Abstract P08: 10x spatial transcriptomics of human AML core bone marrow biopsies reveals the complex remodeling of the non-hematopoietic stromal microenvironment post-treatment
Authors: Pardo Makayla , Bonal Dennis , Lee Seo-Ho , Maiz Daniela , Brown Valeria , Chorzalska Anna , Reagan John , Treaba Diana , Dubielecka Patrycja 
Published: March 2024

Abstract
Acute myeloid leukemia (AML) is a heterogeneous myeloid malignancy with a 5-year survival rate less than 26% due to poor response to treatment and relapse. Leukemic stem cells, largely responsible for relapse, exist in a highly specialized bone marrow (BM) microenvironment. Recent studies have described specific alterations to the non-hematopoietic BM niche following AML progression, such as an increase in mesenchymal stem cells and reduction in osteogenesis. While it is known that stromal cells support development of myeloid malignancies, it remains unclear how they contribute to disease progression and response to treatment. To detail the role of BM niche, we utilized spatial transcriptomics on core bone marrow biopsies (cBMB) to characterize stromal cell interactions and transcriptomic alterations in AML pre- and post-treatment. Previously, through bulk RNA-seq analysis of 29 AML cBMB, we reported the existence of distinct subpopulations of stromal cells, correlating response to 7+3 induction chemotherapy with upregulation of osteo-mesenchymal transcripts in non-responders (≥5% blasts post-treatment) (Treaba et al. 2023). We hypothesize that the prevalence of a subpopulation of osteoblasts allows for the retention of chemotherapy-resistant AML clones in non-responders. Given that expansion of the AML clone leads to retraction of stromal cells at diagnosis, detectability of these cells is diminished even with sensitive genomics approaches. Accounting for that, we reanalyzed our RNA-seq data to include low count (≥10 reads) transcripts. This allowed for detection of stromal genes at diagnosis, identifying a significant upregulation of mesenchymal-associated genes in responders compared to non-responders. Next, to confirm these findings and assess gene expression within the spatial architecture of the AML stroma, we used 10x Visium CytAssist platform to perform spatial transcriptomics (ST) on human AML cBMBs. We are the first group to utilize this technology on human bone marrow samples. The assay was performed in duplicate on decalcified FFPE cBMBs from a responder AML patient at diagnosis and 14 days post-induction chemotherapy. The sample was selected based on RNA DV200 score. ST revealed an abundance of stromal transcripts post-treatment in the endosteal region, with SPP1, BGLAP, COL1A1, IBSP and PTPRD among the top upregulated genes. These stromal genes are not detectable in the diagnostic sample, indicating an increase in osteo-mesenchymal transcripts post-treatment. [PD1] As the stroma is thought to provide protection for the AML clone, there is an urgent need to detail this intricate crosstalk to inform improved therapeutic strategies. While murine models have provided valuable insights, validation in humans is needed. Although assessment of the stromal component in AML is complicated by the low abundance at diagnosis, here we report the successful use of ST to uncover stromal composition on archived cBMB at diagnosis and post-treatment. Further analyses are warranted, to provide key insight into the involvement of the BM niche in AML.
Citation Format: Makayla Pardo, Dennis Bonal, Seo-Ho Lee, Daniela Maiz, Valeria Brown, Anna Chorzalska, John Reagan, Diana Treaba, Patrycja Dubielecka. 10x spatial transcriptomics of human AML core bone marrow biopsies reveals the complex remodeling of the non-hematopoietic stromal microenvironment post-treatment [abstract]. In: Proceedings of the Blood Cancer Discovery Symposium; 2024 Mar 4-6; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(2_Suppl):Abstract nr P08.