Single-Cell Genomics of Haematopoietic Stem Cell Niche Disruption in Sickle Cell Disease: New Mechanistic Insights from Nigerian Patient Samples

Haematopoietic stem and progenitor cell (HSPC) biology in sickle cell disease is incompletely understood, particularly the mechanisms by which the sickling microenvironment disrupts the bone marrow niche and impairs normal haematopoiesis. Single-cell multi-omics technologies provide unprecedented resolution to characterise cell-type-specific transcriptional and chromatin states within the HSPC compartment. This dissertation applied single-cell RNA sequencing (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) to characterise HSPC niche disruption in SCD, using samples from Nigerian patients at Aminu Kano Teaching Hospital and Lagos University Teaching Hospital. Bone marrow aspirates were collected from 20 HbSS patients and 10 healthy HbAA donors. Single-cell libraries were prepared using the 10x Chromium platform and sequenced on the Illumina NovaSeq. Cell type annotation was performed using Seurat and Signac, with reference to the Human Cell Atlas bone marrow reference. Trajectory analysis using Monocle3 and RNA velocity reconstructed aberrant differentiation routes in SCD HSPCs. Chromatin accessibility changes in erythroid commitment regulators were mapped. A novel HSPC subpopulation with a stress erythropoiesis transcriptional signature was identified exclusively in SCD patients. Ligand-receptor communication analysis revealed disrupted CXCL12-CXCR4 niche signalling. These mechanistic insights open new avenues for HSPC-targeted therapy in SCD. Keywords: single-cell genomics, sickle cell disease, haematopoietic stem cells, bone marrow niche, scRNA-seq