Transcriptome research identifies four hub genes related to primary myelofibrosis: a holistic research by weighted gene co-expression network analysis

Weihang Li,Bin Yuan,Ying Zhang,Xiong Xue,Yajun Deng,Ziyi Ding,Chengfei Li,Yingjing Zhao,Guohua Zhang,Kai Wang,Bo Wang,Jun Ma,Dong Wang,Quancheng Liu

doi:10.18632/aging.203619

Abstract

Objectives: This study aimed to identify specific diagnostic as well as predictive targets of primary myelofibrosis (PMF).Methods: The gene expression profiles of GSE26049 were obtained from Gene Expression Omnibus (GEO) dataset, WGCNA was constructed to identify the most related module of PMF. Subsequently, Gene Ontology (GO), Kyoto Encyclopedia Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA) and Protein-Protein interaction (PPI) network were conducted to fully understand the detailed information of the interested green module. Machine learning, Principal component analysis (PCA), and expression pattern analysis including immunohistochemistry and immunofluorescence of genes and proteins were performed to validate the reliability of these hub genes.Results: Green module was strongly correlated with PMF disease after WGCNA analysis. 20 genes in green module were identified as hub genes responsible for the progression of PMF. GO, KEGG revealed that these hub genes were primarily enriched in erythrocyte differentiation, transcription factor binding, hemoglobin complex, transcription factor complex and cell cycle, etc. Among them, EPB42, CALR, SLC4A1 and MPL had the most correlations with PMF. Machine learning, Principal component analysis (PCA), and expression pattern analysis proved the results in this study.Conclusions: EPB42, CALR, SLC4A1 and MPL were significantly highly expressed in PMF samples. These four genes may be considered as candidate prognostic biomarkers and potential therapeutic targets for early stage of PMF. The effects are worth expected whether in the diagnosis at early stage or as therapeutic target.

Highlights

World Health Organization (WHO) revised and updated the hematopoietic tumor classification system in 2016, which confirmed seven major categories of myeloid malignancies including acute myeloid leukemia (AML) and related neoplasms, myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), mastocytosis, eosinophilia-associated myeloid/lymphoid neoplasms with specific mutations, and MDS/MPN overlap and myeloid neoplasms with germline predisposition [1], among which MPNs are clonal hematopoietic disorders characterized by excessive production of differentiated hematopoietic cells in chronic phase [2]
Unqualified samples were eliminated according to the quality control of these gene chips, and standard samples were filtered by calculating the normalized unscaled standard errors (NUSE), NUSE plot was displayed for quality check (Figure 1A)
robust multi-array average (RMA) algorithm was performed for data preprocessing, the boxplot of normalized and background corrected value was plotted (Figure 1B), results showed that the median amount of gene expression in each sample was on a straight line, indicating that the preprocessed data was served as standard data and could be analyzed in the following study

Summary

Introduction

World Health Organization (WHO) revised and updated the hematopoietic tumor classification system in 2016, which confirmed seven major categories of myeloid malignancies including acute myeloid leukemia (AML) and related neoplasms, myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), mastocytosis, eosinophilia-associated myeloid/lymphoid neoplasms with specific mutations, and MDS/MPN overlap and myeloid neoplasms with germline predisposition [1], among which MPNs are clonal hematopoietic disorders characterized by excessive production of differentiated hematopoietic cells in chronic phase [2]. The Philadelphia-negative MPNs contained 3 major diseases including polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF). Among MPNs, PMF is the most essential neoplasms which could evolve from other MPNs such as PV and ET. Later in their courses, both PV and ET disorders may evolve into myelofibrotic phases termed “post polycythemia vera myelofibrosis” or “post-essential thrombocythemia myelofibrosis”, respectively [3, 4]. Both PV and ET disorders may evolve into myelofibrotic phases termed “post polycythemia vera myelofibrosis” or “post-essential thrombocythemia myelofibrosis”, respectively [3, 4] In this situation, PMF is referred to as post-PV MF or post-ET MF.

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