Abstract 5938: High-resolution multi-omic dissection of bone marrow in TP53-mutant acute myeloid leukemia

Abstract TP53-mutated (TP53m) AML is a distinct biological entity with adverse prognosis, characterized by prominent clonal heterogeneity; cells within a patient may exhibit wild type, monoallelic, or biallelic TP53 status, alongside co-occurring genomic alterations and transcriptomic heterogeneity. This complexity poses challenges in accurately aligning genotypes with transcriptomic and epigenomic profiles at single-cell resolution. To address this, we integrated single-cell RNA-seq (10x and long-read Oxford Nanopore, ONT) with open chromatin profiles (scATAC-seq) and whole-genome sequencing (WGS) to capture structural variants (SV), copy number alterations (CNV), and single nucleotide variants (SNV) from bone marrow samples taken from a cohort of 47 TP53m, 7 TP53 wild-type (wt) AML patients, and 4 healthy donors.Cell type annotation for scRNA-seq (335K cells) utilized a bone marrow reference dataset, while scATAC-seq (130K cells) was annotated using the ArchR label-transfer method. Cell type proportions were concordant across modalities (median correlation, ρ = 0.76). SV and CNV profiles showed that TP53m samples displayed frequent loss of Chr5q (72.5%), Chr17p (52.5%), and Chr7q (40%); chromothripsis was present in 16 (40%) samples. All these events were reported to occur in under 3% of TP53wt AMLs. In contrast, TP53m samples showed relative paucity of SNV co-mutations.We leveraged CNV profiles to map genetic gain/loss effect in scRNA and scATAC-seq compared to healthy donors, providing a clear separation of cells with abnormal CNV profiles. In TP53m AML, apart from mature lymphoid populations, 80% of cells including lymphoid progenitors (LMPP), displayed abnormal CNV status. Abnormal CNV cell fractions by sample strongly correlated with orthogonal tumor purity estimations from WGS for scRNA (ρ = 0.81) and ATAC-seq (ρ = 0.84).Single-cell SNV mapping was attempted with the standard 10x pipeline, where we detected driver hotspot mutations in only ∼3% of non-lymphoid cells. To improve mutation calling, we developed a new SNV pipeline using long-read ONT chemistry on full-length cDNA. SNV calling rates rose to 15% in non-lymphoid cells. Mature lymphoid cells showed low alteration rates: SNVs (1-2%), CNVs (5%), while expressing lineage-specific markers, confirming cell-type assignment. Long-read TP53 transcript sequencing also enabled phased variant genotyping. Combined with WGS SV and CNV profiles, we observed that TP53 loss-of-function dosage distinctly associates with the genomic architecture: biallelic loss of TP53 was associated with extensive intrachromosomal breaks and chromothripsis, whereas monoallelic loss primarily induced numerical chromosomal changes. This multi-omic framework enables high-resolution characterization of somatic genomic alterations at the single-cell level in TP53m AML, providing a powerful platform for mechanistic interrogation of disease biology. Citation Format: Gonzalo Lopez Garcia, Felix Andreas Radtke, Sagnik Banerjee, BIJAY JAISWAL, Daiane Hemerich Brennan, Yilin Zhao, Verena Körber, Marlen Metzner, Rachel Moore, Bilyana Stoilova, Junfei Zhao, Bettina Nadorp, David Cruz Hernandez, Batchimeg Usukhbayar, Aimee O’Donohue, Maria Ortiz Estevez, Daniel Lopes de Menezes, Rajasekhar NVS Suragani, Paresh Vyas, Anita Gandhi. High-resolution multi-omic dissection of bone marrow in TP53-mutant acute myeloid leukemia 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 5938.