Differentially expressed genes in CD34+ cells in Ph-negative myeloproliferative neoplasms: bioinformatics meta-analysis of three independent studies

Abstract

Accumulating evidence suggests that the molecular pathobiology of Ph-negative myeloproliferative neoplasms (MPNs) is significantly more complex than expected, with associated somatic mutations failing to fully explain the underlying causes and maintaining a high degree of uncertainty regarding individual disease prognosis. Given the involvement of epigenetic mechanisms of carcinogenesis in altered gene expression, attempts have been made to identify specific transcriptome alterations in hematopoietic cells in MPNs. However, these results often inconsistently reflect the use of different analytical technologies, statistical approaches, and the small number of patients included. Aim – to perform a bioinformatics meta-analysis of available databases of primary results from microarray studies of CD34+ cell RNA profiling in patients with MPNs. The NCBI GEO catalog was used to search for raw data. After searching for the keyword “myeloproliferative neoplasm”, three independent databases were identified that matched the Affymetrix analytical platform and biomaterial type. Processing was performed in the integrated RStudio development environment using the oligo package. Gene expression normalization was performed using the robust multiarray average method. Differential gene expression analysis in CD34+ cells between patient groups was performed using the limma package. To enhance the reliability of the results, a meta-analysis was performed using a combination of Fisher’s and Stauffer’s methods, with the Jackknife procedure used for final filtering. The meta-analysis identified 33 genes common to MPN, as well as 7, 204, and 1806 genes specific to essential thrombocythemia, polycythemia vera, and primary myelofibrosis, respectively, that were differentially expressed. The PIM1 gene expression level significantly varied in the series control → essential thrombocythemia → polycythemia vera → primary myelofibrosis. The functional annotation confirms the pathogenetic mechanisms of the disease: impaired DNA repair, apoptosis, proliferative and functional activation, and the development of inflammatory processes in the bone marrow. It also demonstrates the multilevel nature of the interactions between intracellular signaling pathways and the pleiotropy of regulatory processes in carcinogenesis. Overall, the obtained data are consistent with Dameshek’s biological continuum postulate, which suggests a single pathogenetic mechanism for the evolution of MPNs.