Gene Expression Landscape of Chronic Myeloid Leukemia K562 Cells Overexpressing the Tumor Suppressor Gene PTPRG

Abstract

This study concerns the analysis of the modulation of Chronic Myeloid Leukemia (CML) cell model K562 transcriptome following transfection with the tumor suppressor gene encoding for Protein Tyrosine Phosphatase Receptor Type G (PTPRG) and treatment with the tyrosine kinase inhibitor (TKI) Imatinib. Specifically, we aimed at identifying genes whose level of expression is altered by PTPRG modulation and Imatinib concentration. Statistical tests as differential expression analysis (DEA) supported by gene set enrichment analysis (GSEA) and modern methods of ontological term analysis are presented along with some results of current interest for forthcoming experimental research in the field of the transcriptomic landscape of CML. In particular, we present two methods that differ in the order of the analysis steps. After a gene selection based on fold-change value thresholding, we applied statistical tests to select differentially expressed genes. Therefore, we applied two different methods on the set of differentially expressed genes. With the first method (Method 1), we implemented GSEA, followed by the identification of transcription factors. With the second method (Method 2), we first selected the transcription factors from the set of differentially expressed genes and implemented GSEA on this set. Method 1 is a standard method commonly used in this type of analysis, while Method 2 is unconventional and is motivated by the intention to identify transcription factors more specifically involved in biological processes relevant to the CML condition. Both methods have been equipped in ontological knowledge mining and word cloud analysis, as elements of novelty in our analytical procedure. Data analysis identified RARG and CD36 as a potential PTPRG up-regulated genes, suggesting a possible induction of cell differentiation toward an erithromyeloid phenotype. The prediction was confirmed at the mRNA and protein level, further validating the approach and identifying a new molecular mechanism of tumor suppression governed by PTPRG in a CML context.

Cis‐regulatory control of mammalian Trps1 gene expression

“…To further evaluate the physical regulatory connection between identified CNEs and their precise target promoter, we used Hi‐C data for human embryonic stem cells (H1‐ESC), K562 cells, and GM12878 cells from the 3D genome browser (http://3dgenome.fsm.northwestern.edu/view.php) (Figure 2b and Supporting Information S1: Figures S3 and S4A,B) (Wang et al, 2018). These cell lines are reported to express TRPS1 TF (Joung et al, 2023; Lombardi et al, 2022). The Hi‐C data for H1‐ESC and k562 cells revealed that the TRPS1 gene is embedded in a domain with enhanced interactions compared to surrounding chromatin regions (Figure 2b; Supporting Information S1: Figure S4B).…”

Protein Tyrosine Phosphatase Receptor Gamma as Potential Therapeutic Target for Chronic Myeloid Leukemia Patients

“… 13 More recently, our group had documented that PTPRG overexpression induce a global modification of gene expression and pinpoint the critical role of transcription factor in the reprogramming of CML cells. 15 …”

“…13 More recently, our group had documented that PTPRG overexpression induce a global modification of gene expression and pinpoint the critical role of transcription factor in the reprogramming of CML cells. 15 Ismail et al 16 reported that the restoration of PTPRG protein expression on neutrophil-white blood cells following TKIbased therapy in CML patients was greater in optimal response patients when compared to those who failed treatment. Additionally, higher expression of PTPRG was observed with nilotinib treatment when compared to IM.…”