Single-Cell RNA Sequencing of Bone Marrow Haematopoietic Stem Cell Niches in Aplastic Anaemia: Developing an Original Transcriptomic Classification Framework for Nigerian Patients

This dissertation develops an original transcriptomic classification framework for aplastic anaemia (AA) based on single-cell RNA sequencing (scRNA-seq) of bone marrow haematopoietic stem cell niches in Nigerian patients, addressing a fundamental gap in understanding how stromal niche disruption contributes to haematopoietic failure in this population. Existing AA classification relies on blood count severity criteria without mechanistic insight into niche dysfunction, which limits personalised treatment selection. Using a prospective multi-centre design involving haematology units at Lagos University Teaching Hospital and Aminu Kano Teaching Hospital, bone marrow aspirates from 80 newly diagnosed AA patients, 30 aplasia-recovered patients on immunosuppression, and 40 healthy donors were subjected to 10x Genomics Chromium scRNA-seq. Cell type deconvolution, trajectory analysis, ligand-receptor interaction modelling, and pseudobulk differential expression were applied. The dissertation identifies a previously undescribed stromal mesenchymal subset, termed the Nigerian Aplasia-Associated Stromal Cluster (NASC), characterised by loss of CXCL12 and SCF expression and gain of inflammatory senescence signatures, present in 73 percent of newly diagnosed cases but reduced to 12 percent in responders. Niche transcriptomic signature at diagnosis predicts immunosuppressive therapy response with 81 percent accuracy. An original Haematopoietic Niche Damage Score derived from scRNA-seq data is proposed as a novel disease classification dimension. The framework provides a molecular basis for niche-directed therapeutics and personalised treatment selection in Nigerian aplastic anaemia. Keywords: single-cell RNA sequencing, aplastic anaemia, haematopoietic stem cell niche, transcriptomics, Nigeria.