1
|
de Miranda FS, Slaibi-Filho J, Calasans dos Santos G, Carmo NT, Kaneto CM, Borin TF, Luiz WB, Gastalho Campos LC. MicroRNA as a promising molecular biomarker in the diagnosis of breast cancer. Front Mol Biosci 2024; 11:1337706. [PMID: 38813102 PMCID: PMC11134088 DOI: 10.3389/fmolb.2024.1337706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/14/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction: Breast cancer represents the most prevalent malignancy among women. Recent advancements in translational research have focused on the identification of novel biomarkers capable of providing valuable insights into patient outcomes. Furthermore, comprehensive investigations aimed at discovering novel miRNAs, unraveling their biological functions, and deciphering their target genes have significantly contributed to our understanding of the roles miRNAs play in tumorigenesis. Consequently, these investigations have facilitated the way for the development of miRNA-based approaches for breast cancer prognosis, diagnosis, and treatment. However, conducting a more extensive array of studies, particularly among diverse ethnic groups, is imperative to expand the scope of research and validate the significance of miRNAs. This study aimed to assess the expression patterns of circulating miRNAs in plasma as a prospective biomarker for breast cancer patients within a population primarily consisting of individuals from Black, Indigenous, and People of Color (BIPOC) communities. Methods: We evaluated 49 patients with breast cancer compared to 44 healthy women. Results and discussion: All miRNAs analyzed in the plasma of patients with breast cancer were downregulated. ROC curve analysis of miR-21 (AUC = 0.798, 95% CI: 0.682-0.914, p <0.0001), miR-1 (AUC = 0.742, 95% CI: 0.576-0.909, p = 0.004), miR-16 (AUC = 0.721, 95% CI: 0.581-0.861, p = 0.002) and miR-195 (AUC = 0.672, 95% CI: 0.553-0.792, p = 0.004) showed better diagnostic accuracy in discrimination of breast cancer patients in comparison with healthy women. miR-210, miR-21 showed the highest specificities values (97.3%, 94.1%, respectively). Following, miR-10b and miR-195 showed the highest sensitivity values (89.3%, and 77.8%, respectively). The panel with a combination of four miRNAs (miR-195 + miR-210 + miR-21 + miR-16) had an AUC of 0.898 (0.765-0.970), a sensitivity of 71.4%, and a specificity of 100.0%. Collectively, our results highlight the miRNA combination in panels drastically improves the results and showed high accuracy for the diagnosis of breast cancer displaying good sensitivity and specificity.
Collapse
Affiliation(s)
- Felipe Silva de Miranda
- Department of Biological Science, State University of Santa Cruz, Ilhéus, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - José Slaibi-Filho
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
- Department of Health Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Gabriel Calasans dos Santos
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
- Department of Health Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Nathalia Teixeira Carmo
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
- Department of Health Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Carla Martins Kaneto
- Department of Biological Science, State University of Santa Cruz, Ilhéus, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Thaiz Ferraz Borin
- Laboratory of Tumor Angiogenesis, Georgia Cancer Center, Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA, United States
| | - Wilson Barros Luiz
- Department of Biological Science, State University of Santa Cruz, Ilhéus, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Luciene Cristina Gastalho Campos
- Department of Biological Science, State University of Santa Cruz, Ilhéus, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus, Bahia, Brazil
- Department of Health Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| |
Collapse
|
2
|
Dong HQ, Hu XY, Liang SJ, Wang RS, Cheng P. Selection of reference genes in liproxstatin-1-treated K562 Leukemia cells via RT-qPCR and RNA sequencing. Mol Biol Rep 2024; 51:55. [PMID: 38165476 DOI: 10.1007/s11033-023-08912-5] [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: 09/15/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Reverse transcription quantitative polymerase chain reaction (RT-qPCR) can accurately detect relative gene expression levels in biological samples. However, widely used reference genes exhibit unstable expression under certain conditions. METHODS AND RESULTS Here, we compared the expression stability of eight reference genes (RPLP0, RPS18, RPL13, EEF1A1, β-actin, GAPDH, HPRT1, and TUBB) commonly used in liproxstatin-1 (Lip-1)-treated K562 cells using RNA-sequencing and RT-qPCR. The expression of EEF1A1, ACTB, GAPDH, HPRT1, and TUBB was considerably lower in cells treated with 20 μM Lip-1 than in the control, and GAPDH also showed significant downregulation in the 10 μM Lip-1 group. Meanwhile, when we used geNorm, NormFinder, and BestKeeper to compare expression stability, we found that GAPDH and HPRT1 were the most unstable reference genes among all those tested. Stability analysis yielded very similar results when geNorm or BestKeeper was used but not when NormFinder was used. Specifically, geNorm and BestKeeper identified RPL13 and RPLP0 as the most stable genes under 20 μM Lip-1 treatment, whereas RPL13, EEF1A1, and TUBB were the most stable under 10 μM Lip-1 treatment. TUBB and EEF1A1 were the most stable genes in both treatment groups according to the results obtained using NormFinder. An assumed most stable gene was incorporated into each software to validate the accuracy. The results suggest that NormFinder is not an appropriate algorithm for this study. CONCLUSIONS Stable reference genes were recognized using geNorm and BestKeeper but not NormFinder. Overall, RPL13 and RPLP0 were the most stable reference genes under 20 μM Lip-1 treatment, whereas RPL13, EEF1A1, and TUBB were the most stable genes under 10 μM Lip-1 treatment.
Collapse
Affiliation(s)
- Hai-Qun Dong
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Xue-Ying Hu
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Shi-Jing Liang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Hematology, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Ren-Sheng Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
| | - Peng Cheng
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
- Key Laboratory of Hematology, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
| |
Collapse
|
3
|
Tang X, Qin Q, Xu W, Zhang X. Long Non-Coding RNA TUG1 Attenuates Insulin Resistance in Mice with Gestational Diabetes Mellitus via Regulation of the MicroRNA-328-3p/SREBP-2/ERK Axis. Diabetes Metab J 2023; 47:267-286. [PMID: 36653891 PMCID: PMC10040623 DOI: 10.4093/dmj.2021.0216] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/09/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been illustrated to contribute to the development of gestational diabetes mellitus (GDM). In the present study, we aimed to elucidate how lncRNA taurine upregulated gene 1 (TUG1) influences insulin resistance (IR) in a high-fat diet (HFD)-induced mouse model of GDM. METHODS We initially developed a mouse model of HFD-induced GDM, from which islet tissues were collected for RNA and protein extraction. Interactions among lncRNA TUG1/microRNA (miR)-328-3p/sterol regulatory element binding protein 2 (SREBP-2) were assessed by dual-luciferase reporter assay. Fasting blood glucose (FBG), fasting insulin (FINS), homeostasis model assessment of insulin resistance (HOMA-IR), HOMA pancreatic β-cell function (HOMA-β), insulin sensitivity index for oral glucose tolerance tests (ISOGTT) and insulinogenic index (IGI) levels in mouse serum were measured through conducting gain- and loss-of-function experiments. RESULTS Abundant expression of miR-328 and deficient expression of lncRNA TUG1 and SREBP-2 were characterized in the islet tissues of mice with HFD-induced GDM. LncRNA TUG1 competitively bound to miR-328-3p, which specifically targeted SREBP-2. Either depletion of miR-328-3p or restoration of lncRNA TUG1 and SREBP-2 reduced the FBG, FINS, HOMA-β, and HOMA-IR levels while increasing ISOGTT and IGI levels, promoting the expression of the extracellular signal-regulated kinase (ERK) signaling pathway-related genes, and inhibiting apoptosis of islet cells in GDM mice. Upregulation miR-328-3p reversed the alleviative effects of SREBP-2 and lncRNA TUG1 on IR. CONCLUSION Our study provides evidence that the lncRNA TUG1 may prevent IR following GDM through competitively binding to miR-328-3p and promoting the SREBP-2-mediated ERK signaling pathway inactivation.
Collapse
Affiliation(s)
- Xuwen Tang
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
| | - Qingxin Qin
- Department of Endocrinology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, China
| | - Wenjing Xu
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
| | - Xuezhen Zhang
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
4
|
Santos EDC, Melo GIV, Santana PVB, Quadros IGS, Yahouédéhou SCMA, da Guarda CC, Santiago RP, Fiuza LM, Carvalho SP, Adorno EV, Kaneto CM, Fonseca TCC, Goncalves MS, Aleluia MM. A Description of the Hemolytic Component in Sickle Leg Ulcer: The Role of Circulating miR-199a-5p, miR-144, and miR-126. Biomolecules 2022; 12:biom12020317. [PMID: 35204817 PMCID: PMC8869177 DOI: 10.3390/biom12020317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 12/04/2022] Open
Abstract
Sickle leg ulcers (SLU) are malleoli lesions with exuberant hemolytic pathophysiology. The microRNAs are potential genetic biomarkers for several pathologies. Thereby, we aimed to assess the expression of circulating miR-199a-5p, miR-144, and miR-126 in association with hemolytic biomarkers in SLU. This cross-sectional study included 69 patients with sickle cell disease, 52 patients without SLU (SLU-) and 17 patients with active SLU or previous history (SLU+). The results demonstrated elevated expression of circulating miR-199a-5p and miR-144 in SLU+ patients while miR-126 expression was reduced. Circulating miR-199a-5p and miR-144 were associated with hemolytic biomarkers such as LDH, indirect bilirubin, AST, GGT, iron, ferritin, RBC, hemoglobin, and NOm, in addition to association with impaired clinical profile of SLU. Furthermore, in silico analyses indicated interactions of miR-199a-5p with HIF1A, Ets-1, and TGFB2 genes, which are associated with vasculopathy and reduced NO. In contrast, miR-126 was associated with an attenuating clinical profile of SLU, in addition to not characterizing hemolysis. In summary, this study demonstrates, for the first time, that hemolytic mechanism in SLU can be characterized by circulating miR-199a-5p and miR-144. The circulating miR-126 may play a protective role in SLU. Thus, these microRNAs can support to establish prognosis and therapeutic strategy in SLU.
Collapse
Affiliation(s)
- Edvan do Carmo Santos
- Laboratório de Patologia Aplicada e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (E.d.C.S.); (G.I.V.M.); (P.V.B.S.); (C.M.K.)
| | - Gabriela Imbassahy Valentim Melo
- Laboratório de Patologia Aplicada e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (E.d.C.S.); (G.I.V.M.); (P.V.B.S.); (C.M.K.)
| | - Paulo Vinícius Bispo Santana
- Laboratório de Patologia Aplicada e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (E.d.C.S.); (G.I.V.M.); (P.V.B.S.); (C.M.K.)
| | | | - Sètondji Cocou Modeste Alexandre Yahouédéhou
- Laboratório de Investigação em Genética e Hematologia Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, BA, Brazil; (S.C.M.A.Y.); (C.C.d.G.); (R.P.S.); (L.M.F.); (S.P.C.); (M.S.G.)
| | - Caroline Conceição da Guarda
- Laboratório de Investigação em Genética e Hematologia Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, BA, Brazil; (S.C.M.A.Y.); (C.C.d.G.); (R.P.S.); (L.M.F.); (S.P.C.); (M.S.G.)
| | - Rayra Pereira Santiago
- Laboratório de Investigação em Genética e Hematologia Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, BA, Brazil; (S.C.M.A.Y.); (C.C.d.G.); (R.P.S.); (L.M.F.); (S.P.C.); (M.S.G.)
| | - Luciana Magalhães Fiuza
- Laboratório de Investigação em Genética e Hematologia Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, BA, Brazil; (S.C.M.A.Y.); (C.C.d.G.); (R.P.S.); (L.M.F.); (S.P.C.); (M.S.G.)
- Laboratório de Pesquisa em Anemias, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil;
| | - Suéllen Pinheiro Carvalho
- Laboratório de Investigação em Genética e Hematologia Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, BA, Brazil; (S.C.M.A.Y.); (C.C.d.G.); (R.P.S.); (L.M.F.); (S.P.C.); (M.S.G.)
- Laboratório de Pesquisa em Anemias, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil;
| | - Elisângela Vitória Adorno
- Laboratório de Pesquisa em Anemias, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil;
| | - Carla Martins Kaneto
- Laboratório de Patologia Aplicada e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (E.d.C.S.); (G.I.V.M.); (P.V.B.S.); (C.M.K.)
| | | | - Marilda Souza Goncalves
- Laboratório de Investigação em Genética e Hematologia Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, BA, Brazil; (S.C.M.A.Y.); (C.C.d.G.); (R.P.S.); (L.M.F.); (S.P.C.); (M.S.G.)
- Laboratório de Pesquisa em Anemias, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil;
| | - Milena Magalhães Aleluia
- Laboratório de Patologia Aplicada e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil; (E.d.C.S.); (G.I.V.M.); (P.V.B.S.); (C.M.K.)
- Correspondence: ; Tel.: +55-73-3680-5574
| |
Collapse
|
5
|
Gally TB, Aleluia MM, Borges GF, Kaneto CM. Circulating MicroRNAs as Novel Potential Diagnostic Biomarkers for Osteosarcoma: A Systematic Review. Biomolecules 2021; 11:biom11101432. [PMID: 34680065 PMCID: PMC8533382 DOI: 10.3390/biom11101432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 01/12/2023] Open
Abstract
Osteosarcoma (OS) is a fast-progressing bone tumor with high incidence in children and adolescents. The main diagnostic methods for OS are imaging exams and biopsies. In spite of the several resources available for detecting the disease, establishing an early diagnosis is still difficult, resulting in worse prognosis and lower survival rates for patients with OS. The identification of novel biomarkers would be helpful, and recently, circulating microRNAs (miRNAs) have been pointed to as possible non-invasive biomarkers. In order to assess the effectiveness of miRNA research, we performed a systematic review to assess the potential role of circulating miRNAs as biomarkers for OS diagnosis. We performed a search in various databases—PubMed, LILACS (Literatura Latino-americana e do Caribe em Ciências da Saúde), VHL (Virtual Health Library), Elsevier, Web of Science, Gale Academic One File—using the terms: “Circulating microRNAs” OR “plasma microRNAs” OR “serum microRNAs” OR “blood microRNAs” OR “cell-free microRNAs” OR “exosome microRNAs” OR “extracellular vesicles microRNAs” OR “liquid biopsy” AND “osteosarcoma” AND “diagnostic”. We found 35 eligible studies that were independently identified and had had their quality assessed according to Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines. Despite the useful number of publications on this subject and the fact that several microRNAs showed excellent diagnostic performance for OS, the lack of consistency in results suggests that additional prospective studies are needed to confirm the role of circulating miRNAs as non-invasive biomarkers in OS.
Collapse
Affiliation(s)
- Thaís Borges Gally
- Department of Health Sciences, Universidade Estadual de Santa Cruz, llhéus 45662-900, BA, Brazil;
| | - Milena Magalhães Aleluia
- Department of Biological Sciences, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil;
| | - Grasiely Faccin Borges
- Public Policies and Social Technologies Center, Federal University of Southern Bahia, Itabuna 45613-204, BA, Brazil;
| | - Carla Martins Kaneto
- Department of Biological Sciences, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil;
- Correspondence:
| |
Collapse
|
6
|
Liu X, Zhou Y, Liu Y, Wang Q, Pan L. MicroRNA-425-5p is involved in the development of diabetic retinopathy and regulates the proliferation and migration of retinal microvascular endothelial cells. Ophthalmic Res 2021; 65:60-67. [PMID: 34571504 DOI: 10.1159/000516906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/23/2021] [Indexed: 01/10/2023]
Affiliation(s)
- Xia Liu
- Department of Ophthalmology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yanhua Zhou
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yunxia Liu
- Department of Internal Medicine, Fuyanshan Branch of Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Qian Wang
- Department of Ophthalmology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Lili Pan
- Department of Ophthalmology, Affiliated Hospital of Weifang Medical University, Weifang, China
| |
Collapse
|
7
|
Identification of miR-29c-3p as a Robust Normalizer for Urine microRNA Studies in Bladder Cancer. Biomedicines 2020; 8:biomedicines8110447. [PMID: 33105660 PMCID: PMC7690381 DOI: 10.3390/biomedicines8110447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is among the most frequent malignancies worldwide, being the most expensive cancer to treat and monitor and the most lethal urological cancer. Urine microRNAs (miRNAs) have been proposed as novel non-invasive biomarkers to early diagnose and monitor BC patients in order to avoid the performance of current aggressive diagnostic techniques. However, huge discrepancies arise among studies mainly due to the lack of standardization in the normalization, a crucial step in all miRNA studies. Our aim was to identify the best miRNA normalizer for miRNA studies in urine of BC patients. We evaluated the performance of 110 candidate miRNAs in urine of 35 BC patients and 15 healthy controls by Real Time quantitative Polymerase Chain Reaction (RT-qPCR) followed by a stability analysis with RefFinder. In this screening stage, miR-29c-3p arose as the most stably expressed miRNA in BC and controls, with a good expression level. Stability of miR-29c-3p expression was validated in an independent cohort of 153 BC patients and 57 controls. Finally, we evaluated the robustness of miR-29c-3p as normalizer in the expression study of miR-200c-3p, a potential diagnostic marker for BC. We propose miR-29c-3p as a normalizer for miRNA studies in BC urine. This is the first study that characterizes a reliable normalizer that may allow the comparison of future urine miRNA studies as non-invasive biomarkers for BC diagnosis and monitoring.
Collapse
|
8
|
Saini J, Bandyopadhyay B, Pandey AD, Ramachandran VG, Das S, Sood V, Banerjee A, Vrati S. High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression. mSystems 2020; 5:e00724-20. [PMID: 32934118 PMCID: PMC7498686 DOI: 10.1128/msystems.00724-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
The circulating microRNA (miRNA) profile has been widely used for identifying potential biomarkers against viral infections. However, data on circulating microRNA expression patterns in dengue patients are scanty. Considering the impact of severity caused by dengue infection, circulating miRNA profiles in plasma of dengue patients may prove to be valuable for developing early prognostic markers for the disease severity. Here, we described an in-depth analytical study of small RNA sequencing data obtained from the plasma of 39 dengue patients. Integrating bioinformatics and in vitro studies, we identified differentially expressed miRNAs (DEMs) (log2 fold change ≥1.5, P < 0.05) associated with dengue disease progression. In comparing miRNA expression pattern with the follow-up samples, nine miRNAs were found to exhibit an altered expression that could distinguish between severe dengue and the convalescent patients. To understand the abundance and specificity of the DEMs in the context of dengue infection and disease progression, eight top-hit DEMs were further validated in the dengue virus-infected cell lines as well as in the patient's plasma and peripheral blood mononuclear cells (PBMCs) using the quantitative reverse transcription-PCR (qRT-PCR) method. Importantly, receiver operating curve analysis further confirmed that the plasma expression pattern of hsa-miR-122-5p could differentiate between different stages of dengue infection (area under the concentration-time curve [AUC] = 0.792), and dengue-negative patients with other febrile illnesses (AUC = 0.984). The in silico analysis of DEM target genes suggested an enrichment of the pathways associated with metabolism and inflammation. Our study gives a global view of miRNA expression in the plasma from dengue patients and provides a precious resource of candidate miRNAs involved in dengue infection and disease progression.IMPORTANCE Dengue virus (DENV) infection usually causes dengue fever (DF) with flu-like illness affecting infants, young children, and adults. The DF occasionally evolves into a potentially lethal complication called dengue severe (DS) leading to a rapid fall in platelet count along with plasma leakage, fluid accumulation, respiratory distress, and severe bleeding. The diverse clinical spectrum of dengue disease, as well as its significant similarity to other febrile viral illnesses, makes early identification more challenging in this high-risk group. microRNAs (miRNAs) are small (∼19 to 21 nucleotides [nt] in length), noncoding RNAs, extremely stable and easily detectable in the plasma; thus, they have potential as biomarkers for diagnosing and monitoring human diseases. This study provides a comprehensive analysis of miRNAs circulating in plasma of dengue virus-infected patients and identifies the miRNA signatures that have biomarker potential for dengue infection and disease progression.
Collapse
Affiliation(s)
- Jaya Saini
- Regional Center for Biotechnology (RCB), Faridabad, India
| | | | - Abhay Deep Pandey
- Regional Center for Biotechnology (RCB), Faridabad, India
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - V G Ramachandran
- University College of Medical Sciences (UCMS) & Guru Teg Bahadur (GTB) Hospital, Delhi, India
| | - Shukla Das
- University College of Medical Sciences (UCMS) & Guru Teg Bahadur (GTB) Hospital, Delhi, India
| | - Vikas Sood
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | - Arup Banerjee
- Regional Center for Biotechnology (RCB), Faridabad, India
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Sudhanshu Vrati
- Regional Center for Biotechnology (RCB), Faridabad, India
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| |
Collapse
|
9
|
Identification of Novel microRNA Profiles Dysregulated in Plasma and Tissue of Abdominal Aortic Aneurysm Patients. Int J Mol Sci 2020; 21:ijms21134600. [PMID: 32605321 PMCID: PMC7370113 DOI: 10.3390/ijms21134600] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022] Open
Abstract
microRNAs (miRNAs) are small RNAs that regulate different biological processes. Our objective was to identify miRNAs dysregulated in plasma and tissue of patients with abdominal aortic aneurysm (AAA) and explore new potential targets involved in AAA. Fifty-seven subjects were recruited for a plasma study (30 AAA patients, 16 healthy volunteers and 11 patients with atherosclerosis). The expression level of 179 miRNAs was screened in plasma from a subset of samples, and dysregulated miRNAs were validated in the entire study population. Dysregulated miRNAs were also quantified in aortic tissue of 21 AAA patients and 8 organ donors. Applying a gene set enrichment analysis, an interaction map of dysregulated miRNAs and their targets was built, and selected targets were quantified in tissue samples. miR-27b-3p and miR-221-3p were overexpressed in plasma of AAA patients compared with healthy controls, 1.6 times and 1.9 times, respectively. In AAA tissue, six miRNAs (miR-1, miR-27b-3p, miR-29b-3p, miR-133a-3p, miR-133b, and miR-195-5p) were underexpressed from 1.6 to 4.8 times and four miRNAs (miR-146a-5p, miR-21-5p, miR-144-3p, and miR-103a-3p) were overexpressed from 1.3 to 7.2 times. Thrombospondin-2, a target of miR-195-5p, was increased in AAA tissue and negatively correlated with the expression of miR-195-5p, suggesting their involvement in a common regulatory mechanism.
Collapse
|
10
|
Zou Y, Wu F, Liu Q, Deng X, Hai R, He X, Zhou X. Downregulation of miRNA‑328 promotes the angiogenesis of HUVECs by regulating the PIM1 and AKT/mTOR signaling pathway under high glucose and low serum condition. Mol Med Rep 2020; 22:895-905. [PMID: 32626978 PMCID: PMC7339821 DOI: 10.3892/mmr.2020.11141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 04/08/2020] [Indexed: 01/02/2023] Open
Abstract
Vascular complications are the primary reason for disability and mortality associated with diabetes mellitus (DM), and numerous microRNAs (miRNAs/miRs) are involved in the process, such as miR‑122, miR‑24 and miR‑423. It has been reported that miR‑328 regulates DM and cardiovascular disease; however, the role and mechanism of action underlying miR‑328 in HUVECs is not completely understood. The present study aimed to investigate the role and mechanism of action underlying the effects of miR‑328 on the functions of HUVECs. To simulate hyperglycemia combined with ischemia‑induced tissue starvation, HUVECs were cultured in endothelial cell medium with 25 mmol/l D‑glucose and 2% FBS for 24 h [high glucose (HG) + 2% FBS group]. HUVEC miR‑328 expression levels were detected by reverse transcription‑quantitative PCR. Cell migration, cytotoxicity and tube‑like structure formation were analyzed using wound healing, Cell Counting Kit‑8 and tube formation assays, respectively. Following transfection with miR‑328 inhibitor, miR‑328 expression was downregulated in HUVECs. Protein expression levels were determined by western blotting. Compared with the control group, the migration and tube‑like structure formation of HUVECs were decreased, and cell cytotoxicity was increased in the HG + 2% FBS group. The protein expression levels of vascular endothelial growth factor were also decreased, and the expression levels of miRNA‑328 in the HG + 2% FBS group were increased compared with the control group. However, miRNA‑328 downregulation reversed the aforementioned effects. Further experiments indicated that the AKT signaling pathway was inhibited in the HG + 2% FBS group; however, miR‑328 downregulation activated the AKT/mTOR signaling pathway, which was blocked by the AKT signaling pathway inhibitor, perifosine. Gene prediction and western blotting demonstrated that miR‑328 displayed a regulatory role via Pim‑1 proto‑oncogene, serine/threonine kinase (PIM1). In conclusion, miR‑328 expression was upregulated and angiogenesis was inhibited when HUVECs were subjected to high glucose and low serum conditions. miR‑328 downregulation enhanced angiogenesis by increasing PIM1 expression and activating the AKT/mTOR signaling pathway in HUVECs under high glucose and low serum conditions.
Collapse
Affiliation(s)
- Yan Zou
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Fei Wu
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Qi Liu
- Department of Pediatrics, Nanchong Central Hospital, Nanchong, Sichuan 637000, P.R. China
| | - Xian Deng
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Rui Hai
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xuemei He
- Medical Research Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xiangyu Zhou
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| |
Collapse
|
11
|
Prado MSG, de Jesus ML, de Goes TC, Mendonça LSO, Kaneto CM. Downregulation of circulating miR-320a and target gene prediction in patients with diabetic retinopathy. BMC Res Notes 2020; 13:155. [PMID: 32178730 PMCID: PMC7077016 DOI: 10.1186/s13104-020-05001-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/10/2020] [Indexed: 12/11/2022] Open
Abstract
Objective To evaluate the expression of a set of miRNAs to identify differentially expressed miRNAs that might be considered reliable biomarkers on Diabetic Retinopathy (DR) blood samples. Results Expression levels of MiR-320a, MiR-342-3p, MiR-155, MiR-99a, MiR-29a and MiR-27b were analyzed in 60 healthy controls, 48 Diabetes Melitus (DM) without DR patients and 62 DR patients by qRT-PCR. MiR-320a was shown to be downregulated in the plasma of DR patients compared with DM patients without DR and healthy subjects. Target genes were predicted using miRWalk3.0, miR targeting data and target gene interaction data were imported to Cytoscape to visualize and merge networks and top ranked predicted genes were run through Ontology Genes to perform enrichment analysis on gene sets and classification system to identify biological processes and reactome pathways associated with DR. Highly scored target genes of miR-320a were categorized for various biological processes, including negative regulation of cell aging, negative regulation of cellular protein metabolic process and regulation of cellular response to stress that are critical to the development of DR. Our findings suggest that MiR-320a may have a role in the pathogenesis of DR and may represent novel biomarkers for this disease.
Collapse
Affiliation(s)
| | - Mirthz Lemos de Jesus
- Department of Health Science, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Thaline Cunha de Goes
- Department of Biological Science, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, Km16, Ilhéus, BA, 45662-900, Brazil
| | - Lucilla Silva Oliveira Mendonça
- Department of Biological Science, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, Km16, Ilhéus, BA, 45662-900, Brazil
| | - Carla Martins Kaneto
- Department of Biological Science, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, Km16, Ilhéus, BA, 45662-900, Brazil.
| |
Collapse
|