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

• Published in: Blood 2024-11, Vol.144 (Supplement 1), p.2830-2830
• Main Authors: Lim, Bram S.J., Whitfield, Holly J., Trinh, Mi K., Bloye, Gianna, Thomas, Rebecca, Anderson, Nathaniel D., Wenger, Anna, Hodder, Angus, Treger, Taryn D., Lee-Six, Henry, Coorens, Tim H.H., Parks, Conor, Ogbonnah, Toochi, Pölönen, Petri, Mullighan, Charles G., Teachey, David T., Hagleitner, Melanie M, Kester, Lennart A., van Leeuwen, Frank N., Beattie, Gordon, Mansour, Marc R., Williams, Owen, Bartram, Jack, Adams, Stuart, Jardine, Laura, Behjati, Sam, O'Connor, David
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2024-198354

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 ca