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2830 A Non-Canonical Lymphoblast in Refractory Childhood T-Cell Acute Lymphoblastic Leukemia

Program: Oral and Poster Abstracts
Session: 614. Acute Lymphoblastic Leukemias: Biomarkers, Molecular Markers, and Minimal Residual Disease in Diagnosis and Prognosis: Poster II
Hematology Disease Topics & Pathways:
Research, Fundamental Science, Lymphoid Leukemias, ALL, Translational Research, Genomics, Bioinformatics, Pediatric, Diseases, Lymphoid Malignancies, Computational biology, Biological Processes, Technology and Procedures, Study Population, Human, Measurable Residual Disease , Omics technologies
Sunday, December 8, 2024, 6:00 PM-8:00 PM

Bram S.J. Lim1*, Holly J. Whitfield1*, Mi K. Trinh1*, Gianna Bloye2*, Rebecca Thomas3*, Nathaniel D. Anderson1*, Anna Wenger1*, Angus Hodder, MBBS3,4*, Taryn D. Treger1,5,6*, Henry Lee-Six1,5*, Tim H.H. Coorens, PhD7*, Conor Parks1*, Toochi Ogbonnah1*, Petri Pölönen, PhD8, Charles G. Mullighan, MBBS, MSc, MD8, David T. Teachey, MD9, Melanie M Hagleitner, MD10*, Lennart A. Kester, PhD10*, Frank N. van Leeuwen, PhD11, Gordon Beattie2*, Marc R. Mansour, MD, PhD, FRCPath2,12*, Owen Williams12*, Jack Bartram3*, Stuart Adams3*, Laura Jardine13*, Sam Behjati, BMBCh, PhD1,5,6* and David O'Connor, MD2,3,12*

1Wellcome Sanger Institute, Hinxton, United Kingdom
2UCL Cancer Institute, London, United Kingdom
3Great Ormond Street Hospital for Children, London, United Kingdom
4Wellcome Sanger Institute, London, United Kingdom
5Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
6Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
7Broad Institute of MIT and Harvard, Cambridge, MA
8Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
9Children's Hospital of Philadelphia, Philadelphia, PA
10Princess Maxima Center for pediatric oncology, Utrecht, Netherlands
11Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
12UCL Great Ormond Street Institute of Child Health, London, United Kingdom
13Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom

Childhood T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy which carries a worse clinical prognosis than its B-cell counterpart (B-ALL). Despite extensive genomic characterization, no robust genetic or phenotypic marker has been identified for accurate clinical risk stratification of T-ALL at the point of diagnosis, unlike in B-ALL. Instead, the earliest reliable indicator of high-risk disease is failure to respond to four weeks of induction chemotherapy (minimal residual disease ≥5%), limiting the potential for early intervention. Children with induction failure (i.e. refractory disease) make up 10% of childhood T-ALL cases and constitute a very high-risk group, with only half surviving beyond 5 years.

Here, we studied the transcriptional and phylogenetic profiles of refractory T-ALL. We collected diagnostic bone marrow aspirates from 21 children with T-ALL, including 8 who responded to induction and 13 who were refractory. Crucially, for 8 of the children with induction failure, we collected post-induction bone marrows, allowing analysis of the true refractory blast population. We applied high-throughput single-cell mRNA sequencing to all samples and identified a distinct blast population that was consistently associated with induction failure cases and almost entirely absent in responsive cases. Expression analysis identified a common gene set enriched in this population, spearheaded by the ZBTB16 gene, a transcription factor key to lymphocyte differentiation. Presence of ZBTB16+ blasts at diagnosis heralded refractory disease across independent bulk transcriptome datasets and was associated with survival in the largest reported T-ALL cohort of ~1,300 individuals from the Children’s Oncology Group AALL0434 trial. Additionally, we confirmed the ability to detect the ZBTB16 protein using intracellular flow cytometry, demonstrating its potential utility as a biomarker of high-risk disease.

Previous studies have associated refractory T-ALL with particular T-cell differentiation states, including the early T-cell precursor (ETP). We found that the non-canonical ZBTB16+ blasts have a distinct profile which broadly resembles innate-like lymphocytes such as innate lymphoid cells and natural killer cells as well as unconventional T cells, in strong contrast to responsive T-ALL blasts which resemble conventional T cells and their developing stages. ZBTB16+ blasts exhibited varied T-cell receptor rearrangement status, suggesting that they can arise from maturation block at multiple stages across T-cell development, as opposed to a single fixed point. Moreover, the detection of ZBTB16+ blasts in bulk transcriptomes was able to risk stratify children with T-ALL more reliably than ETP status determined by immunophenotyping or transcriptome profiling.

Refractory cancers may arise either through the acquisition of resistance mechanisms by cancer cells or represent a distinct entity that is intrinsically resistant. In the majority of cases, ZBTB16+ blasts were clearly seen at both diagnostic and post-induction timepoints. However, for one individual, by projecting somatic mutations onto single-cell transcriptomes, we showed that ZBTB16+ blasts were detectable at diagnosis as a minor subclone (~1% of blasts), but expanded dramatically during induction to become the dominant clone, thereby affirming that ZBTB16+ blasts are intrinsically resistant lymphoblasts that are already present at diagnosis.

Overall, our study presents refractory T-ALL as a distinct leukemia that is associated with a previously unknown lymphoblast variant. We believe the presence of ZBTB16+ blasts has the potential to be a powerful clinical predictor at diagnosis of high-risk T-ALL. We therefore suggest that our findings warrant urgent investigation in prospective clinical cohorts.

Disclosures: Teachey: Jazz: Membership on an entity's Board of Directors or advisory committees; NeoImmune Tech: Research Funding; BEAM Therapeutics: Research Funding.

*signifies non-member of ASH