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Trivedi TS, Shaikh AM, Mankad AU, Rawal RM, Patel SK. Genome-Wide Characterization of Fennel (Anethum foeniculum) MiRNome and Identification of its Potential Targets in Homo sapiens and Arabidopsis thaliana: An Inter and Intra-species Computational Scrutiny. Biochem Genet 2024; 62:2766-2795. [PMID: 38017284 DOI: 10.1007/s10528-023-10575-7] [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: 05/29/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
MicroRNAs could be promising biomarkers for various diseases, and small RNA drugs have already been FDA approved for clinical use. This area of research is rapidly expanding and has significant potential for the future. Fennel (Anethum foeniculum) is a highly esteemed spice plant with economic and medicinal benefits, making it an invaluable asset in the pharmaceutical industry. To characterize the fennel miRNAs and their Arabidopsis thaliana and Homo sapience targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the Anethum foeniculum genome and assessed its impact on Arabidopsis thaliana and Homo sapience transcriptomes. In addition, functional enrichment analysis was evaluated for both species' targets. Moreover, PPI network analysis, hub gene identification, and MD simulation analysis of the top hub node with fennel miRNA were incorporated. We have identified 100 miRNAs of fennel and their target genes, which include 2536 genes in Homo sapiens and 1314 genes in Arabidopsis thaliana. Functional enrichment analysis reveals 56 Arabidopsis thaliana targets of fennel miRNAs showed involvement in metabolic pathways. Highly enriched human KEGG pathways were associated with several diseases, especially cancer. The protein-protein interaction network of human targets determined the top ten nodes; from them, seven hub nodes, namely MAPK1, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4, have shown their involvement in the pancreatic cancer pathway. Based on the Blast algorithm, 21 fennel miRNAs are homologs to 16 human miRNAs were predicted; from them, the CSPP1 target was a common target for afo-miR11117a-3p and has-miR-6880-5p homologs miRNAs. Our results are the first to report the 100 fennel miRNAs, and predictions for their endogenous and human target genes provide a basis for further understanding of Anethum foeniculum miRNAs and the biological processes and diseases with which they are associated.
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Affiliation(s)
- Tithi S Trivedi
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Aafrinbanu M Shaikh
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Archana U Mankad
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Rakesh M Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Saumya K Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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Díez-Sainz E, Milagro FI, Aranaz P, Riezu-Boj JI, Lorente-Cebrián S. MicroRNAs from edible plants reach the human gastrointestinal tract and may act as potential regulators of gene expression. J Physiol Biochem 2024:10.1007/s13105-024-01023-0. [PMID: 38662188 DOI: 10.1007/s13105-024-01023-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
MicroRNAs (miRNAs) are small single-stranded non-coding RNA molecules that regulate gene expression at the post-transcriptional level. A cross-kingdom regulatory function has been unveiled for plant miRNAs (xenomiRs), which could shape inter-species interactions of plants with other organisms (bacteria and humans) and thus, be key functional molecules of plant-based food in mammals. However, discrepancies regarding the stability and bioavailability of dietary plant miRNAs on the host cast in doubt whether these molecules could have a significant impact on human physiology. The aim of the present study was to identify miRNAs in edible plants and determine their bioavailability on humans after an acute intake of plant-based products. It was found that plant food, including fruits, vegetables and greens, nuts, legumes, and cereals, contains a wide range of miRNAs. XenomiRs miR156e, miR159 and miR162 were detected in great abundance in edible plants and were present among many plant foods, and thus, they were selected as candidates to analyse their bioavailability in humans. These plant miRNAs resisted cooking processes (heat-treatments) and their relative presence increased in faeces after and acute intake of plant-based foods, although they were not detected in serum. Bioinformatic analysis revealed that these miRNAs could potentially target human and bacterial genes involved in processes such as cell signalling and metabolism. In conclusion, edible plants contain miRNAs, such as miR156e, miR159 and miR162, that could resist degradation during cooking and digestion and reach the distal segments of the gastrointestinal tract. Nevertheless, strategies should be developed to improve their absorption to potentially reach host tissues and organs and modulate human physiology.
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Affiliation(s)
- Ester Díez-Sainz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008, Pamplona, Spain
| | - Fermín I Milagro
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008, Pamplona, Spain.
- Navarra Institute for Health Research (IdiSNA), 31008, Pamplona, Spain.
- Centro de Investigación Biomédica en Red Fisiopatología de La Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Paula Aranaz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008, Pamplona, Spain
| | - José I Riezu-Boj
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, 31008, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008, Pamplona, Spain
| | - Silvia Lorente-Cebrián
- Department of Pharmacology, Physiology and Legal and Forensic Medicine, Faculty of Health and Sport Science, University of Zaragoza, 50009, Saragossa, Spain
- Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, 50013, Saragossa, Spain
- Aragón Health Research Institute (IIS-Aragon), 50009, Saragossa, Spain
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Sahu S, Rao AR, Sahu TK, Pandey J, Varshney S, Kumar A, Gaikwad K. Predictive Role of Cluster Bean ( Cyamopsis tetragonoloba) Derived miRNAs in Human and Cattle Health. Genes (Basel) 2024; 15:448. [PMID: 38674383 PMCID: PMC11049822 DOI: 10.3390/genes15040448] [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: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 04/28/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding conserved molecules with lengths varying between 18-25nt. Plants miRNAs are very stable, and probably they might have been transferred across kingdoms via food intake. Such miRNAs are also called exogenous miRNAs, which regulate the gene expression in host organisms. The miRNAs present in the cluster bean, a drought tolerant legume crop having high commercial value, might have also played a regulatory role for the genes involved in nutrients synthesis or disease pathways in animals including humans due to dietary intake of plant parts of cluster beans. However, the predictive role of miRNAs of cluster beans for gene-disease association across kingdoms such as cattle and humans are not yet fully explored. Thus, the aim of the present study is to (i) find out the cluster bean miRNAs (cb-miRs) functionally similar to miRNAs of cattle and humans and predict their target genes' involvement in the occurrence of complex diseases, and (ii) identify the role of cb-miRs that are functionally non-similar to the miRNAs of cattle and humans and predict their targeted genes' association with complex diseases in host systems. Here, we predicted a total of 33 and 15 functionally similar cb-miRs (fs-cb-miRs) to human and cattle miRNAs, respectively. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the participation of targeted genes of fs-cb-miRs in 24 and 12 different pathways in humans and cattle, respectively. Few targeted genes in humans like LCP2, GABRA6, and MYH14 were predicted to be associated with disease pathways of Yesinia infection (hsa05135), neuroactive ligand-receptor interaction (hsa04080), and pathogenic Escherichia coli infection (hsa05130), respectively. However, targeted genes of fs-cb-miRs in humans like KLHL20, TNS1, and PAPD4 are associated with Alzheimer's, malignant tumor of the breast, and hepatitis C virus infection disease, respectively. Similarly, in cattle, targeted genes like ATG2B and DHRS11 of fs-cb-miRs participate in the pathways of Huntington disease and steroid biosynthesis, respectively. Additionally, the targeted genes like SURF4 and EDME2 of fs-cb-miRs are associated with mastitis and bovine osteoporosis, respectively. We also found a few cb-miRs that do not have functional similarity with human and cattle miRNAs but are found to target the genes in the host organisms and as well being associated with human and cattle diseases. Interestingly, a few genes such as NRM, PTPRE and SUZ12 were observed to be associated with Rheumatoid Arthritis, Asthma and Endometrial Stromal Sarcoma diseases, respectively, in humans and genes like SCNN1B associated with renal disease in cattle.
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Affiliation(s)
- Sarika Sahu
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Atmakuri Ramakrishna Rao
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Indian Council of Agricultural Research, New Delhi 110001, India
| | - Tanmaya Kumar Sahu
- Indian Grassland and Fodder Research Institute, ICAR, Jhansi 284003, India;
| | - Jaya Pandey
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Shivangi Varshney
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Archna Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Kishor Gaikwad
- National Institute for Plant Biotechnology, ICAR, New Delhi 110012, India;
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Habán M, Korczyk-Szabó J, Čerteková S, Ražná K. Lavandula Species, Their Bioactive Phytochemicals, and Their Biosynthetic Regulation. Int J Mol Sci 2023; 24:ijms24108831. [PMID: 37240177 DOI: 10.3390/ijms24108831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
Lavandula species are one of the most useful aromatic and medicinal plants and have great economic potential. The phytopharmaceutical contribution of the secondary metabolites of the species is unquestionable. Most recent studies have been focusing on the elucidation of the genetic background of secondary metabolite production in lavender species. Therefore, knowledge of not only genetic but especially epigenetic mechanisms for the regulation of secondary metabolites is necessary for the modification of those biosynthesis processes and the understanding of genotypic differences in the content and compositional variability of these products. The review discusses the genetic diversity of Lavandula species in relation to the geographic area, occurrence, and morphogenetic factors. The role of microRNAs in secondary-metabolites biosynthesis is described.
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Affiliation(s)
- Miroslav Habán
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Pharmacognosy and Botany, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 83232 Bratislava, Slovakia
| | - Joanna Korczyk-Szabó
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Simona Čerteková
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Katarína Ražná
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
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Trivedi TS, Patel MP, Nanavaty V, Mankad AU, Rawal RM, Patel SK. MicroRNAs from Holarrhena pubescens stems: Identification by small RNA Sequencing and their Potential Contribution to Human Gene Targets. Funct Integr Genomics 2023; 23:149. [PMID: 37148427 DOI: 10.1007/s10142-023-01078-0] [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: 12/31/2022] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/08/2023]
Abstract
Holarrhena pubescens is an effective medicinal plant from the Apocynaceae family, widely distributed over the Indian subcontinent and extensively used by Ayurveda and ethno-medicine systems without apparent side effects. We postulated that miRNAs, endogenous non-coding small RNAs that regulate gene expression at the post-transcriptional level, may, after ingestion into the human body, contribute to the medicinal properties of plants of this species by inducing regulated human gene expression to modulate. However, knowledge is scarce about miRNA in Holarrhena. In addition, to test the hypothesis on the potential pharmacological properties of miRNA, we performed a high-throughput sequencing analysis using the Next Generation Sequencing Illumina platform; 42,755,236 raw reads have been generated from H. pubescens stems from a library of small RNA isolated, identifying 687 known and 50 new miRNAs led. The novel H. pubescens miRNAs were predicted to regulate specific human genes, and subsequent annotations of gene functions suggested a possible role in various biological processes and signaling pathways, such as Wnt, MAPK, PI3K-Akt, and AMPK signaling pathways and endocytosis. The association of these putative targets with many diseases, including cancer, congenital malformations, nervous system disorders, and cystic fibrosis, has been demonstrated. The top hub proteins STAT3, MDM2, GSK3B, NANOG, IGF1, PRKCA, SNAP25, SRSF1, HTT, and SNCA show their interaction with human diseases, including cancer and cystic fibrosis. To our knowledge, this is the first report of uncovering H. pubescens miRNAs based on high-throughput sequencing and bioinformatics analysis. This study has provided new insight into a potential cross-species control of human gene expression. The potential for miRNA transfer should be evaluated as one possible mechanism of action to account for the beneficial properties of this valuable species.
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Affiliation(s)
- Tithi S Trivedi
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Maulikkumar P Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Vishal Nanavaty
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
- Neuberg Centre for Genomic Medicine, Neuberg Supratech Reference Laboratory, Ahmedabad, 380006, Gujarat, India
| | - Archana U Mankad
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Rakesh M Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Saumya K Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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6
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Motwani H, Patel M, Nanavaty V, Dixit N, Rawal RM, Patel SK, Solanki HA. Small RNA sequencing and identification of Andrographis paniculata miRNAs with potential cross‑kingdom human gene targets. Funct Integr Genomics 2023; 23:55. [PMID: 36725761 DOI: 10.1007/s10142-023-00976-7] [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: 12/31/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023]
Abstract
Cross-species post-transcriptional regulatory potential of plant derived small non-coding microRNAs (miRNAs) has been well documented by plenteous studies. MicroRNAs are transferred to host cells via oral ingestion wherein they play a decisive role in regulation of host genes; thus, miRNAs have evolved as the nascent bioactive molecules imparting pharmacological values to traditionally used medicinal plants. The present study aims to investigate small RNA profiling in order to uncover the potential regulatory role of miRNAs derived from Andrographis paniculata, one of the most widely used herb by tribal communities for liver disorders and document the pharmacological properties of A. paniculata miRNAs. In this study, high-throughput sequencing method was used to generate raw data, ~ 60 million sequences were generated from A. paniculata leaves. Using computational tools and bioinformatics approach, analyses of 3,480,097 clean reads resulted in identification of 3440 known and 51 putative novel miRNAs regulating 1365 and 192 human genes respectively. Remarkably, the identified plausible novel miRNAs apa-miR-5, apa-miR-1, apa-miR-26, and apa-miR-30 are projected to target significant host genes including CDK6, IKBKB, TRAF3, CHD4, MECP2, and ADIPOQ. Subsequent annotations revealed probable involvement of the target genes in various pathways for instance p38-MAPK, AKT, AMPK, NF-Kβ, ERK, WNT signalling, MYD88 dependant cascade, and pathways in cancer. Various diseases such as human papilloma virus infection, Alzheimer's, Non-alcoholic Fatty Liver, Alcoholic liver diseases, HepatoCellular Carcinoma (HCC), and numerous other cancers were predominantly found to be linked with target genes. Our findings postulate novel interpretations regarding modulation of human transcripts by A. paniculata miRNAs and exhibit the regulation of human diseases by plant-derived miRNAs. Though our study elucidates miRNAs as novel therapeutic agents, however, experimental validations for assessment of therapeutic potential of these miRNAs are still warranted.
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Affiliation(s)
- Harsha Motwani
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad-380009, Gujarat, India
| | - Maulikkumar Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad-380009, Gujarat, India
| | - Vishal Nanavaty
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad-380009, Gujarat, India
- Neuberg Centre for Genomic Medicine, Neuberg Supratech Reference Laboratory, Ahmedabad, Gujarat, India
| | - Nandan Dixit
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad-380009, Gujarat, India
| | - Rakesh M Rawal
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad-380009, Gujarat, India
| | - Saumya K Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad-380009, Gujarat, India.
| | - Hitesh A Solanki
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad-380009, Gujarat, India.
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MicroRNAs in Medicinal Plants. Int J Mol Sci 2022; 23:ijms231810477. [PMID: 36142389 PMCID: PMC9500639 DOI: 10.3390/ijms231810477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules.
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Moayedi K, Orandi S, Ebrahimi R, Tanhapour M, Moradi M, Abbastabar M, Golestani A. A novel approach to type 3 diabetes mechanism: The interplay between noncoding RNAs and insulin signaling pathway in Alzheimer's disease. J Cell Physiol 2022; 237:2838-2861. [PMID: 35580144 DOI: 10.1002/jcp.30779] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/05/2022] [Accepted: 04/27/2022] [Indexed: 12/06/2022]
Abstract
Today, growing evidence indicates that patients with type 2 diabetes (T2D) are at a higher risk of developing Alzheimer's disease (AD). Indeed, AD as one of the main causes of dementia in people aged more than 65 years can be aggravated by insulin resistance (IR) and other metabolic risk factors related to T2D which are also linked to the function of the brain. Remarkably, a new term called "type 3 diabetes" has been suggested for those people who are diagnosed with AD while also showing the symptoms of IR and T2D. In this regard, the role of genetic and epigenetic changes associated with AD has been confirmed by many studies. On the other hand, it should be noted that the insulin signaling pathway is highly regulated by various mechanisms, including epigenetic factors. Among these, the role of noncoding RNAs (ncRNAs), including microRNAs and long noncoding RNAs has been comprehensively studied with respect to the pathology of AD and the most well-known underlying mechanisms. Nevertheless, the number of studies exploring the association between ncRNAs and the downstream targets of the insulin signaling pathway in the development of AD has notably increased in recent years. With this in view, the present study aimed to review the interplay between different ncRNAs and the insulin signaling pathway targets in the pathogenesis of AD to find a new approach in the field of combining biomarkers or therapeutic targets for this disease.
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Affiliation(s)
- Kiana Moayedi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Orandi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reyhane Ebrahimi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Tanhapour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mona Moradi
- Pediatric Infectious Diseases Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maryam Abbastabar
- Department of Clinical Biochemistry, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Abolfazl Golestani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Jha N, Mangukia N, Gadhavi H, Patel M, Bhavsar M, Rawal R, Patel S. Small RNA sequencing and identification of papaya (Carica papaya L.) miRNAs with potential cross-kingdom human gene targets. Mol Genet Genomics 2022; 297:981-997. [PMID: 35570207 PMCID: PMC9107959 DOI: 10.1007/s00438-022-01904-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/23/2022] [Indexed: 12/11/2022]
Abstract
Several studies have demonstrated potential role of plant-derived miRNAs in cross-kingdom species relationships by transferring into non-plant host cells to regulate certain host cellular functions. How nutrient-rich plants regulate host cellular functions, which in turn alleviate physiological and disease conditions in the host remains to be explored in detail. This computational study explores the potential targets, putative role, and functional implications of miRNAs derived from Carica papaya L., one of the most cultivated tropical crops in the world and a rich source of phytochemicals and enzymes, in human diet. Using the next-generation sequencing, -Illumina HiSeq2500, ~ 30 million small RNA sequence reads were generated from C. papaya young leaves, resulting in the identification of a total of 1798 known and 49 novel miRNAs. Selected novel C. papaya miRNAs were predicted to regulate certain human targets, and subsequent annotation of gene functions indicated a probable role in various biological processes and pathways, such as MAPK, WNT, and GPCR signaling pathways, and platelet activation. These presumptive target gene in humans were predominantly linked to various diseases, including cancer, diabetes, mental illness, and platelet disorder. The computational finding of this study provides insights into how C. papaya-derived miRNAs may regulate certain conditions of human disease and provide a new perspective on human health. However, the therapeutic potential of C. papaya miRNA can be further explored through experimental studies.
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Affiliation(s)
- Neha Jha
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Naman Mangukia
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
- BioInnovations, Bhayander (West), Mumbai, 401101, Maharashtra, India
| | - Harshida Gadhavi
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Maulik Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
- Advait Theragnostics Pvt. Ltd., Ahmedabad, Gujarat, India
| | - Mansi Bhavsar
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Rakesh Rawal
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Saumya Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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Sánchez-Romo D, Hernández-Vásquez CI, Pereyra-Alférez B, García-García JH. Identification of potential target genes in Homo sapiens, by miRNA of Triticum aestivum: A cross kingdom computational approach. Noncoding RNA Res 2022; 7:89-97. [PMID: 35387280 PMCID: PMC8961073 DOI: 10.1016/j.ncrna.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
Plant-derived miRNAs can be found in the human body after dietary intake, and they can affect post-transcriptional gene regulation in human. It is important to identify targets to determine the possible effects in human genes by using computational approach. In this study, 787 possible mRNAs human targets were predicted by 84 miRNAs of wheat. A total of 14 miRNAs were identified with individual binding to 33 mRNAs associated with schizophrenia, epilepsy, neurodevelopmental disorders, and various cancers, located in the 3′UTR of the mRNA. A functional enrichment was carried out, where the results showed associations to pathways such as dopaminergic synapse (hsa04728), and signaling pathways, significantly associated with the target genes. The prediction of target mRNAs in humans by wheat miRNAs, offer candidates that could facilitate the search and verification, which could be of relevance for future projects and therefor contribute in the therapeutic treatment of various human diseases.
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Mangukia N, Rao P, Patel K, Pandya H, Rawal RM. Identifying potential human and medicinal plant microRNAs against SARS-CoV-2 3'UTR region: A computational genomics assessment. Comput Biol Med 2021; 136:104662. [PMID: 34311261 PMCID: PMC8288231 DOI: 10.1016/j.compbiomed.2021.104662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/28/2022]
Abstract
The coronavirus disease of 2019 (COVID-19) began as an outbreak and has taken a toll on human lives. The current pandemic requires scientific attention; hence we designed a systematic computational workflow to identify the cellular microRNAs (miRNAs) from human host possessing the capability to target and silence 3′UTR of SARS-CoV-2 genome. Based on this viewpoint, we extended our miRNA search to medicinal plants like Ocimum tenuiflorum, Zingiber officinale and Piper nigrum, which are well-known to possess antiviral properties, and are often consumed raw or as herbal decoctions. Such an approach, that makes use of miRNA of one species to interact and silence genes of another species including viruses is broadly categorized as cross-kingdom interactions. As a part of our genomics study on host-virus-plant interaction, we identified one unique 3′UTR conserved site ‘GGAAGAG’ amongst 5024 globally submitted SARS-CoV-2 complete genomes, which can be targeted by the human miRNA ‘hsa-miR-1236–3p’ and by Z. officinale miRNA ‘zof-miR2673b’. Additionally, we also predicted that the members of miR477 family commonly found in these three plant genomes possess an inherent potential to silence viral genome RNA and facilitate antiviral defense against SARS-CoV-2 infection. In conclusion, this study reveals a universal site in the SARS-CoV-2 genome that may be crucial for targeted therapeutics to cure COVID-19.
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Affiliation(s)
- Naman Mangukia
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India; BioInnovations, Bhayander (West), Mumbai, 401101, Maharashtra, India.
| | - Priyashi Rao
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
| | - Kamlesh Patel
- Advait Theragnostics, GUSEC, Gujarat University, Ahmedabad, 380009, Gujarat, India.
| | - Himanshu Pandya
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
| | - Rakesh M Rawal
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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12
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Jha N, Mangukia N, Patel MP, Bhavsar M, Gadhavi H, Rawal RM, Patel SK. Exploring the MiRnome of Carica papaya: A cross kingdom approach. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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14
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Dávalos A, Pinilla L, López de Las Hazas MC, Pinto-Hernández P, Barbé F, Iglesias-Gutiérrez E, de Gonzalo-Calvo D. Dietary microRNAs and cancer: A new therapeutic approach? Semin Cancer Biol 2020; 73:19-29. [PMID: 33086083 DOI: 10.1016/j.semcancer.2020.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/26/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022]
Abstract
Cancer is one of the leading causes of premature death and constitutes a challenge for both low- and high-income societies. Previous evidence supports a close association between modifiable risk factors, including dietary habits, and cancer risk. Investigation of molecular mechanisms that mediate the pro-oncogenic and anti-oncogenic effects of diet is therefore fundamental. MicroRNAs (miRNAs) have received much attention in the past few decades as crucial molecular elements of human physiology and disease. Aberrant expression patterns of these small noncoding transcripts have been observed in a wide array of cancers. Interestingly, human miRNAs not only can be modulated by bioactive dietary components, but it has also been proposed that diet-derived miRNAs may contribute to the pool of human miRNAs. Results from independent groups have suggested that these exogenous miRNAs may be functional in organisms. These findings open the door to novel and innovative approaches to cancer therapy. Here, we provide an overview of the biology of miRNAs, with a special focus on plant-derived dietary miRNAs, summarize recent findings in the field of cancer, address the possible applications to clinical practice and discuss obstacles and challenges in the field.
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Affiliation(s)
- Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Crta. de, Carr. de Canto Blanco, nº8, E, 28049 Madrid, Spain
| | - Lucía Pinilla
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - María-Carmen López de Las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Crta. de, Carr. de Canto Blanco, nº8, E, 28049 Madrid, Spain
| | - Paola Pinto-Hernández
- Department of Functional Biology, Physiology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - Eduardo Iglesias-Gutiérrez
- Department of Functional Biology, Physiology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain; Health Research Institute of the Principality of Asturias (ISPA), Av. Roma, s/n, 33011 Oviedo, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Av. de Monforte de Lemos, 5, 28029 Madrid, Spain.
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15
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Samad AFA, Kamaroddin MF, Sajad M. Cross-Kingdom Regulation by Plant microRNAs Provides Novel Insight into Gene Regulation. Adv Nutr 2020; 12:197-211. [PMID: 32862223 PMCID: PMC7850022 DOI: 10.1093/advances/nmaa095] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/08/2020] [Accepted: 07/20/2020] [Indexed: 12/19/2022] Open
Abstract
microRNAs (miRNAs) are well known as major players in mammalian and plant genetic systems that act by regulating gene expression at the post-transcriptional level. These tiny molecules can regulate target genes (mRNAs) through either cleavage or translational inhibition. Recently, the discovery of plant-derived miRNAs showing cross-kingdom abilities to regulate mammalian gene expression has prompted exciting discussions among researchers. After being acquired orally through the diet, plant miRNAs can survive in the digestive tract, enter the circulatory system, and regulate endogenous mRNAs. Here, we review current knowledge regarding the cross-kingdom mechanisms of plant miRNAs, related controversies, and potential applications of these miRNAs in dietary therapy, which will provide new insights for plant miRNA investigations related to health issues in humans.
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Affiliation(s)
| | - Mohd Farizal Kamaroddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Muhammad Sajad
- Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Punjab, Pakistan
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Krishnatreya DB, Baruah PM, Dowarah B, Bordoloi KS, Agarwal H, Agarwala N. Mining of miRNAs from EST data in Dendrobium nobile. Bioinformation 2020; 16:245-255. [PMID: 32308267 PMCID: PMC7147496 DOI: 10.6026/97320630016245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/10/2020] [Accepted: 03/14/2020] [Indexed: 12/05/2022] Open
Abstract
Dendrobium nobile is an orchid species highly popular for its therapeutic properties and is often used as a medicinal herb. Documenting miRNA-target associations in D. nobile is an important step to facilitate functional genomics studies in this species. Therefore, it is of interest to identify miRNA sequences from EST data available in public databases using known techniques and tools. We report 14 potential miRNAs from three ESTs of D. nobile. They belong to 3 miRNA families (miR390, miR528 and miR414) linking to transcription factor regulation, signal transduction, DNA and protein binding, and various cellular processes covering 34 different metabolic networks in KEGG. These results help in the understanding of miRNA-mRNAs functional networks in Dendrobium nobile.
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Affiliation(s)
| | - Pooja Moni Baruah
- Department of Botany, Gauhati University, Guwahati, Assam, India - 7810014
| | - Bhaskar Dowarah
- Department of Botany, Gauhati University, Guwahati, Assam, India - 7810014
| | | | - Heena Agarwal
- Department of Botany, Gauhati University, Guwahati, Assam, India - 7810014
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Guwahati, Assam, India - 7810014
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Correction: Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples. PLoS One 2020; 15:e0230146. [PMID: 32160248 PMCID: PMC7065748 DOI: 10.1371/journal.pone.0230146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0224537.].
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Gadhavi H, Patel M, Mangukia N, Shah K, Bhadresha K, Patel SK, Rawal RM, Pandya HA. Transcriptome-wide miRNA identification of Bacopa monnieri: a cross-kingdom approach. PLANT SIGNALING & BEHAVIOR 2020; 15:1699265. [PMID: 31797719 PMCID: PMC7012157 DOI: 10.1080/15592324.2019.1699265] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bacopa monnieri known as 'Brahmi' is a well-known medicinal plant belonging to Scrophulariaceae family for its nootropic properties. To the best of our knowledge, no characterization data is available on the potential role of micro RNAs (miRNAs) from this plant till date. We present here the first report of computational characterizations of miRNAs from B. monnieri. Owing to the high conservation of miRNAs in nature, new and potential miRNAs can be identified in plants using in silico techniques. Using the plant miRNA sequences present in the miRBase repository, a total of 12 miRNAs were identified from B. monnieri which pertained to 11 miRNA families from the shoot and root transcriptome data. Furthermore, gene ontology analysis of the identified 68 human target genes exhibited significance in various biological processes. These human target genes were associated with signaling pathways like NF-kB and MAPK with TRAF2, CBX1, IL1B, ITGA4 and ITGB1BP1 as the top five hub nodes. This cross-kingdom study provides initial insights about the potential of miRNA-mediated cross-kingdom regulation and unravels the essential target genes of human with implications in numerous human diseases including cancer.
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Affiliation(s)
- Harshida Gadhavi
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
| | - Maulikkumar Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
| | - Naman Mangukia
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
| | - Kanisha Shah
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, India
| | - Kinjal Bhadresha
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, India
| | - Saumya K. Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
| | - Rakesh M. Rawal
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, India
| | - Himanshu A. Pandya
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, India
- CONTACT Himanshu A. Pandya Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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