Comparison of gene expression profiles in MPN subtypes

Myeloproliferative neoplasms (MPN) are known to be heterogeneous disorders that have the potential to progress over time. Essential thrombocythemia (ET) and polycythemia vera (PV) may be considered benign, early stage MPN that can transition to myelofibrosis, which is a more malignant, aggressive disorder. The driver mutations are well-established and additional non-driver mutations have also been associated with increased risk for progression. However, the clinical course and progression of MPN remain difficult to predict and the identification of new molecular targets is of particular interest.

Julian Baumeister and colleagues compared gene expression signatures in CD34⁺ stem and progenitor cells to identify molecular components and potential biomarkers in different MPN subtypes to explore new therapeutic targets and predict the disease progression. The results were presented at the European Hematology Association (EHA) 2021 Virtual Congress¹, and we are pleased to summarize key points here.

Methods

In this study, investigators performed a gene expression analysis of CD34⁺ peripheral blood and bone marrow mononuclear cells from a cohort of 36 samples from patients with MPN and healthy controls. Samples were obtained from individuals with:

• ET (n = 6)
• PV (n = 11)
• primary myelofibrosis (PMF; n = 9)
• secondary myelofibrosis (SMF; n = 4)
• healthy donors (n = 6)

The 36 samples were analyzed using the Affymetrix GeneChip^TM Human Transcriptome Assay 2.0, which provided gene expression, PROGENу, and pathway analyses.

Results

A variety of differentially regulated genes were identified in the MPN subtypes compared with healthy controls:

• PMF (200 genes) and SMF (272 genes) had stronger differences than ET (132 genes) and PV (121 genes) vs healthy controls

PROGENу analysis demonstrated:

• A significant upregulation of NF-κB and TNFα signaling pathways in the late stages of MPN (notably in SMF)
• A reduction of estrogen signaling in PMF and SMF

Gene ontology enrichment analysis demonstrated:

• Induction of inflammatory pathways (notably in PMF and SMF)
• Downregulation of RNA splicing in PMF

The following potential diagnostic or prognostic markers were identified:

• AREG, CYBB, DNTT, TIMD4, and VCAM1
• Members of the S100 family (S100A4/8/9/10/12), which may be associated with a high risk of leukemic transformation

Reverse transcription-quantitative polymerase chain reaction of bone marrow cells demonstrated that deregulation was primarily limited to the CD34⁺ compartment.

In total, 98 genes were deregulated solely in SMF, which may be used to predict the progression into myelofibrosis. The strongest deregulated genes in this group included CLEC1B, CMTM5, CXCL8, DACH1, and RADX (Table 1).

Table 1. Top 10 genes differentially regulated in secondary myelofibrosis versus healthy controls, ranked by fold change*

Conclusion

This first study to investigate gene expression signatures in all classical MPN subtypes revealed a number of findings. Firstly, CD34⁺ cells from patients with myelofibrosis demonstrated stronger differences in gene expression than early-stage MPN (i.e., ET and PV) compared with healthy controls. In addition, inflammatory signaling pathways (NF-κB and TNFα) were strongly activated in all MPN subtypes, particularly SMF, while downregulation of RNA splicing pathways was restricted to PMF. And finally, several deregulated genes and pathways were identified as potential molecular markers for diagnosis and prediction of disease course; particularly CLEC1B, CMTM5, CXCL8, DACH1, and RADX, and genes in the S100 family.