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Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients
Published on: June 16, 2017
Integrated Transcriptomic Analysis and Molecular Modeling Identify ENO1 and Naftopidil as Candidates for Chronic
Minming Li1, Suxia Geng1, Lingji Zeng1
1Department of Hematology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou City, Guangdong Province, 510080, China.
Introduction:
In-depth analysis of the biological status of Hematopoietic Stem Cells (HSCs) may reveal the intrinsic pathological mechanism of Chronic Myelomonocytic Leukemia (CMML).
Materials And Methods:
Single-cell dataset GSE211033 and bulk transcriptomic dataset GSE102312 were analyzed. Single-cell preprocessing was performed using the Seurat package, cell-cell communication was analyzed with CellChat, and HSC-associated co-- expression modules were identified via hdWGCNA. Pathway and candidate-compound analyses were conducted using Enrichr with the DSigDB database. Molecular docking and a 100 ns molecular dynamics simulation were performed with GROMACS 2025, and the function of ENO1 was preliminarily assessed in myeloid leukemia cell lines.
Results:
Ten major cell populations were identified, among which HSCs comprised 14,729 cells. Seven HSC co-expression modules were classified. Among 25 genes represented in the M1 hub-gene network, ENO1 was the only evaluated candidate that showed a distinct difference between CMML samples and healthy controls. ENO1 knockdown reduced the viability of HL-60 and MV-4-11 cells in a time-dependent manner. High ENO1 expression was associated with enrichment of cell-cycle, DNA damage- response, and energy-metabolism pathways. Naftopidil ranked first among the significant HL-60-associated candidates screened from the DSigDB. Molecular docking and 100 ns molecular dynamics simulation revealed that the ligand dynamically interacted with ENO1 following conformational rearrangement, although direct binding remains to be experimentally validated.
Discussion:
ENO1 emerged as an HSC-associated candidate gene with a potential role in supporting the metabolic and proliferative state of CMML-related hematopoietic cells. Naftopidil was computationally predicted as a candidate ENO1-binding compound, but its direct binding and therapeutic activity require experimental validation.
Conclusion:
These findings provide a hypothesis-generating basis for further investigation of ENO1 and naftopidil in CMML-specific models, primary samples, and in vivo studies.
