New genomic study finds rare blood disease in children

Aplastic anemia is a rare, life-threatening blood disorder where patients are unable to make enough blood cells due to the immune system’s attack on blood stem cells. This condition can progress to myelodysplastic syndrome (MDS) and leukemia. A study led by scientists at St. Jude Children’s Research Hospital along with several collaborating institutions used cutting-edge genomic techniques to profile 619 children and adults with aplastic anemia.

They found that different blood stem cells within the same individual independently acquire gene mutations that allow the cells to escape immune attack. In some patients, these “rescue” stem cell clones were enough to restore blood production and provide long-term remission. The work, which involves the largest pediatric cohort of its kind ever reported, is published today nature genetics.

In aplastic anemia, immune cells called autoreactive T cells target and destroy blood stem cells that display peptides on a specific protein on their surface. These are encoded by human leukocyte antigen (HLA) Jean. Every person inherits one copy of this gene from each parent, which may have different variations.

People with aplastic anemia are often at a special “risk” HLA The allele (gene variant) that is believed to trigger the disease. Some blood stem cells escape immune attack by acquiring changes that silence risk. HLA Allele. This can happen through efficiency HLA mutation, or through uniparental isodisomy 6p (UPD6p), where the risk allele is replaced by a non-risk allele.

Two other types of escape in blood stem cells are known: paroxysmal nocturnal hemoglobinuria (PNH) or mutations in the clonal hematopoiesis (CHIP) gene. However, it was not clear whether all of these changes arise in the same stem cell or arise independently to help blood stem cells hide from the immune system. It was also unclear how this process of immune evasion affected clinical outcomes and cancer risk.

We found that in every patient with aplastic anemia who escapes autoimmunity, there are multiple, independent genetic events in his different blood stem cells that allow those cells to escape autoimmunity. Stem cells calm the risks HLA alleles through multiple mechanisms, and our data show that these events are protective, benign events that do not lead to progression to MDS or leukemia, even when rescued clones proliferate and dominate the bone marrow.”

Marcin Wlodarski, MD, PhD, study corresponding author, and associate member, Department of Hematology, St. Jude Children’s Research Hospital

Assessing the risk of blood stem cell ‘clones’

Blood stem cells give rise to all other blood cells, meaning their offspring are genetically identical, including any mutations acquired over time. The relative abundance of genetic “clones” of a specific stem cell measures the genetic diversity of these blood-forming cells. Using single-cell analyses, the researchers showed that the protective mutations occur independently in different blood stem cells and not sequentially within the same cell. These independent clones repopulate the marrow without being detected and killed by the immune system.

“We saw that patients with blood stem cell clones who survived autoimmunity could have improved blood counts,” Wlodarski said. “We also learned that these clones do not indicate an increased risk of leukemia. On the contrary, they often indicate the possibility of long-lasting remission.”

To assess these clones, scientists analyzed bone marrow and blood samples from 619 patients with aplastic anemia (256 children and 363 adults). Overall, 69% of patients had at least one acquired mutation: HLA Mutations or UPD6p clones were found in 16%, PNH clones in 44% and CHIP mutations in 21%.

First author Masanori Yoshida, MD, PhD, St. Jude Department of Hematology, then established and applied a single-cell DNA sequencing assay to simultaneously profile the mutations and cell-surface proteins of 304,902 single cells from 48 samples. The study was complemented by long-read whole-genome sequencing and single-cell whole-genome sequencing.

Experiments showed that acquired mutations are as common in children as in adults, but in pediatric patients, 65% of CHIP mutations occurred in only three genes (BCOR, BCORL1 And ASXL1), compared to 27% in adults. Because age-related CHIP mutations are not expected to be pre-existing in children, these mutations appear to be acquired immune-escape events in response to autoimmune attack.

HLA In aplastic anemia, alleles are lost several times early in life

To understand how these protective events arise and to accurately count them, the authors performed whole-genome sequencing on multiple single blood stem cells. They expected to see one to three programs per person; Instead, they found an average of three per patient, and 15 independent clones in one patient, resulting in a reduced risk. HLA allele, showing convergent evolution to survive a strong immune attack.

That extreme diversity pointed to an unusual, convergent evolutionary process, so scientists reconstructed a phylogenetic “family tree” of individual blood stem cells by reading all the mutations acquired throughout life in a single complete genome. This method enabled them to trace the origin of each clone.

“We expected that these mutations would occur just before the onset of disease,” Wlodarski said. “But we found some of HLA-The loss clones originated many years before clinical diagnosis.”

The team also showed that the longer-lived, rescued clones had higher expression of a surface marker for blood stem and progenitor cells: CD34. This suggests that CD34 enrichment may serve as a biomarker of long-term recovery. Also, clones with disadvantages HLARisk alleles and CHIP mutations almost never co-occur in the same cells, indicating that HLA loss in itself confers sufficient proliferative advantage that additional CHIP mutations, which may predispose to MDS, are not selected for.

Therefore, they appear to act as protective events against their MDS and leukemia development. These results challenge previous assumptions about when and how protective clones arise in aplastic anemia, and their presence may be a factor in restoring hematopoiesis.

“Aplastic anemia shows us convergent evolution in miniature: multiple independent mutational events arise in different cells, leading to the same escape from autoimmunity,” Wlodarski said. “This reflects the amazing nature of human hematopoiesis to heal itself from bad factors like autoimmune T cells and reconstitute the bone marrow.”