P707: mutations in the cohesin gene stag2 are associated with reduced inflammatory geneexpression and an increase in hematopoietic stem cell populations in myelodysplasticsyndrome patients

Background: Mutations in chromatin regulatory genes are frequent in myelodysplastic syndromes (MDS). This includes STAG2, which is a component of the cohesin complex involved in regulating chromatin structure and affecting DNA repair and transcription. STAG2 mutations are associated with poor prognosis. Aims: The overall aim of the study is to gain a better understanding of how STAG2 mutations (STAG2mut) contribute to disease progression by identifying underlying changes in gene expression. Methods: We have analyzed RNA-seq data from total bone marrow samples from 56 healthy individuals and 753 MDS patients (n=809) including 48 (6%) with STAG2mut. Age, gender and survival were used as covariates in the model for evaluating changes in gene expression. Genes were considered differentially expressed when the log2 fold-change was greater than 1.5 and the adjusted p-value was below 0.01. For the functional interpretation, we applied enrichr and fgsea for ranked gene set enrichment of msigDB hallmark sets and xCell to infer the enrichment of different stem and progenitor cell populations. Results: Based on the expression of the top 1000 most variable genes, STAG2mut MDS samples are more similar to each other than samples carrying mutations in genes encoding other chromatin regulators such as TET2, ASXL1 or DNMT3A. Comparing STAG2mut to STAG2 wild type (STAG2wt) MDS samples, we identified 398 differentially expressed genes. While we did not identify any hallmark gene set enriched among upregulated genes, we found that downregulated genes were enriched in inflammatory functions, including the cytokine-encoding gene IL1A. Inflammatory genes were also differentially expressed and enriched by comparing MDS STAG2mut with healthy samples. STAG2 mutations occur late in the course of the disease and in the background of mutations of which ASXL1 and SRSF2 were the most frequent in the analyzed cohort. The STAG2 association with reduced inflammatory gene expression held true when comparing co-mutated samples with samples carrying only the other mutations, for instance when comparing STAG2 and ASXL1 co-mutants (n=37) versus only ASXL1 mutants (n=114) but not when comparing the frequently co-mutated gene with non-mutant samples (e.g. ASXL1 mutant versus non-ASXL1 mutant). The transcriptomic data was generated from total bone marrow aspirates. Clustering all 753 MDS samples based on the inferred enrichment of stem and progenitor cell populations showed that most STAG2mut are part of a cluster enriched in hematopoietic stem cells (HSC). In line with this, we found the HSC self-renewal gene FLT3 to be upregulated in STAG2mut samples compared to STAG2wt, while the B-cell lineage commitment genes VPREB3 and PAX5 were downregulated. At the same time, also various genes encoding hemoglobins expressed in mature cells of the erythroid lineage, were downregulated in STAG2mut Summary/Conclusion: In MDS, STAG2 mutations are associated with changes in gene expression that suggest a down-regulation of inflammatory signals and an enrichment of stem and progenitor cell populations with reduced B-cell differentiation. The latter is in line with previously reported results in a mouse model (Viny et al., doi: 10.1016/j.stem.2019.08.003) and MDS samples (Sternberg et al,doi.org/10.1182/blood-2005-04-1543; Nováková et al, 10.3324/haematol.2015.137711). Our ongoing work aims to understand whether these two observations are linked. Keywords: Myelodysplastic syndrome, MDS/AML, Inflammation, HSC