Abstract A018 Transcriptional evolution from normal foetal haematopoiesis to myeloid leukaemia in Down syndrome

Abstract Children born with Down syndrome (DS), a genetic condition caused by the presence of an additional chromosome 21 (trisomy 21 or T21), have a substantially higher risk of developing childhood leukaemia. Approximately 30% of DS infants develop a preleukemic condition called transient abnormal myelopoiesis (TAM). TAM is strictly associated with GATA1 truncating mutations on a T21 background. Most TAM cases spontaneously resolve within the first few months of life. However, by the age of five, approximately 10% of cases progress to megakaryoblastic/erythroid leukaemia, known as myeloid leukaemia of DS (ML-DS). This final step of transformation is often driven by specific third-hit somatic mutations, most of which affects genes encoding JAK kinases, cohesin complexes, or epigenetic regulators. These well-defined stepwise genetic aberrations associated with ML-DS pathogenesis provide a unique and highly tractable system to elucidate the molecular changes underlying leukaemogenesis. Using single-cell mRNA sequencing of primary human samples, we directly interrogate the transcriptional changes underpinning the multi-step pathogenesis of ML-DS. We observe an expansion of megakaryocyte-erythrocyte progenitors (MEPs) specifically in T21 foetal liver compared to diploid or other trisomies. However, it is the GATA1 mutation that accounts for the majority of the transcriptomic changes towards that of the leukaemic blasts. Furthermore, investigation of an aggressive TAM case reveals an enrichment in expression of the leukaemogenic gene module associated with the full-blown leukaemia state ML-DS. We also demonstrate that TAM and ML-DS blasts still retain transcriptional signatures of normal haematopoiesis, showing heterogeneous features of differentiation towards erythrocytes, megakaryocytes, and mast cells. Finally, by integrating genomic and transcriptomic data, we directly defined the genomic evolution, and its corresponding transcriptional consequences, that underpins a treatment-refractory case of ML-DS. Overall, we have generated the first comprehensive single-cell mRNA atlas of TAM / ML-DS, enabling unbiased quantitative characterisation of the transcriptional transformation along ML-DS pathogenesis. Our study explores the molecular signature associated with progression of TAM to ML-DS, as well as the mechanism underlying differences in treatment response. These insights offer the possibility of more meaningful clinical interpretations and potential to explore novel therapeutic targets for these conditions. Citation Format: Mi K. Trinh, Matthew D. Young, Conor Parks, Agnes Oszlanczi, Toochi Ogbonnah, Di Zhou, Angus Hodder, Konstantin Schuschel, Hasan Issa, Laura Jardine, Jan-Henning Klusmann, Jack Bartram, Sam Behjati. Transcriptional evolution from normal foetal haematopoiesis to myeloid leukaemia in Down syndrome [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr A018.