1
|
Huang F, Ming C, Jiang Y, Li C, Tan C. Construction and validation of key genes-related prognosis model in children with acute myeloid leukaemia. Int J Lab Hematol 2024; 46:678-686. [PMID: 38600718 DOI: 10.1111/ijlh.14272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/24/2024] [Indexed: 04/12/2024]
Abstract
INTRODUCTION To identify the differentially expressed genes of acute myeloid leukaemia (AML) and construct and verify a survival prognosis model combined with patient survival information. METHODS The TARGET database was searched to identify differentially expressed peripheral blood genes in children with AML and healthy children. A gene set functional analysis and pathway analysis were performed using gene ontology and the KEGG pathway. A prognostic model for children with AML was constructed using univariate Cox, LASSO Cox regression and multivariate Cox regression analyses. Time-dependent receiver operating characteristic (ROC) curves were adopted to assess the predictive capacity of the prognostic models. RESULTS In total, 1640 differentially expressed genes were screened (1119 upregulated and 521 downregulated genes). The differentially expressed genes were mainly involved in nutrient metabolism and cytochrome P450 metabolism. Six key genes related to the prognosis of AML, FAM157A, GPR78, IRX5, RP4-800G7.1, RP11-179H18.5 and RP11-61N20.3, were identified. Kaplan-Meier curves indicated that 3-year and 5-year overall survival was significantly higher in the low-risk group than in the high-risk group. The area under the ROC curve was 0.722. At different stages of AML, FAM157A and RP4-800G7.1 exhibited significant differences in expression. The expression levels of FAM157A were significantly decreased in AML, whereas the expression levels of GPR78, IRX5, RP4-800G7.1, RP11-179H18.5 and RP11-61N20.3 were significantly increased in AML. CONCLUSION A prognosis-related gene model of AML was successfully constructed, and the expression levels of the model genes varied with AML stage.
Collapse
Affiliation(s)
- Fan Huang
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chuan Ming
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yuqian Jiang
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chenli Li
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Cheng Tan
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
2
|
Comparison of high-resolution melting analysis with direct sequencing for detection of FLT3-TKD, FLT3-ITD and WT1 mutations in acute myeloid leukemia. Cancer Treat Res Commun 2021; 28:100432. [PMID: 34303121 DOI: 10.1016/j.ctarc.2021.100432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/28/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Acute Myeloid Leukemia (AML) is a group of hematologic diseases characterized by a variety of clinically important genetic alterations. Genetic mutations affecting the FMS-like receptor tyrosine kinase-3 (FLT3) and Wilm's tumor (WT-1) genes are associated with poor prognosis in AML. In this work, efficiency of HRM method for detection of FLT3-ITD, FLT3-TKD, and WT-1 mutations was assessed in comparison with direct sequencing. METHOD A total of 58 formalin-fixed, paraffin-embedded BM biopsy specimens of AML patients were analyzed. Mutation detection was performed by HRM method and the results were consequently compared with direct sequencing RESULTS: FLT3 and WT-1 mutations were detected in 21 (36.2%) and 3 (5.17%) samples, respectively. Among all FLT3 mutations, 10 (17.2%) and 11 (18.2%) samples were harboring the FLT3-ITD and-TKD gene mutations, respectively. Frequency of the FLT3-ITD was not statistically different in females (51%) and males (49%). Also, FLT3-TKD was more common in males although the differences in gender distribution were not statistically significant (P = 0.721 and P = 0.626, respectively). CONCLUSIONS Regarded as the desirable characteristic, the present study is generally distinguished by the similar previous ones due to assessing the FFPE BM tissue from the perspective of the type of assessed sample. This discrepancy between our results and those in prior studies may be due to the disparity of the studied population size, adopted methods as well as the sample type. In this survey, regarding to low amount of extracted DNA from the paraffinized samples, the HRM method was efficient in determining the mentioned mutations.
Collapse
|
3
|
El-Gamal RAER, Hashem AES, Habashy DM, Abou Elwafa MAZ, Boshnak NH. Flow cytometry in detection of Nucleophosmin 1 mutation in acute myeloid leukemia patients: A reproducible tertiary hospital experience. Int J Lab Hematol 2020; 43:68-75. [PMID: 32856429 DOI: 10.1111/ijlh.13317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/18/2020] [Accepted: 07/29/2020] [Indexed: 12/08/2022]
Abstract
INTRODUCTION Nucleophosmin 1 (NPM1) mutation is one of the most frequent gene mutations in adult acute myeloid leukemia (AML), being detected in 35% of all cases and in up to 60% of patients with normal karyotype AML. AML with mutated NPM1 has distinct pathology, immunophenotyping, and confirmed favorable prognostic significance. Hence, AML with mutated NPM1 is a separate entity in the revised 2016 World Health Organization classification. This study aimed to evaluate the use of a reproducible flow cytometry approach in the assay of mutant NPM1 protein in AML patients and to correlate flow cytometric results with the NPM1 gene mutation. METHODS Eighty-nine newly diagnosed AML patients were evaluated for the expression of mutant NPM1 using flow cytometry and for the presence of NPM1 exon 12 mutations using high-resolution melting polymerase chain reaction (HRM PCR). RESULTS The NPM1 mutation was found in 35 (39.3%) patients by HRM PCR. These patients showed a significantly higher level of percentage of positive-stained cells (% positive cells) and normalized median fluorescence intensity (MFI) for mutant NPM1 by flow cytometry than the negative mutation group. CONCLUSION Flow cytometric detection of mutant NPM1 offers a possible tool to indicate NPM1 mutational status.
Collapse
Affiliation(s)
| | - Azza El-Sayed Hashem
- Department of Clinical Pathology, Hematology Unit, Ain Shams University, Cairo, Egypt
| | - Deena Mohamed Habashy
- Department of Clinical Pathology, Hematology Unit, Ain Shams University, Cairo, Egypt
| | | | - Noha Hussein Boshnak
- Department of Clinical Pathology, Hematology Unit, Ain Shams University, Cairo, Egypt
| |
Collapse
|
4
|
Ariza MJ, Pérez-López C, Almagro F, Sánchez-Tévar AM, Muñiz-Grijalvo O, Álvarez-Sala Walter LA, Rioja J, Sánchez-Chaparro MÁ, Valdivielso P. Genetic variants in the LPL and GPIHBP1 genes, in patients with severe hypertriglyceridaemia, detected with high resolution melting analysis. Clin Chim Acta 2019; 500:163-171. [PMID: 31669931 DOI: 10.1016/j.cca.2019.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/02/2019] [Accepted: 10/14/2019] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Pathogenic variants in lipoprotein lipase (LPL) and glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 (GPIHBP1) have been described in patients with severe hypertriglyceridaemia. We aimed to optimise high resolution melting (HRM) assays to detect the presence of functional variants in these genes. METHODS One hundred and sixteen patients with severe hypertriglyceridaemia were studied. HRM assays were optimised to scan exons and splice junctions in LPL and GPIHBP1. Sanger sequencing was the reference method. Next-generation-sequencing (NGS) was performed in five patients, including one with Familial Chylomicronemia syndrome (FCS). RESULTS We identified 15 different variants in LPL and 6 in GPIHBP1. The variants revealed with NGS were also detected with HRM, including a rare premature stop codon in LPL (p.Trp421*) and two LPL pathogenic variants in the patient with FCS (p.His80Arg + p.Gly215Glu). Having multiple functional variant alleles was associated with pancreatitis onset at younger ages and higher baseline triglycerides. CONCLUSIONS Our HRM assays detected the presence of functional gene variants that were confirmed with Sanger and NGS sequencing. The presence of multiple functional variant alleles was associated with differences in the clinical profile. Therefore, these assays represent a reliable, cost-effective tool that can be used to complement the NGS approach for gene scanning.
Collapse
Affiliation(s)
- María José Ariza
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain.
| | - Carmen Pérez-López
- Internal Medicine Unit, University Hospital Virgen de la Victoria, Campus de Teatinos, S/N, 29010 Málaga, Spain
| | - Fátima Almagro
- Lipids Unit, Internal Medicine, University Hospital Donostia, San Sebastian, Begiristain Doktorea Pasealekua, 107-115, 20014 Donostia, Gipuzkoa, Spain
| | - Ana María Sánchez-Tévar
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain
| | - Ovidio Muñiz-Grijalvo
- UCERV-UCAMI, Internal Medicine Department, University Hospital Virgen del Rocío, Av. Manuel Siurot, S/n, 41013 Sevilla, Spain
| | - Luis Antonio Álvarez-Sala Walter
- Lipids Unit, Internal Medicine, Hospital General Universitario Gregorio Marañón, IiSGM, Calle del Dr. Esquerdo, 46, 28007 Madrid, Spain; Department of Medicine, School of Medicine, Universidad Complutense, Av. Séneca, 2, 28040 Madrid, Spain
| | - José Rioja
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain
| | - Miguel Ángel Sánchez-Chaparro
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain; Internal Medicine Unit, University Hospital Virgen de la Victoria, Campus de Teatinos, S/N, 29010 Málaga, Spain
| | - Pedro Valdivielso
- Department of Medicine and Dermatology, Lipids and Atherosclerosis Laboratory, Centro de Investigaciones Médico Sanitarias (CIMES), Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, C/Marqués de Beccaria n° 3, 29010 Málaga, Spain; Internal Medicine Unit, University Hospital Virgen de la Victoria, Campus de Teatinos, S/N, 29010 Málaga, Spain
| |
Collapse
|
5
|
Prognostic significance of FLT3-ITD in pediatric acute myeloid leukemia: a meta-analysis of cohort studies. Mol Cell Biochem 2016; 420:121-8. [PMID: 27435859 DOI: 10.1007/s11010-016-2775-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/09/2016] [Indexed: 01/20/2023]
Abstract
The purpose of the study was to assess the effect of the internal tandem duplication in FMS-like tyrosine kinase 3 (FLT3-ITD) on the outcome in pediatric acute myeloid leukemia (AML) patients. We identified eligible studies from several databases including PubMed, Embase, and Cochrane Central Register of Controlled Trials (CENTRAL) (from January 1995 to July 2015). Ten studies of 1661 pediatric patients with AML were included in exploring the relationship between the FLT3-ITD and overall survival (OS)/event free survival (EFS). Pediatric patients with AML with FLT3-ITD had worse OS [HR = 2.19 (1.60-3.01)]/EFS [HR = 1.70 (1.37-2.11)] than those patients without FLT3-ITD. Furthermore, FLT3-ITD had unfavorable effect on OS/EFS in the subgroups of NOS, uni/multivariate model, number of patients, the length of following-up, and patient source. The findings of this meta-analysis indicated that FLT3-ITD had negative impact on pediatric patients with AML.
Collapse
|
6
|
Nagy A, Černíková L, Vitásková E, Křivda V, Dán Á, Dirbáková Z, Jiřincová H, Procházka B, Sedlák K, Havlíčková M. MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay. PLoS One 2016; 11:e0151204. [PMID: 27031831 PMCID: PMC4816343 DOI: 10.1371/journal.pone.0151204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/23/2016] [Indexed: 12/05/2022] Open
Abstract
In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence.
Collapse
Affiliation(s)
- Alexander Nagy
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
- * E-mail:
| | - Lenka Černíková
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
| | - Eliška Vitásková
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
| | - Vlastimil Křivda
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
- Department of Virology and Serology, State Veterinary Institute Prague, Prague, Czech Republic
| | - Ádám Dán
- National Food Chain Safety Office, Veterinary Diagnostic Directorate, Molecular Biology Laboratory, Budapest, Hungary
| | - Zuzana Dirbáková
- Department of Virology, State Veterinary Institute Zvolen, Zvolen, Slovak Republic
| | - Helena Jiřincová
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
| | - Bohumír Procházka
- Department of Informatics and Biostatistics, National Institute of Public Health, Prague, Czech Republic
| | - Kamil Sedlák
- Department of Virology and Serology, State Veterinary Institute Prague, Prague, Czech Republic
| | - Martina Havlíčková
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
| |
Collapse
|
7
|
Berenstein R. Class III Receptor Tyrosine Kinases in Acute Leukemia - Biological Functions and Modern Laboratory Analysis. Biomark Insights 2015; 10:1-14. [PMID: 26309392 PMCID: PMC4527365 DOI: 10.4137/bmi.s22433] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease caused by deregulation of multiple signaling pathways. Mutations in class III receptor tyrosine kinases (RTKs) have been implicated in alteration of cell signals concerning the growth and differentiation of leukemic cells. Point mutations, insertions, or deletions of RTKs as well as chromosomal translocations induce constitutive activation of the receptor, leading to uncontrolled proliferation of undifferentiated myeloid blasts. Aberrations can occur in all domains of RTKs causing either the ligand-independent activation or mimicking the activated conformation. The World Health Organization recommended including RTK mutations in the AML classification since their detection in routine laboratory diagnostics is a major factor for prognostic stratification of patients. Polymerase chain reaction (PCR)-based methods are well-validated for the detection of fms-related tyrosine kinase 3 (FLT3) mutations and can easily be applied for other RTKs. However, when methodological limitations are reached, accessory techniques can be applied. For a higher resolution and more quantitative approach compared to agarose gel electrophoresis, PCR fragments can be separated by capillary electrophoresis. Furthermore, high-resolution melting and denaturing high-pressure liquid chromatography are reliable presequencing screening methods that reduce the sample amount for Sanger sequencing. Because traditional DNA sequencing is time-consuming, next-generation sequencing (NGS) is an innovative modern possibility to analyze a high amount of samples simultaneously in a short period of time. At present, standardized procedures for NGS are not established, but when this barrier is resolved, it will provide a new platform for rapid and reliable laboratory diagnostic of RTK mutations in patients with AML. In this article, the biological and physiological role of RTK mutations in AML as well as possible laboratory methods for their detection will be reviewed.
Collapse
Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|