lncRNA CRNDE204 regulates erythropoiesis and myelopoiesis by binding to PUS1

Abstract

Hematopoiesis is a crucial process that produces all cells within the hematopoietic system. Mutations in genes that disrupt normal hematopoiesis can cause bone marrow failure disorders ranging from myelodysplastic syndromes (MDS) to leukemia. Recent studies have pointed out the association between ribosomopathy and hematopoietic failure, and hematopoietic deficiency is a common clinical manifestation of multiple ribosomopathies, including Shwachman Diamond Syndrome and Diamond-Blackfan anemia (DBA). Shwachman Diamond Syndrome (SDS) is a rare and inherited form of ribosomopathy that is caused by mutations in SBDS gene, and patients with SDS lack myeloid progenitor cells, which causes severe anemia and neutropenia, and have increased risk of developing MDS or acute myeloid leukemia in later stages of life. Although standard care for SDS and other forms of MDS can relieve the symptoms, patients usually require lifelong treatment and multiple hospital visits to monitor their current status. Until now, the only cure for SDS is hematopoietic stem cell transplantation, yet due to its high risk of side effects, this is not widely used for treating SDS patients and is only considered if the patient has severe symptoms or starting to develop malignancies. The absence of curative treatment of SDS suggests there is a need to understand the molecular mechanism of SDS pathogenesis. The Novina Lab published the first map of SDS hematopoiesis at single cell resolution. Analysis of this SDS patient data identified a lncRNA first described in colorectal cancers, called colorectal neoplasia differentially expressed (CRNDE), as the most downregulated genes during SDS hematopoiesis and the expression of it is increased in acute myeloid leukemia. Our data points out the role of CRNDE in promoting normal erythropoiesis. In vitro experiments show that one splice variant isoform of CRNDE, CRNDE204, can promote differentiation of erythrocytes and megakaryocytes in K562 cells. However, another isoform, CRNDE201, represses differentiation. Based on these observations, we performed RNA-seq and proteomics analysis and found that CRNDE204 regulates key erythropoiesis and myelopoiesis genes and pathways. In addition, a yeast three-hybrid screen identified 24 proteins that could bind to CRNDE204, including PUS1 which is the key regulator of erythrocyte development and its mutation causes sideroblastic anemia. This is further validated by computational analysis and knock-down assays, and knock-down of PUS1 result in a decrease in both erythroid and megakaryocyte differentiation in K562 cells. Collectively, our findings pinpoint that CRNDE204 regulates erythropoiesis and myelopoiesis by interacting with PUS1, which makes CRNDE204 reintroduction as promising genetic therapy target for bone marrow failure disorders.