Abstract TP53-mutated (TP53m) Acute myeloid leukemia (AML) represents a clinically intractable and biologically distinct disease. To study the molecular basis of this disease through hemopoiesis, we integrated single-cell RNA-seq (10x and long-read Oxford Nanopore sequencing) with open chromatin profiles (scATAC-seq), whole-genome (WGS) to capture structural variants and copy number alterations, and deep panel DNA sequencing from bone marrow samples taken from a cohort of 49 TP53m AML patients, 7 TP53 wild type (WT) AML patients, and 4 healthy donors. Phased genotyping plus WGS revealed biallelic loss to be associated with intrachromosomal breakage, whereas monoallelic loss favored numerical chromosomal alterations. TP53m clones pervaded stem/progenitors and myeloerythroid lineages but were proportionally depleted in mature lymphocytes. While co-occurring AML driver mutations influence the lineage biases of TP53m clones, we observed expansion of HSC/MPP, LMPP, and late erythroid compartments. In HSC/MPP dominant disease, TP53m cells displayed suppression of translational and mitochondrial-respiratory programs, with enrichment of a “p53-LSC” signature linked to chronic inflammatory stress. This suggests adaptation through metabolic quiescence, conferring persistence under inflammatory pressure. In LMPP-dominant expansion, we observed enriched MYC/E2F targets. Transcriptomic neighborhood analysis with pseudotime showed the erythroid compartment to be heterogeneous, with less mature basophilic cells enriched for TP53m clones, whereas more mature orthochromatic cells were enriched for TP53wt clones, nominating this transition as a tipping point for differentiation delay/arrest. Consistently, in erythroid dominant patients, late-stage erythroid cells demonstrated impaired GATA-1 and KLF1 (erythroid TFs) activities, and TP53m clones showed heightened GATA2, SPI1, and CEBPD regulon activity. TP53m versus TP53wt clones in erythroid differentiation showed heightened transcriptional activity of the EIF2AK1(HRI)→eIF2α mediated integrated stress response (ISR). Differential expression analysis within the aforementioned erythroid compartment showed ISR activation in TP53m clones; SESN2, DDIT4, and DDIT3/CHOP significantly up, with ATF3, and XBP1, up-trending, together with increased GATA2. Replication/mitochondrial-handling components (GINS2, RPA3, ABCB8) were significantly downregulated. These data together support a model in which deficient GATA-1/KLF1 function underpins the intra erythroid arrest of TP53m clones possibly due to activated HRI-ISR circuitry. These detailed molecular differentiation stage specific analyses of TP53m AML provide mechanistic insights and a platform for functional and synthetic lethal studies to specifically target TP53m leukemic cells. Citation Format: Felix A. Radtke, Bijay S. Jaiswal, Gonzalo Lopez, Junfei Zhao, Sagnik Banerjee, Daiane Hemerich Brennan, Yilin Zhao, Verena Körber, Marlen Metzner, Rachel Moore, Bilyana Stoilova, Batchimeg Usukhbayar, David Cruz Hernandez, Maria Ortiz Estevez, Aimee O’Donohue, Daniel Lopes de Menezes, Rajasekhar NVS Suragani, Anita K. Gandhi, Paresh Vyas. Dependent lineage regulatory programs in TP53-mutated acute myeloid leukemia revealed through deep single-cell multi-omic profiling of patient samples abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7500.
Radtke et al. (Fri,) studied this question.