Nestin/CXCL12 immunohistochemistry and RNA sequencing map the bone marrow microenvironment in aplastic anemia

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. Here, we analyzed 29 bone marrow biopsies from patients with moderate (mAA), severe (sAA) and very severe (vsAA) AA, along with 12 unaffected 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. Patients with sAA exhibited a significantly increased number of nestin+ niches compared to patients with 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 immune injury and compensatory, yet dysfunctional, stromal remodeling. These data underline the importance of the bone marrow microenvironment in AA.