclerc; Charles A Whittaker; Rebecca C Larson; Audrey J Muscato; Kathleen B Yates; Juan Dubrot; John G Doench; Aviv Regev; Matthew G Vander Heiden; Marcela V Maus; Robert T Manguso; Michael E Birnbaum; Michael T Hemann

doi:10.1038/s41467-023-43790-2

Leukemia-intrinsic determinants of CAR-T response revealed by iterative in vivo genome-wide CRISPR screening

Nat Commun. 2023 Dec 5;14(1):8048. doi: 10.1038/s41467-023-43790-2.

Authors

Azucena Ramos^#^{1

2}, Catherine E Koch^#^{1

2}, Yunpeng Liu-Lupo^#^{1

2}, Riley D Hellinger¹, Taeyoon Kyung^{1

3}, Keene L Abbott^{1

2}, Julia Fröse¹, Daniel Goulet¹, Khloe S Gordon^{1

3}, Keith P Eidell¹, Paul Leclerc¹, Charles A Whittaker¹, Rebecca C Larson^{4

5}, Audrey J Muscato^{6

7}, Kathleen B Yates^{6

7}, Juan Dubrot^{6

7

8}, John G Doench⁷, Aviv Regev^{2

7

9

10}, Matthew G Vander Heiden^{1

2

11}, Marcela V Maus^{4

5

6

7

12}, Robert T Manguso^{5

6

7}, Michael E Birnbaum^{1

3}, Michael T Hemann^{13

14}

Affiliations

¹ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
² Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
³ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁴ Cellular Immunotherapy Program, Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
⁵ Immunology Program, Harvard Medical School, Boston, MA, USA.
⁶ Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.
⁷ Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, 02142, USA.
⁸ Solid Tumors Program, Division of Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
⁹ Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹⁰ Howard Hughes Medical Institute, Chevy Chase, MD, USA.
¹¹ Dana-Farber Cancer Institute, Boston, MA, USA.
¹² Ragon Institute of MIT, MGH, and Harvard, Cambridge, MA, USA.
¹³ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. hemann@mit.edu.
¹⁴ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. hemann@mit.edu.

^# Contributed equally.

Abstract

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.

MeSH terms

Animals
Burkitt Lymphoma*
Humans
Immunotherapy, Adoptive
Leukemia*
Mice
Precursor B-Cell Lymphoblastic Leukemia-Lymphoma* / genetics
Precursor B-Cell Lymphoblastic Leukemia-Lymphoma* / therapy
RNA, Guide, CRISPR-Cas Systems
Receptors, Chimeric Antigen*
T-Lymphocytes
Tumor Microenvironment

Substances

Receptors, Chimeric Antigen
RNA, Guide, CRISPR-Cas Systems

Abstract

MeSH terms

Substances

Grants and funding