Aplastic anemia remains a disease entity shrouded in mystery. Although there is not a clear or universal trigger, it is generally accepted that the disease is mediated by an autoimmune attack of marrow precursors by lymphocytes. This notion is further validated by the disease’s consistent but not absolute response to immunosuppressive therapies. In a comprehensive effort to describe the changes in the marrow compartment during treatment of severe aplastic anemia (SAA), Zhijie Wu, MD, PhD, and colleagues used mass cytometry, single-cell RNA sequencing, and paired T-cell receptor/B-cell receptor (TCR/BCR) sequencing to analyze bone marrow samples obtained prospectively from 20 treatment-naive SAA patients enrolled in a combined horse anti-thymocyte globulin (ATG)-cyclosporine-eltrombopag protocol as well as from four healthy donors. Their multimodal atlas simultaneously captured the target (hematopoietic precursors) and effector (immune) compartments before therapy and at six-month follow-up, at which time 15 out of the 20 patients had achieved a complete response.
Shift in Cellular Architecture
Pretreatment marrows showed a reproducible distortion in cell-type abundances compared to healthy donors: before therapy, CD34+ hemopoietic stem and progenitor cells (HSPCs) were profoundly depleted while effector-memory CD8+ and CD4+ T cells were expanded. Immunotherapy reversed these trends — granulocyte-monocyte progenitors, common myeloid progenitors, and lymphoid progenitors rebounded, while activated cytotoxic lymphocytes contracted. Importantly, long-term HSPCs failed to normalize, indicating that recovery likely emanated from later multipotent progenitors rather than true stem cells.
Clonal T-Cell Dynamics Dictate Recovery
TCR analysis revealed an oligoclonal expansion (defined as a clonotype found in two or more cells with an identical TCR) in 25% of all T cells measured at baseline, compared to 10% in controls (BCR clonal expansion was not observed). Importantly, these expanded TCR clones were almost always individual-private, meaning they were only very rarely seen across patients. The expanded T-cell clones harbored a cytotoxic gene signature (PRF1, GZMB) and expressed high levels after therapy. Post-therapy, the overall clonal burden persisted (23%), but individual trajectories diverged. Patients whose dominant clones shrank exhibited more robust neutrophil and platelet recoveries, while the emergence of novel clones was associated with blunted count rises and a higher relapse risk.
Cell–Cell Cross-Talk Amplifies Damage
Ligand-receptor analysis highlighted a pronounced interferon gamma (IFNG)–IFNG receptor circuit linking CD8+ T/natural killer (NK) cells to neutrophils, monocytes, and HSPCs. Immunosuppression dampened these interactions in parallel with clinical response. Notably, new post-therapy clones engaged the same cytokine circuitry as extinguished clones, suggesting persistent antigenic drive. Interestingly, these circuits were detectible in healthy patients.
Genetic Susceptibility Converges on Cytotoxic Effectors
Integrating single-cell expression with genome-wide association studies signals, the authors show that SAA risk variants are enriched in genes regulating lymphocyte activation (e.g., S1PR5, NFKB1). S1PR5+ NK and CD8+ subsets, as well as NFKB1+ myeloid cells, were overrepresented in patients and transcriptionally primed for cytotoxicity; their frequency decreased with treatment, underscoring the role of germline contributions in immune dysregulation.
In Brief
Dr. Wu and colleagues deliver the most granular view yet of human aplastic anemia in response to therapy. Their data confirm the long-held hypothesis that SAA is driven by IFNG-charged effector-memory T cells that prune HSPCs, leaving downstream progenitors capable of rebound once immune pressure abates. However, in SAA, immunosuppression can act as a double-edged sword: while it may suppress existing clones, it permits new ones to rise, potentially restraining complete marrow regeneration and seeding relapse or clonal evolution. Future trials should combine ATG-based regimens with targeted agents that eliminate pathogenic clones or directly modulate the IFNG axis to achieve durable hematopoietic reconstitution.
Disclosure Statement
Dr. Furlan indicated no relevant conflicts of interest.
