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Nascimento A, Valadão de Souza DR, Pessôa R, Pietrobon AJ, Nukui Y, Pereira J, Casseb J, Penalva de Oliveira AC, Loureiro P, da Silva Duarte AJ, Clissa PB, Sanabani SS. Global expression of noncoding RNome reveals dysregulation of small RNAs in patients with HTLV-1-associated adult T-cell leukemia: a pilot study. Infect Agent Cancer 2021; 16:4. [PMID: 33422115 PMCID: PMC7797118 DOI: 10.1186/s13027-020-00343-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/29/2020] [Indexed: 12/19/2022] Open
Abstract
Background Adult T cell lymphoma/leukemia (ATLL) is a peripheral T-cell neoplasm caused by human T-cell lymphotropic virus-1 (HTLV-1). Small RNAs (sRNAs), including microRNAs (miRNAs), play a pivotal role in the initiation and development of hematological malignancies and may represent potential therapeutic target molecules. However, little is known about how these molecules impact the pathogenesis of ATLL. In this study, we aimed to identify sRNA expression signatures associated with ATLL and to investigate their potential implication in the pathophysiology of the disease. Methods Small-RNAseq analysis was performed in peripheral blood mononuclear cells from HTLV-1- associated ATLL (n = 10) in comparison to asymptomatic carriers (n = 8) and healthy controls (n = 5). Sequencing was carried out using the Illumina MiSeq platform, and the deregulation of selected miRNAs was validated by real-time PCR. Pathway analyses of most deregulated miRNA were performed and their global profiling was combined with transcriptome data in ATLL. Results The sequencing identified specific sRNAs signatures associated with ATLL patients that target pathways relevant in ATLL, such as the transforming growth factor-(βTGF-β), Wnt, p53, apoptosis, and mitogen-activated protein kinase (MAPK) signaling cascades. Network analysis revealed several miRNAs regulating highly connected genes within the ATLL transcriptome. miR-451-3p was the most downregulated miRNA in active patients. Conclusions Our findings shed light on the expression of specific sRNAs in HTLV-1 associated ATLL, which may represent promising candidates as biomarkers that help monitor the disease activity. Supplementary Information The online version contains supplementary material available at 10.1186/s13027-020-00343-2.
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Affiliation(s)
- Andrezza Nascimento
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Instituto de Medicina Tropical de São Paulo, Faculty of Medicine, University of São Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3° andar, São Paulo, 05403 000, Brazil
| | - Daniela Raguer Valadão de Souza
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Instituto de Medicina Tropical de São Paulo, Faculty of Medicine, University of São Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3° andar, São Paulo, 05403 000, Brazil
| | - Rodrigo Pessôa
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Instituto de Medicina Tropical de São Paulo, Faculty of Medicine, University of São Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3° andar, São Paulo, 05403 000, Brazil
| | - Anna Julia Pietrobon
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Instituto de Medicina Tropical de São Paulo, Faculty of Medicine, University of São Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3° andar, São Paulo, 05403 000, Brazil
| | - Youko Nukui
- Department of Hematology, Faculty of Medicine, University of São Paulo, São Paulo, 05403 000, Brazil
| | - Juliana Pereira
- Department of Hematology, Faculty of Medicine, University of São Paulo, São Paulo, 05403 000, Brazil
| | - Jorge Casseb
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Instituto de Medicina Tropical de São Paulo, Faculty of Medicine, University of São Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3° andar, São Paulo, 05403 000, Brazil
| | | | - Paula Loureiro
- Pernambuco State Center of Hematology and Hemotherapy, Recife, Pernambuco, CEP 52011900, Brazil
| | - Alberto José da Silva Duarte
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology, Instituto de Medicina Tropical de São Paulo, Faculty of Medicine, University of São Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3° andar, São Paulo, 05403 000, Brazil
| | | | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation Unit 03, Clinics Hospital, Faculty of Medicine, University of São Paulo, São Paulo, 05403 000, Brazil.
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Wu S, Wu F, Jiang Z. Identification of hub genes, key miRNAs and potential molecular mechanisms of colorectal cancer. Oncol Rep 2017; 38:2043-2050. [PMID: 28902367 PMCID: PMC5652954 DOI: 10.3892/or.2017.5930] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/17/2017] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is the most common cancer of the digestive system. The aim of the present study was to identify the potential biomarkers and uncover the underlying mechanisms. The gene and miRNA expression profiles were obtained from GEO database. The differentially expressed genes (DEGs) and miRNAs (DE miRNAs) were identified by GEO2R. The Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by KOBAS 3.0. The protein-protein interaction (PPI) network and miRNA-gene network were constructed by Cytoscape software. Then, the identified genes were verified by quantitative real-time PCR in both CRC tissue samples and cell lines. A total of 600 upregulated DEGs, 283 downregulated DEGs, 13 upregulated DE miRNAs and 7 downregulated DE miRNAs were identified. GO analysis results showed that upregulated DEGs were significantly enriched in binding, organelle and cellular process. Downregulated DEGs were enriched in binding, extracellular region and chemical homeostasis. KEGG analysis showed that the DEGs were mostly enriched in cell cycle and pathways in cancer. A total of eight genes were identified as biomarkers, including CAD, ITGA2, E2F3, BCL2, PRKACB, IGF1, SGK1 and NR3C1. Experimental validation showed that seven of the eight identified genes had the same expression trend as predicted, except for ITGA2. Besides, hsa-miR-552 and hsa-miR-30a were identified as key miRNAs. The present study provides a series of biomarkers and mechanisms for the diagnosis and therapy of CRC. We also prove that although bioinformatics analysis is a wonderful approach, experiment validation is necessary.
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Affiliation(s)
- Shasha Wu
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Feixiang Wu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Zheng Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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