1
|
Yao F, Zhao C, Zhong F, Qin T, Li S, Liu J, Huang B, Wang X. Bioinformatics analysis and identification of hub genes and immune-related molecular mechanisms in chronic myeloid leukemia. PeerJ 2022; 10:e12616. [PMID: 35111390 PMCID: PMC8781323 DOI: 10.7717/peerj.12616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/18/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Chronic myeloid leukemia (CML) is a malignant hyperplastic tumor of the bone marrow originating from pluripotent hematopoietic stem cells. The advent of tyrosine kinase inhibitors (TKIs) has greatly improved the survival rate of patients with CML. However, TKI-resistance leads to the disease recurrence and progression. This study aimed to identify immune-related genes (IRGs) associated with CML progression. METHODS We extracted the gene's expression profiles from the Gene Expression Omnibus (GEO). Bioinformatics analysis was used to determine the differentially expressed IRGs of CML and normal peripheral blood mononuclear cells (PBMCs). Functional enrichment and gene set enrichment analysis (GSEA) were used to explore its potential mechanism. Hub genes were identified using Molecular Complex Detection (MCODE) and the CytoHubba plugin. The hub genes' diagnostic value was evaluated using the receiver operating characteristic (ROC). The relative proportions of infiltrating immune cells in each CML sample were evaluated using CIBERSORT. Quantitative real-time PCR (RT-qPCR) was used to validate the hub gene expression in clinical samples. RESULTS A total of 31 differentially expressed IRGs were identified. GO analyses revealed that the modules were typically enriched in the receptor ligand activity, cytokine activity, and endopeptidase activity. KEGG enrichment analysis of IRGs revealed that CML involved Th17 cell differentiation, the NF-kappa B signaling pathway, and cytokine-cytokine receptor interaction. A total of 10 hub genes were selected using the PPI network. GSEA showed that these hub genes were related to the gamma-interferon immune response, inflammatory response, and allograft rejection. ROC curve analysis suggested that six hub genes may be potential biomarkers for CML diagnosis. Further analysis indicated that immune cells were associated with the pathogenesis of CML. The RT-qPCR results showed that proteinase 3 (PRTN3), cathepsin G (CTSG), matrix metalloproteinase 9 (MMP9), resistin (RETN), eosinophil derived neurotoxin (RNase2), eosinophil cationic protein (ECP, RNase3) were significantly elevated in CML patients' PBMCs compared with healthy controls. CONCLUSION These results improved our understanding of the functional characteristics and immune-related molecular mechanisms involved in CML progression and provided potential diagnostic biomarkers and therapeutic targets.
Collapse
|
2
|
Depreter B, De Moerloose B, Vandepoele K, Uyttebroeck A, Van Damme A, Terras E, Denys B, Dedeken L, Dresse MF, Van der Werff Ten Bosch J, Hofmans M, Philippé J, Lammens T. Deciphering molecular heterogeneity in pediatric AML using a cancer vs. normal transcriptomic approach. Pediatr Res 2021; 89:1695-1705. [PMID: 33069162 DOI: 10.1038/s41390-020-01199-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/30/2020] [Accepted: 09/25/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Still 30-40% of pediatric acute myeloid leukemia (pedAML) patients relapse. Delineation of the transcriptomic profile of leukemic subpopulations could aid in a better understanding of molecular biology and provide novel biomarkers. METHODS Using microarray profiling and quantitative PCR validation, transcript expression was measured in leukemic stem cells (LSC, n = 24) and leukemic blasts (L-blast, n = 25) from pedAML patients in comparison to hematopoietic stem cells (HSCs, n = 19) and control myeloblasts (C-blast, n = 20) sorted from healthy subjects. Gene set enrichment analysis was performed to identify relevant gene set enrichment signatures, and functional protein associations were identified by STRING analysis. RESULTS Highly significantly overexpressed genes in LSC and L-blast were identified with a vast majority not studied in AML. CDKN1A, CFP, and CFD (LSC) and HOMER3, CTSA, and GADD45B (L-blast) represent potentially interesting biomarkers and therapeutic targets. Eleven LSC downregulated targets were identified that potentially qualify as tumor suppressor genes, with MYCT1, PBX1, and PTPRD of highest interest. Inflammatory and immune dysregulation appeared to be perturbed biological networks in LSC, whereas dysregulated metabolic profiles were observed in L-blast. CONCLUSION Our study illustrates the power of taking into account cell population heterogeneity and reveals novel targets eligible for functional evaluation and therapy in pedAML. IMPACT Novel transcriptional targets were discovered showing a significant differential expression in LSCs and blasts from pedAML patients compared to their normal counterparts from healthy controls. Deregulated pathways, including immune and metabolic dysregulation, were addressed for the first time in children, offering a deeper understanding of the molecular pathogenesis. These novel targets have the potential of acting as biomarkers for risk stratification, follow-up, and targeted therapy. Multiple LSC-downregulated targets endow tumor suppressor roles in other cancer entities, and further investigation whether hypomethylating therapy could result into LSC eradication in pedAML is warranted.
Collapse
Affiliation(s)
- Barbara Depreter
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.
| | - Barbara De Moerloose
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Karl Vandepoele
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Anne Uyttebroeck
- Department of Pediatrics, University Hospital Gasthuisberg, Leuven, Belgium
| | - An Van Damme
- Department of Pediatric Hematology Oncology, University Hospital Saint-Luc, Brussels, Belgium
| | - Eva Terras
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara Denys
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Laurence Dedeken
- Department of Pediatric Hematology Oncology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | | | | | - Mattias Hofmans
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Jan Philippé
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tim Lammens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| |
Collapse
|
3
|
Citalan-Madrid AF, Cabral-Pacheco GA, Martinez-de-Villarreal LE, Villarreal-Martinez L, Ibarra-Ramirez M, Garza-Veloz I, Cardenas-Vargas E, Marino-Martinez I, Martinez-Fierro ML. Proteomic tools and new insights for the study of B-cell precursor acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2019; 24:637-650. [PMID: 31514680 DOI: 10.1080/16078454.2019.1664127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a hematological malignancy of immature B-cell precursors, affecting children more often than adults. The etiology of BCP-ALL is still unknown, but environmental factors, sex, race or ethnicity, and genomic alterations influence the development of the disease. Tools based on protein detection, such as flow cytometry, mass spectrometry, mass cytometry and reverse phase protein array, represent an opportunity to investigate BCP-ALL pathogenesis and to identify new biomarkers of disease. This review aims to document the recent advancements with respect to applications of proteomic technologies to study mechanisms of leukemogenesis, how this information could be used in the discovery of biological targets, and finally we describe the challenges of application of proteomic tools for the approach of BCP-ALL.
Collapse
Affiliation(s)
- Alí F Citalan-Madrid
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico
| | - Griselda A Cabral-Pacheco
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico
| | | | - Laura Villarreal-Martinez
- Hematology Service, Hospital Universitario 'Dr. José Eleuterio González', Universidad Autonoma de Nuevo Leon , Monterrey , Mexico
| | - Marisol Ibarra-Ramirez
- Departamento de Genetica, Facultad de Medicina, Universidad Autónoma de Nuevo Leon , Monterrey , Mexico
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico
| | - Edith Cardenas-Vargas
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Hospital General Zacatecas 'Luz González Cosío' , Zacatecas , Mexico
| | - Ivan Marino-Martinez
- Departamento de Patologia, Facultad de Medicina, Universidad Autonoma de Nuevo Leon , Monterrey , Mexico
| | - Margarita L Martinez-Fierro
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico
| |
Collapse
|