Aging-Related Gene Expression Signatures Define Likelihood of Disease Progression in Patients with Lower-Risk Myelodysplastic Syndromes

Abstract

Myelodysplastic syndromes (MDS) are a heterogeneous clonal bone marrowdisorders occurring mostly in the elderly. The Revised International PrognosticSystem (IPSS-R) groups MDS patients according to the risk of transformation intoacute myeloid leukemia. For treatment decision-making, patients are usuallydivided into two groups: lower- and higher-risk with the cutpoint of 3.5 accordingto the IPSS-R. However, part of lower-risk MDS patients (LR-MDS) progressesrapidly. Recently, we demonstrated that DNA damage response (DDR) activationand the ensuing senescence form an anti-tumor barrier in CD34+ cells of LR-MDSpatients, and that this barrier can be breached by

RUNX1 mutations (Kaisrlikova M,et al., Leukemia. 2022; 36:1898). As an extension, we analyzed transcriptomes ofLR-MDS patients regardless of their driver mutation, with and without rapidprogression (within 2 years of diagnosis), to determine molecular mechanismsunderlying the progression. Because MDS is associated with aging, and many anti-tumor barrier mechanisms (DDR, checkpoint activation, senescence) lead to a pro-aging phenotype, we questioned whether aging-related gene expressionsignatures defi ne the likelihood of disease progression in patients with LR-MDS.

We performed RNA-seq on CD34+ cells of 61 LR-MDS diagnostic samples (53patients without rapid progression (NRP) and 8 patients with rapid progression(RP)) with a median age of 65 years.

The diff erential expression analysis showed 1,701 up- and 1,569 downregulatedgenes in NRP (FDR<0.01). According to the GO Biological Processes (GO BP) and

Abstract #168503

Aging-Related Gene Expression SignaturesDefi ne Likelihood of Disease Progression inPatients with Lower-Risk MyelodysplasticSyndromes 1,2

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REACTOME databases, the most signifi cantly upregulated pathways were relatedto macromolecular metabolic processes such as DNA repair, replication, proteinmetabolism, cell cycle, chromosome organization, including regulation of geneexpression, and telomere organization (Fig. 1). The pathways of rRNA expressionregulation, splicing, and RNA metabolism were deregulated as well as thepathways related to apoptosis, cellular senescence and cellular response to stress,immune response, and mitochondrial metabolism. Furthermore, we foundderegulation of crucial signaling pathways mediated by NOTCH, RHO GTPases, NF-kB, MAPK, b-catenin, and WNT.

Although 1,569 genes were upregulated in RP, only seventeen GO BP termsconsisted of regulation of metabolic processes, cytoskeleton organization,phosphorylation, and signal transduction were upregulated.

The NRP results are consistent with the hallmarks of aging (López-Otín C, et al.,Cell. 2013; 153:1194). In GSEA, 36/37 and 120/143 gene sets were upregulated inNRP for the datasets consisting of gene sets chosen according to the keyword'aging' and 'stress', respectively (Fig. 2). Among them, gene sets associated withreplication stress, DNA damage, oxidative stress and unfolded protein responsewere signifi cant (FDR1.7).

Abnormal splicing is associated with cellular aging. Therefore, we conducted adiff erential alternative splicing analysis using rMATS. We found signifi cantdiff erences in 1,356 alternative splicing events (FDR10%) between NRP and RP.

Finally, we performed analysis of healthy controls (n=7) and age-matched NRP(NRP-age) (n=13) samples. We observed 70 up- and 209 downregulated genes inNRP-age (FDR<0.05). Only the splicing pathways were upregulated and theimmune pathways downregulated. In GSEA, no gene sets were signifi cant(FDR<0.1) for aging and stress datasets.

To conclude, these results show increased signatures of aging in CD34+ cells fromNRP, which correspond to an increased level of the intrinsic ability of CD34+ cellsto suppress malignant progression through anti-tumor barrier activation. This isconsistent with the current understanding that most aging phenotypes are knownto be the products of DDR and tumor suppression. Based on our data, wehypothesize that the progression of LR-MDS patients represents a cell-autonomously and perhaps also non-cell-autonomously-mediated failure ofappropriate cellular stress response mechanisms. Our data also show similarity atthe transcriptome level between age-matched NRP and healthy controls.