Differential Expression of Genes Associated with Oncogene-Induced Senescence and Senescence Associated Secretory Phenotype in the Absence of Differential Expression of High Molecular Risk Genes and Genes Associated with JAK-STAT Pathway in Sorted Cells of Patients with Polycythemia Vera and Primary Myelofibrosis

Introduction

Despite significant progress in the understanding of the molecular pathogenesis of myeloproliferative neoplasms (MPN) and the identification of high molecular risk (HMR) genes (i.e. ASXL1, EZH2, IDH1 and IDH2 genes), the mechanisms by which different cell types predominate in the different disease subtypes and their implications for prognosis remain uncertain. Given the recently described association of senescence and fibrosis in a number of pathologies by Menoz-Espin et al, we hypothesized that genes implicated in oncogene-induced senescence (OIS) and senescence associated secretory phenotype (SASP) may contribute to the pathogenesis of these neoplastic bone marrow disorders that frequently show evidence of fibrosis. Specifically, we were interested in the gene expression levels in different disease subtypes, at a cell-type level, and whether these patterns of differential expression were distinct from the transforming JAK-STAT pathway and the HMR genes.

Aim

To elucidate the role of OIS and SASP genes in the pathogenesis of MPN subtypes by determining the differential expression of the genes in specific cell types in patients with MPN.

Methods

We performed gene expression profiling on normal controls (NC) and patients with MPN who were diagnosed with essential thrombocythemia (ET), polycythemia vera (PV) and primary myelofibrosis (PMF) according to the 2008 WHO diagnostic criteria. Two cohorts of patients, the patient and validation cohorts, from 3 tertiary-level hospitals were recruited prospectively over 3 years. Peripheral blood samples were taken and sorted into polymorphonuclear cells (PMN), mononuclear cells (MNC) and T cells. RNA was extracted from each cell population. Gene expression profiling of the human transcriptome was performed using microarray and RNA sequencing on the patient and validation cohorts respectively. Gene expression analyses (GEA) were performed on 4 sets of genes derived from publicly available or custom derived gene set enrichment analysis: 92 OIS genes, 88 SASP genes (Gil et al), 4 HMR genes, and 126 genes associated with JAK-STAT pathway. Gene expression levels for each cell type in each disease were compared with NC to obtain the differential expression of the genes. RNA-seq analysis of samples from the validation cohort was used to validate the microarray results from the patient cohort.

Results

Twenty-eight patients (10 ET, 11 PV and 7 PMF) and 11 NC were recruited into the patient cohort. Twelve patients (4 ET, 4 PV and 4 PMF) and 4 NC were recruited into the validation cohort. After combination of the microarray and RNA-seq datasets, GEA of the OIS genes revealed the differential expressions of MCTP1 and SULT1B1 genes by PMN in PV but of none in PMF. In contrast, the BEX1 gene was identified as differentially expressed by MNC in PMF but none in PV. GEA of the SASP genes revealed differential expression of THBS1 gene by MNC in PMF but of none in PV. None of the SASP genes were differentially expressed by PMN in either PV or PMF. No differentially expressed genes were identified by PMN or MNC in ET, or by T cells in any of the diseases. Notably, GEA of the HMR genes and genes associated with the JAK-STAT pathways did not show any differential expression in any disease subtype by any cell type.

Conclusions

We have found strikingly distinct patterns of differential expression of senescence associated genes by PMN (in PV) and MNC (in PMF). These results provide a novel insight into the mechanisms underlying the different phenotype of the MPN subtypes and also to the cells responsible for mediating the differences. The lack of differential expression of OIS and SASP genes in ET may reflect the milder clinical phenotype of the disease. Although mutations in the HMR genes are associated with poor prognosis in PMF, the lack of differential expression in these genes and genes associated with the JAK-STAT pathway is in keeping with their mutated status and suggests that they give rise to the disease phenotypes via altering downstream expression of genes associated in other pathways such as the senescence pathways studied here. Further studies are warranted to investigate the role of these genes and the pathways involved in senescence at a cell-type specific level in order to gain further insight into how they can potentially give rise to the various disease phenotypes in MPN and unmask potential therapeutic targets.