PURPOSE Gamma delta T-cell receptor-positive acute lymphoblastic leukemia (γδ T-ALL) is a high-risk but poorly characterized disease.

METHODS We studied clinical features of 200 pediatric γδ T-ALL, and compared the prognosis of 93 cases to 1,067 protocol-matched non-γδ T-ALL. Genomic features were defined by transcriptome and genome sequencing. Experimental modeling was used to examine the mechanistic impacts of genomic alterations. Therapeutic vulnerabilities were identified by high throughput drug screening of cell lines and xenografts.

RESULTS γδ T-ALL in children under three was extremely high-risk with 5-year event-free survival (33% v. 70% [age 3-<10] and 73% [age ≥10], P=9.5 x 10-5) and 5-year overall survival (49% v. 78% [age 3-<10] and 81% [age ≥10], P=0.002), differences not observed in non-γδ T-ALL. γδ T-ALL in this age group was enriched for genomic alterations activating LMO2 activation and inactivating STAG2 inactivation (STAG2/LMO2). Mechanistically, we show that inactivation of STAG2 profoundly perturbs chromatin organization by altering enhancer-promoter looping resulting in deregulation of gene expression associated with T-cell differentiation. Drug screening showed resistance to prednisolone, consistent with clinical slow treatment response, but identified a vulnerability in DNA repair pathways arising from STAG2 inactivation, which was efficaciously targeted by Poly(ADP-ribose) polymerase (PARP) inhibition, with synergism with HDAC inhibitors. Ex-vivo drug screening on PDX cells validated the efficacy of PARP inhibitors as well as other potential targets including nelarabine.

CONCLUSION γδ T-ALL in children under the age of three is extremely high-risk and enriched for STAG2/LMO2 ALL. STAG2 loss perturbs chromatin conformation and differentiation, and STAG2/LMO2 ALL is sensitive to PARP inhibition. These data provide a diagnostic and therapeutic framework for pediatric γδ T-ALL.

SUPPORT The authors are supported by the American and Lebanese Syrian Associated Charities of St Jude Children’s Research Hospital, NCI grants R35 CA197695, P50 CA021765 (C.G.M.), the Henry Schueler 41&9 Foundation (C.G.M.), and a St. Baldrick’s Foundation Robert J. Arceci Innovation Award (C.G.M.), Gabriella Miller Kids First X01HD100702 (D.T.T and C.G.M.) and R03CA256550 (D.T.T. and C.G.M.), F32 5F32CA254140 (L.M.), and a Garwood Postdoctoral Fellowship of the Hematological Malignancies Program of the St Jude Children’s Research Hospital Comprehensive Cancer Center (S.K.). This project was supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: U10CA180820, UG1CA189859, U24CA114766, U10CA180899, U10CA180866 and U24CA196173.

DISCLAIMER The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funding agencies were not directly involved in the design of the study, gathering, analysis and interpretation of the data, writing of the manuscript, or decision to submit the manuscript for publication.

D.T.T. received research funding from BEAM Therapeutics, NeoImmune Tech and serves on advisory boards for BEAM Therapeutics, Janssen, Servier, Sobi, and Jazz. D.T.T. has multiple patents pending on CAR-T. I.I. received honoraria from Amgen and Mission Bio. M.Kicinski received research funding from MSD, BMS, Pierre Fabre, JnJ, and Immunocore. C.G.M. received research funding from Loxo Oncology, Pfizer, AbbVie; honoraria from Amgen and Illumina, and holds stock in Amgen. There are no conflicts of interest with the work presented in this manuscript.

The authors are supported by the American and Lebanese Syrian Associated Charities of St Jude Children's Research Hospital, NCI grants R35 CA197695, P50 CA021765 (C.G.M.), the Henry Schueler 41&9 Foundation (C.G.M.), and a St. Baldrick's Foundation Robert J. Arceci Innovation Award (C.G.M.), Gabriella Miller Kids First X01HD100702 (D.T.T and C.G.M.) and R03CA256550 (D.T.T. and C.G.M.), F32 5F32CA254140 (L.M.), and a Garwood Postdoctoral Fellowship of the Hematological Malignancies Program of the St Jude Children's Research Hospital Comprehensive Cancer Center (S.K.). This project was supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: U10CA180820, UG1CA189859, U24CA114766, U10CA180899, U10CA180866 and U24CA196173.

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

All clinical trials were approved by institutional review boards or ethics committees. This study was ethically approved by the Institutional Review Board of St. Jude Children's Research Hospital.

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Primary sample whole-genome and transcriptome data have been deposited in the European Genome-phenome Archive (EGA) with accession number EGAS50000000018, in the database of genotypes and phenotypes (dbGaP; http://www.ncbi.nlm.nih.gov/gap) under accession number phs002276.v2.p1 (phs000218, phs000464), in the Kids First data portal (https://portal.kidsfirstdrc.org/dashboard), and in the National Bioscience Database Center (NBDC) database with accession number JGAS000090. HiChIP and ChIP-seq data have been deposited at GSE243776. Reference ChIP-seq and HiChIP data used in this study have been deposited at EGAS50000000016 and GSE165209.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243776