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Wang P, Zhou Y, Wang J, Zhou Y, Zhang X, Liu Y, Li A, He Y, Chen S, Qian A, Wang X, Nie Y, Fan D, Cao T, Lu Y, Zhao X. miR-107 reverses the multidrug resistance of gastric cancer by targeting the CGA/EGFR/GATA2 positive feedback circuit. J Biol Chem 2024; 300:107522. [PMID: 38960034 PMCID: PMC11345541 DOI: 10.1016/j.jbc.2024.107522] [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: 12/27/2023] [Revised: 06/02/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Chemotherapy is still the main therapeutic strategy for gastric cancer (GC). However, most patients eventually acquire multidrug resistance (MDR). Hyperactivation of the EGFR signaling pathway contributes to MDR by promoting cancer cell proliferation and inhibiting apoptosis. We previously identified the secreted protein CGA as a novel ligand of EGFR and revealed a CGA/EGFR/GATA2 positive feedback circuit that confers MDR in GC. Herein, we outline a microRNA-based treatment approach for MDR reversal that targets both CGA and GATA2. We observed increased expression of CGA and GATA2 and increased activation of EGFR in GC samples. Bioinformatic analysis revealed that miR-107 could simultaneously target CGA and GATA2, and the low expression of miR-107 was correlated with poor prognosis in GC patients. The direct interactions between miR-107 and CGA or GATA2 were validated by luciferase reporter assays and Western blot analysis. Overexpression of miR-107 in MDR GC cells increased their susceptibility to chemotherapeutic agents, including fluorouracil, adriamycin, and vincristine, in vitro. Notably, intratumor injection of the miR-107 prodrug enhanced MDR xenograft sensitivity to chemotherapies in vivo. Molecularly, targeting CGA and GATA2 with miR-107 inhibited EGFR downstream signaling, as evidenced by the reduced phosphorylation of ERK and AKT. These results suggest that miR-107 may contribute to the development of a promising therapeutic approach for the treatment of MDR in GC.
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Affiliation(s)
- Pei Wang
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China; Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yelu Zhou
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Juan Wang
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yun Zhou
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xiaohui Zhang
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yanxing Liu
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Ang Li
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yangsong He
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Shuyi Chen
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China; School of Basic Medical Sciences, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Airong Qian
- Key Laboratory for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xin Wang
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yongzhan Nie
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Daiming Fan
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Tianyu Cao
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Yuanyuan Lu
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Xiaodi Zhao
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China.
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2
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Awuson-David B, Williams AC, Wright B, Hill LJ, Di Pietro V. Common microRNA regulated pathways in Alzheimer's and Parkinson's disease. Front Neurosci 2023; 17:1228927. [PMID: 37719162 PMCID: PMC10502311 DOI: 10.3389/fnins.2023.1228927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in gene regulation. Recently, miRNA dysregulation has been found in neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). The diagnosis of Alzheimer's and Parkinson's is currently challenging, mainly occurring when pathology is already present, and although treatments are available for both diseases, the role of treatment is primarily to prevent or delay the progress of the diseases instead of fully overcoming the diseases. Therefore, the challenge in the near future will be to determine effective drugs to tackle the dysregulated biological pathways in neurodegenerative diseases. In the present study, we describe the dysregulation of miRNAs in blood of Alzheimer's and Parkinson's patients with the aim to identify common mechanisms between the 2 pathologies and potentially to identify common therapeutic targets which can stop or delay the progression of two most frequent neuropathologies. Two independent systematic reviews, bioinformatic analysis, and experiment validation were performed to identify whether AD and PD share common pathways. A total of 15 common miRNAs were found in the literature and 13 common KEGG pathways. Among the common miRNAs, two were selected for validation in a small cohort of AD and PD patients. Let-7f-5p and miR-29b-3p showed to be good predictors in blood of PD patients.
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Affiliation(s)
- Betina Awuson-David
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Adrian C. Williams
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Benjamin Wright
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Lisa J. Hill
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Valentina Di Pietro
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
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3
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Carapito R, Bernardo SC, Pereira MM, Neves MC, Freire MG, Sousa F. Multimodal ionic liquid-based chromatographic supports for an effective RNA purification. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2023.123676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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4
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Baptista B, Oliveira ASR, Mendonça P, Serra AC, Coelho JFJ, Sousa F. pH-responsive nanoparticles based on POEOMA-b-PDPA block copolymers for RNA encapsulation, protection and cell delivery. BIOMATERIALS ADVANCES 2023; 145:213267. [PMID: 36599197 DOI: 10.1016/j.bioadv.2022.213267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
The use of gene-based products, such as DNA or RNA, is increasingly being explored for various innovative therapies. However, the success of these strategies is highly dependent on the effective delivery of these biomolecules to target cells. Therefore, the development of pH-responsive nanoparticles comprises the creation of intelligent delivery systems with high therapeutic efficiency. In this work, the pH-responsiveness of the poly(2-(diisopropylamino)ethyl methacrylate)) (PDPA) block was investigated for the encapsulation and delivery of small RNAs (sRNA) to cancer cells. The pH responsiveness was dependent on the protonation profile of the tertiary amines of PDPA, which directly affected the electrostatic interactions established with RNA. Thus, block copolymers based on poly(oligo(ethylene oxide) methyl ether methacrylate) (POEOMA) and PDPA, POEOMA-b-PDPA, were synthesized by supplemental activator and reducing agent atom transfer radical polymerization (SARA ATRP). The structure of the block copolymers was characterized by size exclusion chromatography and 1H NMR spectroscopy. The copolymers allowed effective complexation of model sRNAs and a pre-miRNA with efficiencies of about 89 % and 91 %, respectively. The characterization by dynamic light scattering revealed that these systems had sizes between 76 and 1375 nm. It was also found that the morphology of the polyplexes depended on the pH, since the preparation at a pH lower than the pKa of the copolymers resulted in spherical but polydisperse particles, while higher pH values resulted in nanoparticles with more homogeneous size, but altered morphology. Moreover, due to pH-responsiveness, it was achieved the release of RNA at pH higher than the pKa of the copolymers, while maintaining its integrity. The polyplexes also showed a high potential to protect RNA from RNases. The transfection of a lung cancer model (A549) and fibroblast cell lines showed that these polyplexes did not cause cell toxicity. In addition, the polyplexes enabled the effective transfection of the A549 cell line with pre-miRNA-29b and miRNA-29b, resulting in a decrease of expression levels of the target DNMT3B gene by approximately 51 % and 47 %, respectively. Overall, the POEOMA-b-PDPA copolymers proved to be a promising strategy for developing responsive delivery systems, that can play a critical role in some diseases, such as cancer, where pH varies between the intra and extracellular environments.
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Affiliation(s)
- Bruno Baptista
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Andreia S R Oliveira
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Chemical Engineering, Rua Sílvio Lima-Polo II, 3030-790 Coimbra, Portugal
| | - Patrícia Mendonça
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Chemical Engineering, Rua Sílvio Lima-Polo II, 3030-790 Coimbra, Portugal
| | - Arménio C Serra
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Chemical Engineering, Rua Sílvio Lima-Polo II, 3030-790 Coimbra, Portugal
| | - Jorge F J Coelho
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Chemical Engineering, Rua Sílvio Lima-Polo II, 3030-790 Coimbra, Portugal
| | - Fani Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
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5
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Traber GM, Yu AM. RNAi-Based Therapeutics and Novel RNA Bioengineering Technologies. J Pharmacol Exp Ther 2023; 384:133-154. [PMID: 35680378 PMCID: PMC9827509 DOI: 10.1124/jpet.122.001234] [Citation(s) in RCA: 78] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 01/26/2023] Open
Abstract
RNA interference (RNAi) provides researchers with a versatile means to modulate target gene expression. The major forms of RNAi molecules, genome-derived microRNAs (miRNAs) and exogenous small interfering RNAs (siRNAs), converge into RNA-induced silencing complexes to achieve posttranscriptional gene regulation. RNAi has proven to be an adaptable and powerful therapeutic strategy where advancements in chemistry and pharmaceutics continue to bring RNAi-based drugs into the clinic. With four siRNA medications already approved by the US Food and Drug Administration (FDA), several RNAi-based therapeutics continue to advance to clinical trials with functions that closely resemble their endogenous counterparts. Although intended to enhance stability and improve efficacy, chemical modifications may increase risk of off-target effects by altering RNA structure, folding, and biologic activity away from their natural equivalents. Novel technologies in development today seek to use intact cells to yield true biologic RNAi agents that better represent the structures, stabilities, activities, and safety profiles of natural RNA molecules. In this review, we provide an examination of the mechanisms of action of endogenous miRNAs and exogenous siRNAs, the physiologic and pharmacokinetic barriers to therapeutic RNA delivery, and a summary of the chemical modifications and delivery platforms in use. We overview the pharmacology of the four FDA-approved siRNA medications (patisiran, givosiran, lumasiran, and inclisiran) as well as five siRNAs and several miRNA-based therapeutics currently in clinical trials. Furthermore, we discuss the direct expression and stable carrier-based, in vivo production of novel biologic RNAi agents for research and development. SIGNIFICANCE STATEMENT: In our review, we summarize the major concepts of RNA interference (RNAi), molecular mechanisms, and current state and challenges of RNAi drug development. We focus our discussion on the pharmacology of US Food and Drug Administration-approved RNAi medications and those siRNAs and miRNA-based therapeutics that entered the clinical investigations. Novel approaches to producing new true biological RNAi molecules for research and development are highlighted.
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Affiliation(s)
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, University of California (UC) Davis School of Medicine, Sacramento, California
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6
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Carapito R, Valente JFA, Queiroz JA, Sousa F. Arginine-Affinity Chromatography for Nucleic Acid (DNA and RNA) Isolation. Methods Mol Biol 2022; 2466:135-144. [PMID: 35585316 DOI: 10.1007/978-1-0716-2176-9_10] [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] [Indexed: 06/15/2023]
Abstract
Nucleic acid-based therapy has been emerging as a new strategy with great potential for the treatment of numerous diseases, especially those caused by gene defects. In this context, biotechnology plays a critical role on establishing suitable processes for biopharmaceuticals manufacturing, while the purification step still imposes a major burden. Affinity chromatography using amino acids as specific ligands has been successfully applied for plasmid DNA purification. In this protocol, we describe the process for nucleic acids production and extraction, as well as the chromatographic matrix synthesis for separation between DNA and RNA. This novel arginine-macroporous support presents excellent binding capacity and great robustness for nucleic acids isolation.
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Affiliation(s)
- Rita Carapito
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Joana F A Valente
- CDRSP-IPLEIRIA - Centre for Rapid and Sustainable Product Development, Instituto Politécnico de Leiria, Marinha Grande, Portugal
| | - João A Queiroz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal.
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7
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Baptista B, Carapito R, Laroui N, Pichon C, Sousa F. mRNA, a Revolution in Biomedicine. Pharmaceutics 2021; 13:2090. [PMID: 34959371 PMCID: PMC8707022 DOI: 10.3390/pharmaceutics13122090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/23/2022] Open
Abstract
The perspective of using messenger RNA (mRNA) as a therapeutic molecule first faced some uncertainties due to concerns about its instability and the feasibility of large-scale production. Today, given technological advances and deeper biomolecular knowledge, these issues have started to be addressed and some strategies are being exploited to overcome the limitations. Thus, the potential of mRNA has become increasingly recognized for the development of new innovative therapeutics, envisioning its application in immunotherapy, regenerative medicine, vaccination, and gene editing. Nonetheless, to fully potentiate mRNA therapeutic application, its efficient production, stabilization and delivery into the target cells are required. In recent years, intensive research has been carried out in this field in order to bring new and effective solutions towards the stabilization and delivery of mRNA. Presently, the therapeutic potential of mRNA is undoubtedly recognized, which was greatly reinforced by the results achieved in the battle against the COVID-19 pandemic, but there are still some issues that need to be improved, which are critically discussed in this review.
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Affiliation(s)
- Bruno Baptista
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (B.B.); (R.C.)
| | - Rita Carapito
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (B.B.); (R.C.)
| | - Nabila Laroui
- Centre de Biophysique Moléculaire (CBM), UPR 4301 CNRS, University of Orléans, 45071 Orléans, France;
| | - Chantal Pichon
- Centre de Biophysique Moléculaire (CBM), UPR 4301 CNRS, University of Orléans, 45071 Orléans, France;
| | - Fani Sousa
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (B.B.); (R.C.)
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8
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New RNA-Based Breakthroughs in Alzheimer's Disease Diagnosis and Therapeutics. Pharmaceutics 2021; 13:pharmaceutics13091397. [PMID: 34575473 PMCID: PMC8471423 DOI: 10.3390/pharmaceutics13091397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 01/25/2023] Open
Abstract
Dementia is described as the fifth leading cause of death worldwide and Alzheimer’s disease (AD) is recognized as the most common, causing a huge impact on health costs and quality of patients’ lives. The main hallmarks that are commonly associated with the pathologic process are amyloid deposition, pathologic Tau phosphorylation and neurodegeneration. It is still unclear how these events are linked to the disease progression, due to the complex pathologic mechanisms. Nevertheless, several hypotheses have been proposed for a better understanding of AD. The AD diagnosis is performed by using a combination of several tools to detect β-amyloid peptide (Aβ) deposits and modifications in cognitive performance, sometimes being expensive and invasive. In the treatment field, there is still an absence of effective treatments to delay or stop the progression of the disease, with most of the approved drugs used to relieve symptoms, and all of them with significant adverse side effects. Considering all limitations, the need to establish new and more effective diagnostic and therapeutic strategies becomes clear. This review aims not only to describe the disease and its impact but also to collect the currently available diagnostic and therapeutic strategies, highlighting new promising RNA-based strategies for AD.
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Laham-Karam N, Pinto GP, Poso A, Kokkonen P. Transcription and Translation Inhibitors in Cancer Treatment. Front Chem 2020; 8:276. [PMID: 32373584 PMCID: PMC7186406 DOI: 10.3389/fchem.2020.00276] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Transcription and translation are fundamental cellular processes that govern the protein production of cells. These processes are generally up regulated in cancer cells, to maintain the enhanced metabolism and proliferative state of these cells. As such cancerous cells can be susceptible to transcription and translation inhibitors. There are numerous druggable proteins involved in transcription and translation which make lucrative targets for cancer drug development. In addition to proteins, recent years have shown that the "undruggable" transcription factors and RNA molecules can also be targeted to hamper the transcription or translation in cancer. In this review, we summarize the properties and function of the transcription and translation inhibitors that have been tested and developed, focusing on the advances of the last 5 years. To complement this, we also discuss some of the recent advances in targeting oncogenes tightly controlling transcription including transcription factors and KRAS. In addition to natural and synthetic compounds, we review DNA and RNA based approaches to develop cancer drugs. Finally, we conclude with the outlook to the future of the development of transcription and translation inhibitors.
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Affiliation(s)
- Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Gaspar P. Pinto
- International Clinical Research Center, St. Anne University Hospital, Brno, Czechia
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- University Hospital Tübingen, Department of Internal Medicine VIII, University of Tübingen, Tübingen, Germany
| | - Piia Kokkonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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10
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Yu AM, Batra N, Tu MJ, Sweeney C. Novel approaches for efficient in vivo fermentation production of noncoding RNAs. Appl Microbiol Biotechnol 2020; 104:1927-1937. [PMID: 31953559 PMCID: PMC7385725 DOI: 10.1007/s00253-020-10350-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/26/2019] [Accepted: 01/03/2020] [Indexed: 01/07/2023]
Abstract
Genome-derived noncoding RNAs (ncRNAs), including microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs), play an essential role in the control of target gene expression underlying various cellular processes, and dysregulation of ncRNAs is involved in the pathogenesis and progression of various diseases in virtually all species including humans. Understanding ncRNA biology has opened new avenues to develop novel RNA-based therapeutics. Presently, ncRNA research and drug development is dominated by the use of ncRNA mimics that are synthesized chemically in vitro and supplemented with extensive and various types of artificial modifications and thus may not necessarily recapitulate the properties of natural RNAs generated and folded in living cells in vivo. Therefore, there are growing interests in developing novel technologies for in vivo production of RNA molecules. The two most recent major breakthroughs in achieving an efficient, large-scale, and cost-effective fermentation production of recombinant or bioengineered RNAs (e.g., tens of milligrams from 1 L of bacterial culture) are (1) using stable RNA carriers and (2) direct overexpression in RNase III-deficient bacteria, while other approaches offer a low yield (e.g., nano- to microgram scales per liter). In this article, we highlight these novel microbial fermentation-based technologies that have shifted the paradigm to the production of true biological ncRNA molecules for research and development.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA.
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - Colleen Sweeney
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
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11
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Kikuchi Y, Umekage S. Extracellular nucleic acids of the marine bacterium Rhodovulum sulfidophilum and recombinant RNA production technology using bacteria. FEMS Microbiol Lett 2019; 365:4705897. [PMID: 29228187 DOI: 10.1093/femsle/fnx268] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
Extracellular nucleic acids of high molecular weight are detected ubiquitously in seawater. Recent studies have indicated that these nucleic acids are, at least in part, derived from active production by some bacteria. The marine bacterium Rhodovulum sulfidophilum is one of those bacteria. Rhodovulumsulfidophilum is a non-sulfur phototrophic marine bacterium that is known to form structured communities of cells called flocs, and to produce extracellular nucleic acids in culture media. Recently, it has been revealed that this bacterium produces gene transfer agent-like particles and that this particle production may be related to the extracellular nucleic acid production mechanism. This review provides a summary of recent physiological and genetic studies of these phenomena and also introduces a new method for extracellular production of artificial and biologically functional RNAs using this bacterium. In addition, artificial RNA production using Escherichia coli, which is related to this topic, will also be described.
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Affiliation(s)
- Yo Kikuchi
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
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12
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Bioengineering of a single long noncoding RNA molecule that carries multiple small RNAs. Appl Microbiol Biotechnol 2019; 103:6107-6117. [PMID: 31187211 DOI: 10.1007/s00253-019-09934-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
Noncoding RNAs (ncRNAs), including microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs), regulate target gene expression and can be used as tools for understanding biological processes and identifying new therapeutic targets. Currently, ncRNA molecules for research and therapeutic use are limited to ncRNA mimics made by chemical synthesis. We have recently established a high-yield and cost-effective method of producing bioengineered or biologic ncRNA agents (BERAs) through bacterial fermentation, which is based on a stable tRNA/pre-miR-34a carrier (~ 180 nt) that accommodates target small RNAs. Nevertheless, it remains a challenge to heterogeneously express longer ncRNAs (e.g., > 260 nt), and it is unknown if single BERA may carry multiple small RNAs. To address this issue, we hypothesized that an additional human pre-miR-34a could be attached to the tRNA/pre-miR-34a scaffold to offer a new tRNA/pre-miR-34a/pre-miR-34a carrier (~ 296 nt) for the accommodation of multiple small RNAs. We thus designed ten different combinatorial BERAs (CO-BERAs) that include different combinations of miRNAs, siRNAs, and antagomirs. Our data showed that all target CO-BERAs were successfully expressed in Escherichia coli at high levels, greater than 40% in total bacterial RNAs. Furthermore, recombinant CO-BERAs were purified to a high degree of homogeneity by fast protein liquid chromatography methods. In addition, CO-BERAs exhibited strong anti-proliferative activities against a variety of human non-small cell lung cancer cell lines. These results support the production of long ncRNA molecules carrying different warhead small RNAs for multi-targeting which may open avenues for developing new biologic RNAs as experimental, diagnostic, and therapeutic tools.
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13
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Abstract
Small-molecule and protein/antibody drugs mainly act on genome-derived proteins to exert pharmacological effects. RNA based therapies hold the promise to expand the range of druggable targets from proteins to RNAs and the genome, as evidenced by several RNA drugs approved for clinical practice and many others under active trials. While chemo-engineered RNA mimics have found their success in marketed drugs and continue dominating basic research and drug development, these molecules are usually conjugated with extensive and various modifications. This makes them completely different from cellular RNAs transcribed from the genome that usually consist of unmodified ribonucleotides or just contain a few posttranscriptional modifications. The use of synthetic RNA mimics for RNA research and drug development is also in contrast with the ultimate success of protein research and therapy utilizing biologic or recombinant proteins produced and folded in living cells instead of polypeptides or proteins synthesized in vitro. Indeed, efforts have been made recently to develop RNA bioengineering technologies for cost-effective and large-scale production of biologic RNA molecules that may better capture the structures, functions, and safety profiles of natural RNAs. In this article, we provide an overview on RNA therapeutics for the treatment of human diseases via RNA interference mechanisms. By illustrating the structural differences between natural RNAs and chemo-engineered RNA mimics, we focus on discussion of a novel class of bioengineered/biologic RNA agents produced through fermentation and their potential applications to RNA research and drug development.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
| | - Chao Jian
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Allan H Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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14
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Pedro AQ, Pereira P, Quental MJ, Carvalho AP, Santos SM, Queiroz JA, Sousa F, Freire MG. Cholinium-based Good's buffers ionic liquids as remarkable stabilizers and recyclable preservation media for recombinant small RNAs. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2018; 6:16645-16656. [PMID: 30949418 PMCID: PMC6443033 DOI: 10.1021/acssuschemeng.8b03900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
RNA is a biopolymer of high relevance in the biopharmaceuticals field and in fundamental and applied research; however, the preservation of the RNA stability is still a remarkable challenge. Herein, we demonstrate the enhanced potential of aqueous solutions of self-buffering cholinium-based Good's buffers ionic liquids (GB-ILs), at 20 and 50 % (w/w), as alternative preservation media of recombinant small RNAs. The thermal stability of RNA is highly enhanced by GB-ILs, with an increase of 14 °C in the biopolymer melting temperature - the highest increase observed up to date with ILs. Most GB-ILs investigated improve the stability of RNA at least up to 30-days, both at 25 °C and at 4 °C, without requiring the typical samples freezing. Molecular dynamics simulations were applied to better understand the molecular-level mechanisms responsible for the observed RNA improved stability. The number of IL cations surrounding the RNA chain is similar, yet with differences found for the IL anions, which are responsible for the overall charge of the biopolymer first solvation sphere. No cytotoxicity of the studied solutions containing RNA and ILs at 20 % (w/w) was observed onto two distinct human cell lines, reinforcing their potential to act as preservation media when foreseeing biopharmaceutical applications. Finally, RNA was successfully recovered from the ILs aqueous solutions, without changes in its structural integrity, and the ILs successfully recycled and reused.
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Affiliation(s)
- Augusto Q. Pedro
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Patrícia Pereira
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria J. Quental
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - André P. Carvalho
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Sérgio M. Santos
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - João A. Queiroz
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
- Corresponding Authors: ; Tel: +351-234-401422; Fax: +351-234-370084; ; Tel: +351-275-329074
| | - Mara G. Freire
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Complexo de Laboratórios Tecnológicos, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Corresponding Authors: ; Tel: +351-234-401422; Fax: +351-234-370084; ; Tel: +351-275-329074
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15
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Baronti L, Karlsson H, Marušič M, Petzold K. A guide to large-scale RNA sample preparation. Anal Bioanal Chem 2018; 410:3239-3252. [PMID: 29546546 PMCID: PMC5937877 DOI: 10.1007/s00216-018-0943-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 12/30/2022]
Abstract
RNA is becoming more important as an increasing number of functions, both regulatory and enzymatic, are being discovered on a daily basis. As the RNA boom has just begun, most techniques are still in development and changes occur frequently. To understand RNA functions, revealing the structure of RNA is of utmost importance, which requires sample preparation. We review the latest methods to produce and purify a variation of RNA molecules for different purposes with the main focus on structural biology and biophysics. We present a guide aimed at identifying the most suitable method for your RNA and your biological question and highlighting the advantages of different methods. Graphical abstract In this review we present different methods for large-scale production and purification of RNAs for structural and biophysical studies.
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Affiliation(s)
- Lorenzo Baronti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, 17177, Stockholm, Sweden
| | - Hampus Karlsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, 17177, Stockholm, Sweden
| | - Maja Marušič
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, 17177, Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, 17177, Stockholm, Sweden.
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16
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Ho PY, Duan Z, Batra N, Jilek JL, Tu MJ, Qiu JX, Hu Z, Wun T, Lara PN, DeVere White RW, Chen HW, Yu AM. Bioengineered Noncoding RNAs Selectively Change Cellular miRNome Profiles for Cancer Therapy. J Pharmacol Exp Ther 2018; 365:494-506. [PMID: 29602831 DOI: 10.1124/jpet.118.247775] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/28/2018] [Indexed: 12/16/2022] Open
Abstract
Noncoding RNAs (ncRNAs) produced in live cells may better reflect intracellular ncRNAs for research and therapy. Attempts were made to produce biologic ncRNAs, but at low yield or success rate. Here we first report a new ncRNA bioengineering technology using more stable ncRNA carrier (nCAR) containing a pre-miR-34a derivative identified by rational design and experimental validation. This approach offered a remarkable higher level expression (40%-80% of total RNAs) of recombinant ncRNAs in bacteria and gave an 80% success rate (33 of 42 ncRNAs). New FPLC and spin-column based methods were also developed for large- and small-scale purification of milligrams and micrograms of recombinant ncRNAs from half liter and milliliters of bacterial culture, respectively. We then used two bioengineered nCAR/miRNAs to demonstrate the selective release of target miRNAs into human cells, which were revealed to be Dicer dependent (miR-34a-5p) or independent (miR-124a-3p), and subsequent changes of miRNome and transcriptome profiles. miRNA enrichment analyses of altered transcriptome confirmed the specificity of nCAR/miRNAs in target gene regulation. Furthermore, nCAR assembled miR-34a-5p and miR-124-3p were active in suppressing human lung carcinoma cell proliferation through modulation of target gene expression (e.g., cMET and CDK6 for miR-34a-5p; STAT3 and ABCC4 for miR-124-3p). In addition, bioengineered miRNA molecules were effective in controlling metastatic lung xenograft progression, as demonstrated by live animal and ex vivo lung tissue bioluminescent imaging as well as histopathological examination. This novel ncRNA bioengineering platform can be easily adapted to produce various ncRNA molecules, and biologic ncRNAs hold the promise as new cancer therapeutics.
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Affiliation(s)
- Pui Yan Ho
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Zhijian Duan
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Joseph L Jilek
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Jing-Xin Qiu
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Zihua Hu
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Theodore Wun
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Primo N Lara
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Ralph W DeVere White
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Hong-Wu Chen
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
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