Fig. 1: ZBTB16 defines refractory blasts in T-ALL.

A Schematic illustrating the clinical course of T-ALL and overview of study design. Created in BioRender. Behjati, S. (2025) https://www.biorender.com/4eu223k. B Heatmap indicating data generated for each patient and clinical information (ETP status, induction outcome, genomic subtype). C UMAP (uniform manifold approximation and projection) of 216,507 cells, including 160,327 leukaemia blasts (coloured) and 56,180 normal cells (grey). Day 0 blasts from patients who responded to induction treatment (blue); day 0 blasts from patients with induction failure (orange); day 28 refractory blasts from patients with induction failure (red). Circles and arrows highlight that day 28 blasts from patients P030 and P058 clustered separately from their respective day 0 blasts on the UMAP. D Analytical schematic. Overlapping the top 100 upregulated genes of the day 28 blasts from the two patients (P030 and P058) yielded eight genes, of which ZBTB16 had the highest log-fold increase. E UMAP showing the expression of ZBTB16 in day 0 and day 28 blasts from P058. ZBTB16 expression is largely absent in day 0 blasts, apart from a small cluster (65/9668 blasts) indicated by an arrowhead, whereas most day 28 blasts expressed ZBTB16 (692/709 blasts). F ZBTB16 expression in blasts across 29 samples from 21 children with T-ALL. Samples comprise diagnostic day 0 blasts from responsive cases (8 children), diagnostic day 0 blasts from induction failure cases (13 children) and refractory day 28 blasts from induction failure cases (8 children). Top: Median ZBTB16 expression of each cluster of blasts within each sample; size of circle indicates cluster size; arrowhead indicates a small cluster of day 0 blasts from P058 expressing ZBTB16. Middle: Box plots and swarm plots of ZBTB16 expression at single-cell resolution. Box plots show the first and third quartiles (boxes), as well as median values (central lines). Whiskers extend to the most extreme values within 1.5 times the interquartile range above and below the boxes. Bottom: Fraction of blasts expressing ZBTB16. G ZBTB16 expression in blasts from induction failure patients with paired day 0 (orange) and day 28 samples (red). Left: Fraction of blasts expressing ZBTB16. Right: Median ZBTB16 expression in ZBTB16+ blasts. H Flow cytometry measurement of ZBTB16 in blasts from diagnostic samples of responsive patient P108 and induction failure patient P018. MRD minimal residual disease, scRNA-seq single cell mRNA sequencing, scTCR-seq single cell T-cell receptor sequencing, WGS whole genome sequencing, ETP early T-cell precursor, NK natural killer cell. Source data are provided as a Source Data file.