Figure 1.

Venetoclax-based therapies drive selection of novel BAX variants in relapsed AML. (A) Patients with either primary refractory or relapsed AML divided according to whether venetoclax (VEN) was combined with lower intensity (hypomethylating agent or low-dose cytarabine [LDAC]) or high intensity (infusional cytarabine + idarubicin) chemotherapy. The venetoclax dose used is indicated, along with the FLT3 and TP53 mutation status and BM blast percentage at the time of treatment failure. The time spent in remission (months) is shown as a green bar. Treatment failure is shown as a pink-colored bar cap. Patients refractory to therapy spent no time in remission. No BAX variants were identified among patients with primary refractory disease. At relapse, 7 patients (ID number shown) were found to harbor ≥1 BAX variant (red star within pink cap) and the dominant predicted BAX protein change is shown. (B) The distribution of BAX variant allele frequencies (yellow circles) at relapse are shown in the venetoclax-resistant cohort (n = 41), along with a control population of patients with AML relapsing after prior intensive chemotherapy (n = 34). The predicted protein change is indicated for BAX variants with variant allele frequencies (VAFs) ≥5%. (C) Schematic overview of BAX variants. Protein domain structure of BAX and identified variants observed in patients treated with venetoclax or standard chemotherapy. The presence of four BCL-2 homology (BH) domains and the transmembrane domain (TM) are indicated along with the location of each of the nine alpha helices. The red bar indicates the position of the hydrophobic groove. Missense variants, frameshift/nonsense variants, and splice site variants are denoted by pink, green, and blue circles, respectively. (D-G) Fishplot representation of selected patients with BAX variants (also refer to supplemental Figure 1). Clonal architecture presented in fishplot format was inferred from bulk sequencing showing clonal dynamics of leukemic or preleukemic clones in serial samples from 4 venetoclax-treated patients with detected BAX mutations. The dominant BAX subpopulation is shown in red in each case. (D-E) BAX variants emerging with leukemic relapse. (F) A BAX mutation emerges in remission, suggesting presence in an expanded preleukemic population after suppression of the original diagnostic AML clone. (G) BAX mutation is present at diagnosis and persists in remission after venetoclax-based therapy, despite suppression of several AML-related mutations. Duration of therapy is denoted by the gray arrow, clinical status including first complete remission (CR1), CR2, or measurable residual disease (MRD). Available cytogenetic, BM blast information, and time elapsed to remission and relapse are indicated below each fishplot. ∗indicates time points verified by single-cell DNA sequencing. Freq, frequency.