High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression
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 mi...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2020-10-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSystems.00724-20 |
| _version_ | 1819035602980438016 |
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| author | Jaya Saini Bhaswati Bandyopadhyay Abhay Deep Pandey V. G. Ramachandran Shukla Das Vikas Sood Arup Banerjee Sudhanshu Vrati |
| author_facet | Jaya Saini Bhaswati Bandyopadhyay Abhay Deep Pandey V. G. Ramachandran Shukla Das Vikas Sood Arup Banerjee Sudhanshu Vrati |
| author_sort | Jaya Saini |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T07:52:15Z |
| format | Article |
| id | doaj.art-3be4c808cb0d468eb918b617a11aeeed |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-21T07:52:15Z |
| publishDate | 2020-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-3be4c808cb0d468eb918b617a11aeeed2022-12-21T19:11:03ZengAmerican Society for MicrobiologymSystems2379-50772020-10-015510.1128/mSystems.00724-20High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease ProgressionJaya Saini0Bhaswati Bandyopadhyay1Abhay Deep Pandey2V. G. Ramachandran3Shukla Das4Vikas Sood5Arup Banerjee6Sudhanshu Vrati7Regional Center for Biotechnology (RCB), Faridabad, IndiaCalcutta School of Tropical Medicine (STM), Kolkata, IndiaRegional Center for Biotechnology (RCB), Faridabad, IndiaUniversity College of Medical Sciences (UCMS) & Guru Teg Bahadur (GTB) Hospital, Delhi, IndiaUniversity College of Medical Sciences (UCMS) & Guru Teg Bahadur (GTB) Hospital, Delhi, IndiaTranslational Health Science and Technology Institute (THSTI), Faridabad, IndiaRegional Center for Biotechnology (RCB), Faridabad, IndiaRegional Center for Biotechnology (RCB), Faridabad, IndiaABSTRACT 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.https://journals.asm.org/doi/10.1128/mSystems.00724-20dengueRNA sequencingcirculating miRNAplasma microRNA |
| spellingShingle | Jaya Saini Bhaswati Bandyopadhyay Abhay Deep Pandey V. G. Ramachandran Shukla Das Vikas Sood Arup Banerjee Sudhanshu Vrati High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression mSystems dengue RNA sequencing circulating miRNA plasma microRNA |
| title | High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression |
| title_full | High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression |
| title_fullStr | High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression |
| title_full_unstemmed | High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression |
| title_short | High-Throughput RNA Sequencing Analysis of Plasma Samples Reveals Circulating microRNA Signatures with Biomarker Potential in Dengue Disease Progression |
| title_sort | high throughput rna sequencing analysis of plasma samples reveals circulating microrna signatures with biomarker potential in dengue disease progression |
| topic | dengue RNA sequencing circulating miRNA plasma microRNA |
| url | https://journals.asm.org/doi/10.1128/mSystems.00724-20 |
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