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Teixeira EB, Khayat AS, Assumpção PP, Casseb SM, Moreira-Nunes CA, Moreira FC. EndoGeneAnalyzer: A tool for selection and validation of reference genes. PLoS One 2024; 19:e0299993. [PMID: 38568963 PMCID: PMC10990236 DOI: 10.1371/journal.pone.0299993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024] Open
Abstract
The selection of proper reference genes is critical for accurate gene expression analysis in all fields of biological and medical research, mainly because there are many distinctions between different tissues and specimens. Given this variability, even in known classic reference genes, demands of a comprehensive analysis platform is needed to identify the most suitable genes for each study. For this purpose, we present an analysis tool for assisting in decision-making in the analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) data. EndoGeneAnalyzer, an open-source web tool for reference gene analysis in RT-qPCR studies, was used to compare the groups/conditions under investigation. This interactive application offers an easy-to-use interface that allows efficient exploration of datasets. Through statistical and stability analyses, EndoGeneAnalyzer assists in the select of the most appropriate reference gene or set of genes for each condition. It also allows researchers to identify and remove unwanted outliers. Moreover, EndoGeneAnalyzer provides a graphical interface to compare the evaluated groups, providing a visually informative differential analysis.
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Affiliation(s)
| | - André Salim Khayat
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Caroline Aquino Moreira-Nunes
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
- Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Department of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Clementino Fraga Group, Central Unity, Molecular Biology Laboratory, Fortaleza, CE, Brazil
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Wang Y, Liu Q, Liang S, Yao M, Zheng H, Hu D, Wang Y. Genetically predicted telomere length and the risk of 11 hematological diseases: a Mendelian randomization study. Aging (Albany NY) 2024; 16:4270-4281. [PMID: 38393686 DOI: 10.18632/aging.205583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
OBJECTIVE Previous studies have demonstrated that various hematologic diseases (HDs) induce alterations in telomere length (TL). The aim of this study is to investigate whether genetically predicted changes in TL have an impact on the risk of developing HDs. METHODS GWAS data for TL and 11 HDs were extracted from the database. The R software package "TwoSampleMR" was employed to conduct a two-sample Mendelian randomization (MR) analysis, in order to estimate the influence of TL changes on the risk of developing the 11 HDs. RESULTS We examined the effect of TL changes on the risk of developing the 11 HDs. The IVW results revealed a significant causal association between genetically predicted longer TL and the risk of developing acute lymphocytic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MANTLE), and hodgkin lymphoma (HODGKIN). However, there was no significant causal relationship observed between TL changes and the risk of developing chronic myeloid leukemia (CML), diffuse large b-cell lymphoma (DLBCL), marginal zone b-cell lymphoma (MARGINAL), follicular lymphoma (FOLLICULAR), monocytic leukemia (MONOCYTIC), and mature T/NK-cell lymphomas (TNK). CONCLUSIONS The MR analysis revealed a positive association between genetically predicted longer TL and an increased risk of developing ALL, AML, CLL, MANTLE, and HODGKIN. This study further supports the notion that cells with longer TL have greater proliferative and mutational potential, leading to an increased risk of certain HDs.
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Affiliation(s)
- Yimin Wang
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qi Liu
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shibing Liang
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Minghao Yao
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Huimin Zheng
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Dongqing Hu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yifei Wang
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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da Mota THA, Camargo R, Biojone ER, Guimarães AFR, Pittella-Silva F, de Oliveira DM. The Relevance of Telomerase and Telomere-Associated Proteins in B-Acute Lymphoblastic Leukemia. Genes (Basel) 2023; 14:genes14030691. [PMID: 36980962 PMCID: PMC10048576 DOI: 10.3390/genes14030691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/04/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Telomeres and telomerase are closely linked to uncontrolled cellular proliferation, immortalization and carcinogenesis. Telomerase has been largely studied in the context of cancer, including leukemias. Deregulation of human telomerase gene hTERT is a well-established step in leukemia development. B-acute lymphoblastic leukemia (B-ALL) recovery rates exceed 90% in children; however, the relapse rate is around 20% among treated patients, and 10% of these are still incurable. This review highlights the biological and clinical relevance of telomerase for B-ALL and the implications of its canonical and non-canonical action on signaling pathways in the context of disease and treatment. The physiological role of telomerase in lymphocytes makes the study of its biomarker potential a great challenge. Nevertheless, many works have demonstrated that high telomerase activity or hTERT expression, as well as short telomeres, correlate with poor prognosis in B-ALL. Telomerase and related proteins have been proven to be promising pharmacological targets. Likewise, combined therapy with telomerase inhibitors may turn out to be an alternative strategy for B-ALL.
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Affiliation(s)
- Tales Henrique Andrade da Mota
- Laboratory of Molecular Pathology of Cancer, University of Brasilia, Brasilia 70910-900, Brazil
- Laboratory of Molecular Analysis, Faculty of Ceilândia, University of Brasilia, Brasilia 72220-275, Brazil
- Correspondence:
| | - Ricardo Camargo
- Brasília Children’s Hospital José Alencar, Brasilia 70684-831, Brazil
| | | | - Ana Flávia Reis Guimarães
- Laboratory of Molecular Analysis, Faculty of Ceilândia, University of Brasilia, Brasilia 72220-275, Brazil
| | - Fabio Pittella-Silva
- Laboratory of Molecular Pathology of Cancer, University of Brasilia, Brasilia 70910-900, Brazil
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Gadelha RB, Machado CB, Pessoa FMCDP, Pantoja LDC, Barreto IV, Ribeiro RM, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira-Nunes CA. The Role of WRAP53 in Cell Homeostasis and Carcinogenesis Onset. Curr Issues Mol Biol 2022; 44:5498-5515. [PMID: 36354684 PMCID: PMC9688736 DOI: 10.3390/cimb44110372] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/30/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2023] Open
Abstract
The WD repeat containing antisense to TP53 (WRAP53) gene codifies an antisense transcript for tumor protein p53 (TP53), stabilization (WRAP53α), and a functional protein (WRAP53β, WDR79, or TCAB1). The WRAP53β protein functions as a scaffolding protein that is important for telomerase localization, telomere assembly, Cajal body integrity, and DNA double-strand break repair. WRAP53β is one of many proteins known for containing WD40 domains, which are responsible for mediating a variety of cell interactions. Currently, WRAP53 overexpression is considered a biomarker for a diverse subset of cancer types, and in this study, we describe what is known about WRAP53β's multiple interactions in cell protein trafficking, Cajal body formation, and DNA double-strand break repair and its current perspectives as a biomarker for cancer.
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Affiliation(s)
- Renan Brito Gadelha
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Caio Bezerra Machado
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Flávia Melo Cunha de Pinho Pessoa
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Laudreísa da Costa Pantoja
- Department of Pediatrics, Octávio Lobo Children’s Hospital, Belém 60430-275, PA, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
| | - Igor Valentim Barreto
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | | | - Manoel Odorico de Moraes Filho
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Maria Elisabete Amaral de Moraes
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
| | - Caroline Aquino Moreira-Nunes
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
- Northeast Biotechnology Network (RENORBIO), Itaperi Campus, Ceará State University, Fortaleza 60740-903, CE, Brazil
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段 一, 文 飞. Recent research on the association between signal transducer and activator of transcription 5 and childhood acute lymphoblastic leukemia. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:942-947. [PMID: 36036135 PMCID: PMC9425862 DOI: 10.7499/j.issn.1008-8830.2203117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Signal transducer and activator of transcription 5 (STAT5) can be involved in the processes such as cell proliferation, differentiation, apoptosis, and hematopoiesis, and its dysregulation is closely associated with the development and progression of malignant tumors including leukemia and may affect the treatment outcome and prognosis of pediatric patients. Identification of STAT5 can facilitate targeted therapy to improve the response rate of children with acute lymphoblastic leukemia. This article reviews the impact of STAT5 on the development/progression, targeted therapy strategies and the prognosis of childhood acute lymphoblastic leukemia.
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