Single-Cell RNA Sequencing Elucidates Cellular Origin and Heterogeneity in Acute Myeloid Leukemia

Introduction:

Acute myeloid leukemia (AML) is a heterogeneous malignancy arising from hematopoietic stem and progenitor cells (HSPCs) that acquire genetic abnormalities during hematopoiesis. Understanding the heterogeneous nature of AML is crucial, and predicting the cell of origin for each AML subtype could significantly enhance our comprehension of the disease. Recent studies utilizing single-cell RNA sequencing (scRNA-seq) have characterized hematopoiesis at single-cell resolution. However, many scRNA-seq studies involve a limited number of patients and lack comprehensive clinical information. Investigating large-scale bulk RNA-seq data with clinical annotations based on scRNA-seq studies will provide deeper insights into the heterogeneous nature of AML.

Methods:

A reference transcriptomic map of hematopoiesis was created using publicly available scRNA-seq data from the Human Cell Atlas and Tabula Sapiens. Data from various studies were aggregated using BBKNN and Scanorama and visualized using UMAP. Bulk RNA-seq data from the BeatAML project were projected onto the reference UMAP and clustered based on the annotations from the reference map to infer the cell of origin for each AML patient. This classification was validated using Pearson correlation of pooled transcriptomic data from the reference cells and NMF factorization of gene expression of reference cell types.

Results:

The reference map comprised 330,000 cells, capturing a wide variety of hematopoietic processes. UMAP projection of bulk RNA samples primarily divided the samples into granulocytic and monocytic origins with varying degrees of differentiation inferred from pseudotime analysis. Overall survival analysis revealed a favorable outcome for diseases originating from granulocytic lineages. To investigate transcriptomic changes from initial diagnosis to relapse, 30 paired initial and relapsed bulk RNA-seq samples were compared. Relapse samples were more likely to be located in proximal pseudotime, indicating a loss of differentiation, and showed a mixture of cell origins, indicating a loss of original transcriptomic characteristics.

Discussion:

This study provides a comprehensive single-cell resolution map of hematopoiesis and reclassifies existing AML bulk RNA-seq data based on the cell of origin. This reclassification allows for comparison of clinical outcomes, such as overall survival and relapse rates, between different groups. Furthermore, the investigation of transcriptomic changes from initial diagnosis to relapse offers insights into the evolution of AML and highlights the importance of targeting specific subpopulations for therapy.

Park:ImpriMed, Inc.: Consultancy, Current holder of stock options in a privately-held company. Kim:BL&H: Research Funding; AbbVie, Astellas, BMS, Handok, Novartis, AML-Hub, Jazz Pharmaceuticals and Takeda: Honoraria, Speakers Bureau; AbbVie, AIMS Bioscience, AML-Hub, Astellas, BMS & Celgene, Boryung Pharm Co., Daiichi Sankyo, Janssen, Handok, LG Chem, Novartis, Pfizer, SL VaxiGen, VigenCell, Aston Bioscience, Ingenium, Amgen, Sanofi Genzyme, Takeda, Meiji Pharm Co. and GreenCross Phar: Consultancy; BMS & Celgene, Novartis, APLC, AbbVie, Astellas, Janssen, Handok, Pfizer, Sanofi Genzyme, AML-Hub, Daiichi Sankyo and APBMT: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals, Takeda, Astellas, AbbVie and APLC: Other: Travel; AML-Hub, APBMT, ICBMT, APLC, Novartis and BMS: Other: and leadership or fiduciary roles in other board, society, committee or advocacy group .