Adaptive clonal hematopoiesis in bone marrow failure and leukemia predisposition
Hematology, Oncology
Final Report Abstract
Inherited bone marrow failure syndromes (IBMFS) are congenital disorders characterized by ineffective hematopoiesis, non-hematologic anomalies, and an increased risk of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Recent studies have identified maladaptive clonal pathways driving progression to MDS and adaptive clonal pathways resulting in somatic genetic rescue of the germline defect. Shwachman-Diamond Syndrome (SDS) is an IBMFS caused by biallelic mutations in the SBDS gene, which functions in ribosome assembly. SDS carries a high risk of MDS/AML and survival is low. SDS patients frequently acquire somatic mutations in TP53 and EIF6. In addition, interstitial deletions of chromosome 20q (del20q), encompassing the EIF6 gene, are also frequent in SDS patients. Functional studies revealed that EIF6 inactivation rescued the underlying ribosomal defect and EIF6-mutated clones did not progress to MDS/AML, reflecting an adaptive mechanism. TP53 inactivation did not rescue the ribosomal defect and biallelic TP53 inactivation was associated with MDS/AML development, representing a maladaptive pathway. We hypothesized that the identification and characterization of pathways downstream of somatic EIF6 inactivation may lead to novel therapeutic approaches to improve hematopoiesis and reduce the risk of MDS/AML. We integrated single-cell long-read nanopore sequencing to identify somatic mutations with single-cell RNA sequencing of an SDS patient with a somatic EIF6 mutation. The EIF6 mutation was present in lymphoid and myeloid cells, consistent with a likely common origin from a multipotent hematopoietic stem/progenitor cell, and showed a myeloid bias. In contrast, singlecell studies in an SDS patient with a somatic TP53 mutation showed that TP53-mutant cells were evenly distributed in all cell types. Annotation of cells without a mutation was difficult due to potential allelic drop-out. We pursued an orthogonal approach analyzing three SDS patients with del20q. Del20q single cells, identified by the copy number variant tool Numbat, were present in myeloid and lymphoid lineages and had a myeloid bias. We observed high numbers of monocytes +/- del20q, which have been implicated in inflammation and age-related clonal hematopoiesis. Further analysis revealed a significant downregulation of inflammatory/immune pathways/genes in CD14+ monocytes with del20q. Our data shows that somatic EIF6 inactivation is more prevalent in myeloid cells and leads to downregulation of immune/inflammatory pathways. We are currently analyzing additional BM samples of SDS patients with somatic EIF6 mutations and del20q to increase our statistical power for downstream analysis. I will then perform functional studies to confirm the relevance of downstream effectors/pathways of somatic EIF6 inactivation in SDS. We hope that our studies will identify new therapeutic targets to treat bone marrow failure and reduce leukemia risk in SDS and develop non-invasive surveillance testing to flag high-risk patients and inform transplant timing.
Publications
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Transient Monosomy 7 Is a Rare Event in Young Children with SAMD9L Syndrome. Blood, 140(Supplement 1), 8678-8679.
Andresen, Felicia; Sukova, Martina; Stary, Jan; De Moerloose, Barbara; Van Der Werff Ten Bosch, Jutte; Dworzak, Michael; Seidel, Markus G.; Polychronopoulou, Sophia; Beier, Rita; Kratz, Christian P.; Nathrath, Michaela; Frühwald, Michael C.; Göhring, Gudrun; Bergmann, Anke K.; Mayerhofer, Christina; Rotari, Natalia; Lebrecht, Dirk; Ramamoorthy, Senthilkumar; Yoshimi, Ayami ... & Erlacher, Miriam
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Spontaneous remission and loss of monosomy 7: a window of opportunity for young children with SAMD9L syndrome. Haematologica, 109(2), 422-430.
Erlacher, Miriam; Andresen, Felicia; Sukova, Martina; Stary, Jan; De Moerloose, Barbara; Van Der Werff Ten Bosch, Jutte; Dworzak, Michael; Seidel, Markus G.; Polychronopoulou, Sophia; Beier, Rita; Kratz, Christian P.; Nathrath, Michaela; Frühwald, Michael C.; Göhring, Gudrun; Bergmann, Anke K.; Mayerhofer, Christina; Lebrecht, Dirk; Ramamoorthy, Senthilkumar; Yoshimi, Ayami ... & Niemeyer, Charlotte M.
