Bone marrow microenvironment in aplastic anemia: insights from Nestin/CXCL12 immunohistochemistry and RNA-sequencing

Aplastic anemia (AA) is a rare bone marrow failure syndrome characterized by immune-mediated destruction of hematopoietic stem and progenitor cells (HSPCs). The contribution of the bone marrow microenvironment remains incompletely understood. We analyzed 29 bone marrow biopsies from patients with moderate (mAA), severe (sAA), and very severe AA (vsAA), along with 12 healthy controls and seven subcortical pseudohypocellular samples. Immunohistochemistry for nestin and CXCL12 was performed to quantify stromal niches. RNA sequencing was carried out to investigate immune and niche-related gene expression patterns. sAA patients exhibited a significantly increased number of nestin+ niches compared to mAA and controls. CXCL12+ niches showed no significant differences between groups. RNA sequencing revealed upregulation of immune response genes, as well as pathways related to interferon-gamma signaling, JAK-STAT3 activation, and antigen presentation. Downregulated genes and pathways pointed to impaired DNA repair, cell cycle regulation, and epigenetic stability. Our findings support a model in which AA pathogenesis is driven by both immune injury and compensatory, yet dysfunctional, stromal remodeling. These data underline the importance of the bone marrow microenvironment in AA.